--- /dev/null
+/*
+ * 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.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 $Revision$ $Date$
+ */
+public class Alignment extends org.vamsas.client.object
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _alignmentAnnotations
+ */
+ private org.vamsas.objects.core.AlignmentAnnotations _alignmentAnnotations;
+
+ /**
+ * Field _treeList
+ */
+ private java.util.Vector _treeList;
+
+ /**
+ * Field _alignmentSequenceList
+ */
+ private java.util.Vector _alignmentSequenceList;
+
+ /**
+ * Field _provenance
+ */
+ private org.vamsas.objects.core.Provenance _provenance;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Alignment()
+ {
+ super();
+ _treeList = new Vector();
+ _alignmentSequenceList = new Vector();
+ } //-- org.vamsas.objects.core.Alignment()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addAlignmentSequence
+ *
+ *
+ *
+ * @param vAlignmentSequence
+ */
+ public void addAlignmentSequence(org.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _alignmentSequenceList.addElement(vAlignmentSequence);
+ } //-- void addAlignmentSequence(org.vamsas.objects.core.AlignmentSequence)
+
+ /**
+ * Method addAlignmentSequence
+ *
+ *
+ *
+ * @param index
+ * @param vAlignmentSequence
+ */
+ public void addAlignmentSequence(int index, org.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _alignmentSequenceList.insertElementAt(vAlignmentSequence, index);
+ } //-- void addAlignmentSequence(int, org.vamsas.objects.core.AlignmentSequence)
+
+ /**
+ * Method addTree
+ *
+ *
+ *
+ * @param vTree
+ */
+ public void addTree(org.vamsas.objects.core.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _treeList.addElement(vTree);
+ } //-- void addTree(org.vamsas.objects.core.Tree)
+
+ /**
+ * Method addTree
+ *
+ *
+ *
+ * @param index
+ * @param vTree
+ */
+ public void addTree(int index, org.vamsas.objects.core.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _treeList.insertElementAt(vTree, index);
+ } //-- void addTree(int, org.vamsas.objects.core.Tree)
+
+ /**
+ * Method enumerateAlignmentSequence
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateAlignmentSequence()
+ {
+ return _alignmentSequenceList.elements();
+ } //-- java.util.Enumeration enumerateAlignmentSequence()
+
+ /**
+ * Method enumerateTree
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateTree()
+ {
+ return _treeList.elements();
+ } //-- java.util.Enumeration enumerateTree()
+
+ /**
+ * Note: hashCode() has not been overriden
+ *
+ * @param obj
+ * @return boolean
+ */
+ public boolean equals(java.lang.Object obj)
+ {
+ if ( this == obj )
+ return true;
+
+ if (super.equals(obj)==false)
+ return false;
+
+ if (obj instanceof Alignment) {
+
+ Alignment temp = (Alignment)obj;
+ if (this._alignmentAnnotations != null) {
+ if (temp._alignmentAnnotations == null) return false;
+ else if (!(this._alignmentAnnotations.equals(temp._alignmentAnnotations)))
+ return false;
+ }
+ else if (temp._alignmentAnnotations != null)
+ return false;
+ if (this._treeList != null) {
+ if (temp._treeList == null) return false;
+ else if (!(this._treeList.equals(temp._treeList)))
+ return false;
+ }
+ else if (temp._treeList != null)
+ return false;
+ if (this._alignmentSequenceList != null) {
+ if (temp._alignmentSequenceList == null) return false;
+ else if (!(this._alignmentSequenceList.equals(temp._alignmentSequenceList)))
+ return false;
+ }
+ else if (temp._alignmentSequenceList != null)
+ return false;
+ if (this._provenance != null) {
+ if (temp._provenance == null) return false;
+ else if (!(this._provenance.equals(temp._provenance)))
+ return false;
+ }
+ else if (temp._provenance != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Returns the value of field 'alignmentAnnotations'.
+ *
+ * @return AlignmentAnnotations
+ * @return the value of field 'alignmentAnnotations'.
+ */
+ public org.vamsas.objects.core.AlignmentAnnotations getAlignmentAnnotations()
+ {
+ return this._alignmentAnnotations;
+ } //-- org.vamsas.objects.core.AlignmentAnnotations getAlignmentAnnotations()
+
+ /**
+ * Method getAlignmentSequence
+ *
+ *
+ *
+ * @param index
+ * @return AlignmentSequence
+ */
+ public org.vamsas.objects.core.AlignmentSequence getAlignmentSequence(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _alignmentSequenceList.size())) {
+ throw new IndexOutOfBoundsException("getAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index);
+ } //-- org.vamsas.objects.core.AlignmentSequence getAlignmentSequence(int)
+
+ /**
+ * Method getAlignmentSequence
+ *
+ *
+ *
+ * @return AlignmentSequence
+ */
+ public org.vamsas.objects.core.AlignmentSequence[] getAlignmentSequence()
+ {
+ int size = _alignmentSequenceList.size();
+ org.vamsas.objects.core.AlignmentSequence[] mArray = new org.vamsas.objects.core.AlignmentSequence[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.AlignmentSequence[] getAlignmentSequence()
+
+ /**
+ * Method getAlignmentSequenceCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getAlignmentSequenceCount()
+ {
+ return _alignmentSequenceList.size();
+ } //-- int getAlignmentSequenceCount()
+
+ /**
+ * Returns the value of field 'provenance'.
+ *
+ * @return Provenance
+ * @return the value of field 'provenance'.
+ */
+ public org.vamsas.objects.core.Provenance getProvenance()
+ {
+ return this._provenance;
+ } //-- org.vamsas.objects.core.Provenance getProvenance()
+
+ /**
+ * Method getTree
+ *
+ *
+ *
+ * @param index
+ * @return Tree
+ */
+ public org.vamsas.objects.core.Tree getTree(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _treeList.size())) {
+ throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
+ } //-- org.vamsas.objects.core.Tree getTree(int)
+
+ /**
+ * Method getTree
+ *
+ *
+ *
+ * @return Tree
+ */
+ public org.vamsas.objects.core.Tree[] getTree()
+ {
+ int size = _treeList.size();
+ org.vamsas.objects.core.Tree[] mArray = new org.vamsas.objects.core.Tree[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.Tree[] getTree()
+
+ /**
+ * Method getTreeCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getTreeCount()
+ {
+ return _treeList.size();
+ } //-- int getTreeCount()
+
+ /**
+ * Method isValid
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean isValid()
+ {
+ try {
+ validate();
+ }
+ catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ } //-- boolean isValid()
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param out
+ */
+ public void marshal(java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, out);
+ } //-- void marshal(java.io.Writer)
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param handler
+ */
+ public void marshal(org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, handler);
+ } //-- void marshal(org.xml.sax.ContentHandler)
+
+ /**
+ * Method removeAlignmentSequence
+ *
+ *
+ *
+ * @param index
+ * @return AlignmentSequence
+ */
+ public org.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int index)
+ {
+ java.lang.Object obj = _alignmentSequenceList.elementAt(index);
+ _alignmentSequenceList.removeElementAt(index);
+ return (org.vamsas.objects.core.AlignmentSequence) obj;
+ } //-- org.vamsas.objects.core.AlignmentSequence removeAlignmentSequence(int)
+
+ /**
+ * Method removeAllAlignmentSequence
+ *
+ */
+ public void removeAllAlignmentSequence()
+ {
+ _alignmentSequenceList.removeAllElements();
+ } //-- void removeAllAlignmentSequence()
+
+ /**
+ * Method removeAllTree
+ *
+ */
+ public void removeAllTree()
+ {
+ _treeList.removeAllElements();
+ } //-- void removeAllTree()
+
+ /**
+ * Method removeTree
+ *
+ *
+ *
+ * @param index
+ * @return Tree
+ */
+ public org.vamsas.objects.core.Tree removeTree(int index)
+ {
+ java.lang.Object obj = _treeList.elementAt(index);
+ _treeList.removeElementAt(index);
+ return (org.vamsas.objects.core.Tree) obj;
+ } //-- org.vamsas.objects.core.Tree removeTree(int)
+
+ /**
+ * Sets the value of field 'alignmentAnnotations'.
+ *
+ * @param alignmentAnnotations the value of field
+ * 'alignmentAnnotations'.
+ */
+ public void setAlignmentAnnotations(org.vamsas.objects.core.AlignmentAnnotations alignmentAnnotations)
+ {
+ this._alignmentAnnotations = alignmentAnnotations;
+ } //-- void setAlignmentAnnotations(org.vamsas.objects.core.AlignmentAnnotations)
+
+ /**
+ * Method setAlignmentSequence
+ *
+ *
+ *
+ * @param index
+ * @param vAlignmentSequence
+ */
+ public void setAlignmentSequence(int index, org.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _alignmentSequenceList.size())) {
+ throw new IndexOutOfBoundsException("setAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]");
+ }
+ _alignmentSequenceList.setElementAt(vAlignmentSequence, index);
+ } //-- void setAlignmentSequence(int, org.vamsas.objects.core.AlignmentSequence)
+
+ /**
+ * Method setAlignmentSequence
+ *
+ *
+ *
+ * @param alignmentSequenceArray
+ */
+ public void setAlignmentSequence(org.vamsas.objects.core.AlignmentSequence[] alignmentSequenceArray)
+ {
+ //-- copy array
+ _alignmentSequenceList.removeAllElements();
+ for (int i = 0; i < alignmentSequenceArray.length; i++) {
+ _alignmentSequenceList.addElement(alignmentSequenceArray[i]);
+ }
+ } //-- void setAlignmentSequence(org.vamsas.objects.core.AlignmentSequence)
+
+ /**
+ * Sets the value of field 'provenance'.
+ *
+ * @param provenance the value of field 'provenance'.
+ */
+ public void setProvenance(org.vamsas.objects.core.Provenance provenance)
+ {
+ this._provenance = provenance;
+ } //-- void setProvenance(org.vamsas.objects.core.Provenance)
+
+ /**
+ * Method setTree
+ *
+ *
+ *
+ * @param index
+ * @param vTree
+ */
+ public void setTree(int index, org.vamsas.objects.core.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _treeList.size())) {
+ throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
+ }
+ _treeList.setElementAt(vTree, index);
+ } //-- void setTree(int, org.vamsas.objects.core.Tree)
+
+ /**
+ * Method setTree
+ *
+ *
+ *
+ * @param treeArray
+ */
+ public void setTree(org.vamsas.objects.core.Tree[] treeArray)
+ {
+ //-- copy array
+ _treeList.removeAllElements();
+ for (int i = 0; i < treeArray.length; i++) {
+ _treeList.addElement(treeArray[i]);
+ }
+ } //-- void setTree(org.vamsas.objects.core.Tree)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return Alignment
+ */
+ public static org.vamsas.objects.core.Alignment unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.Alignment) Unmarshaller.unmarshal(org.vamsas.objects.core.Alignment.class, reader);
+ } //-- org.vamsas.objects.core.Alignment unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * 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.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 AlignmentAnnotations.
+ *
+ * @version $Revision$ $Date$
+ */
+public class AlignmentAnnotations extends org.vamsas.client.object
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _graph
+ */
+ private boolean _graph;
+
+ /**
+ * keeps track of state for field: _graph
+ */
+ private boolean _has_graph;
+
+ /**
+ * Field _annotationElementList
+ */
+ private java.util.Vector _annotationElementList;
+
+ /**
+ * Field _label
+ */
+ private java.lang.String _label;
+
+ /**
+ * Field _description
+ */
+ private java.lang.String _description;
+
+ /**
+ * Field _provenance
+ */
+ private org.vamsas.objects.core.Provenance _provenance;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public AlignmentAnnotations()
+ {
+ super();
+ _annotationElementList = new Vector();
+ } //-- org.vamsas.objects.core.AlignmentAnnotations()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addAnnotationElement
+ *
+ *
+ *
+ * @param vAnnotationElement
+ */
+ public void addAnnotationElement(org.vamsas.objects.core.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _annotationElementList.addElement(vAnnotationElement);
+ } //-- void addAnnotationElement(org.vamsas.objects.core.AnnotationElement)
+
+ /**
+ * Method addAnnotationElement
+ *
+ *
+ *
+ * @param index
+ * @param vAnnotationElement
+ */
+ public void addAnnotationElement(int index, org.vamsas.objects.core.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _annotationElementList.insertElementAt(vAnnotationElement, index);
+ } //-- void addAnnotationElement(int, org.vamsas.objects.core.AnnotationElement)
+
+ /**
+ * Method deleteGraph
+ *
+ */
+ public void deleteGraph()
+ {
+ this._has_graph= false;
+ } //-- void deleteGraph()
+
+ /**
+ * Method enumerateAnnotationElement
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateAnnotationElement()
+ {
+ return _annotationElementList.elements();
+ } //-- java.util.Enumeration enumerateAnnotationElement()
+
+ /**
+ * Note: hashCode() has not been overriden
+ *
+ * @param obj
+ * @return boolean
+ */
+ public boolean equals(java.lang.Object obj)
+ {
+ if ( this == obj )
+ return true;
+
+ if (super.equals(obj)==false)
+ return false;
+
+ if (obj instanceof AlignmentAnnotations) {
+
+ AlignmentAnnotations temp = (AlignmentAnnotations)obj;
+ if (this._graph != temp._graph)
+ return false;
+ if (this._has_graph != temp._has_graph)
+ return false;
+ if (this._annotationElementList != null) {
+ if (temp._annotationElementList == null) return false;
+ else if (!(this._annotationElementList.equals(temp._annotationElementList)))
+ return false;
+ }
+ else if (temp._annotationElementList != null)
+ return false;
+ if (this._label != null) {
+ if (temp._label == null) return false;
+ else if (!(this._label.equals(temp._label)))
+ return false;
+ }
+ else if (temp._label != null)
+ return false;
+ if (this._description != null) {
+ if (temp._description == null) return false;
+ else if (!(this._description.equals(temp._description)))
+ return false;
+ }
+ else if (temp._description != null)
+ return false;
+ if (this._provenance != null) {
+ if (temp._provenance == null) return false;
+ else if (!(this._provenance.equals(temp._provenance)))
+ return false;
+ }
+ else if (temp._provenance != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Method getAnnotationElement
+ *
+ *
+ *
+ * @param index
+ * @return AnnotationElement
+ */
+ public org.vamsas.objects.core.AnnotationElement getAnnotationElement(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _annotationElementList.size())) {
+ throw new IndexOutOfBoundsException("getAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index);
+ } //-- org.vamsas.objects.core.AnnotationElement getAnnotationElement(int)
+
+ /**
+ * Method getAnnotationElement
+ *
+ *
+ *
+ * @return AnnotationElement
+ */
+ public org.vamsas.objects.core.AnnotationElement[] getAnnotationElement()
+ {
+ int size = _annotationElementList.size();
+ org.vamsas.objects.core.AnnotationElement[] mArray = new org.vamsas.objects.core.AnnotationElement[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.AnnotationElement[] getAnnotationElement()
+
+ /**
+ * Method getAnnotationElementCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getAnnotationElementCount()
+ {
+ return _annotationElementList.size();
+ } //-- int getAnnotationElementCount()
+
+ /**
+ * Returns the value of field 'description'.
+ *
+ * @return String
+ * @return the value of field 'description'.
+ */
+ public java.lang.String getDescription()
+ {
+ return this._description;
+ } //-- java.lang.String getDescription()
+
+ /**
+ * Returns the value of field 'graph'.
+ *
+ * @return boolean
+ * @return the value of field 'graph'.
+ */
+ public boolean getGraph()
+ {
+ return this._graph;
+ } //-- boolean getGraph()
+
+ /**
+ * Returns the value of field 'label'.
+ *
+ * @return String
+ * @return the value of field 'label'.
+ */
+ public java.lang.String getLabel()
+ {
+ return this._label;
+ } //-- java.lang.String getLabel()
+
+ /**
+ * Returns the value of field 'provenance'.
+ *
+ * @return Provenance
+ * @return the value of field 'provenance'.
+ */
+ public org.vamsas.objects.core.Provenance getProvenance()
+ {
+ return this._provenance;
+ } //-- org.vamsas.objects.core.Provenance getProvenance()
+
+ /**
+ * Method hasGraph
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasGraph()
+ {
+ return this._has_graph;
+ } //-- boolean hasGraph()
+
+ /**
+ * Method isValid
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean isValid()
+ {
+ try {
+ validate();
+ }
+ catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ } //-- boolean isValid()
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param out
+ */
+ public void marshal(java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, out);
+ } //-- void marshal(java.io.Writer)
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param handler
+ */
+ public void marshal(org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, handler);
+ } //-- void marshal(org.xml.sax.ContentHandler)
+
+ /**
+ * Method removeAllAnnotationElement
+ *
+ */
+ public void removeAllAnnotationElement()
+ {
+ _annotationElementList.removeAllElements();
+ } //-- void removeAllAnnotationElement()
+
+ /**
+ * Method removeAnnotationElement
+ *
+ *
+ *
+ * @param index
+ * @return AnnotationElement
+ */
+ public org.vamsas.objects.core.AnnotationElement removeAnnotationElement(int index)
+ {
+ java.lang.Object obj = _annotationElementList.elementAt(index);
+ _annotationElementList.removeElementAt(index);
+ return (org.vamsas.objects.core.AnnotationElement) obj;
+ } //-- org.vamsas.objects.core.AnnotationElement removeAnnotationElement(int)
+
+ /**
+ * Method setAnnotationElement
+ *
+ *
+ *
+ * @param index
+ * @param vAnnotationElement
+ */
+ public void setAnnotationElement(int index, org.vamsas.objects.core.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _annotationElementList.size())) {
+ throw new IndexOutOfBoundsException("setAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]");
+ }
+ _annotationElementList.setElementAt(vAnnotationElement, index);
+ } //-- void setAnnotationElement(int, org.vamsas.objects.core.AnnotationElement)
+
+ /**
+ * Method setAnnotationElement
+ *
+ *
+ *
+ * @param annotationElementArray
+ */
+ public void setAnnotationElement(org.vamsas.objects.core.AnnotationElement[] annotationElementArray)
+ {
+ //-- copy array
+ _annotationElementList.removeAllElements();
+ for (int i = 0; i < annotationElementArray.length; i++) {
+ _annotationElementList.addElement(annotationElementArray[i]);
+ }
+ } //-- void setAnnotationElement(org.vamsas.objects.core.AnnotationElement)
+
+ /**
+ * Sets the value of field 'description'.
+ *
+ * @param description the value of field 'description'.
+ */
+ public void setDescription(java.lang.String description)
+ {
+ this._description = description;
+ } //-- void setDescription(java.lang.String)
+
+ /**
+ * Sets the value of field 'graph'.
+ *
+ * @param graph the value of field 'graph'.
+ */
+ public void setGraph(boolean graph)
+ {
+ this._graph = graph;
+ this._has_graph = true;
+ } //-- void setGraph(boolean)
+
+ /**
+ * Sets the value of field 'label'.
+ *
+ * @param label the value of field 'label'.
+ */
+ public void setLabel(java.lang.String label)
+ {
+ this._label = label;
+ } //-- void setLabel(java.lang.String)
+
+ /**
+ * Sets the value of field 'provenance'.
+ *
+ * @param provenance the value of field 'provenance'.
+ */
+ public void setProvenance(org.vamsas.objects.core.Provenance provenance)
+ {
+ this._provenance = provenance;
+ } //-- void setProvenance(org.vamsas.objects.core.Provenance)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return AlignmentAnnotations
+ */
+ public static org.vamsas.objects.core.AlignmentAnnotations unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.AlignmentAnnotations) Unmarshaller.unmarshal(org.vamsas.objects.core.AlignmentAnnotations.class, reader);
+ } //-- org.vamsas.objects.core.AlignmentAnnotations unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * 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.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 AlignmentSequence.
+ *
+ * @version $Revision$ $Date$
+ */
+public class AlignmentSequence extends org.vamsas.objects.core.SequenceType
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _id
+ */
+ private java.lang.Object _id;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public AlignmentSequence()
+ {
+ super();
+ } //-- org.vamsas.objects.core.AlignmentSequence()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Note: hashCode() has not been overriden
+ *
+ * @param obj
+ * @return boolean
+ */
+ public boolean equals(java.lang.Object obj)
+ {
+ if ( this == obj )
+ return true;
+
+ if (super.equals(obj)==false)
+ return false;
+
+ if (obj instanceof AlignmentSequence) {
+
+ AlignmentSequence temp = (AlignmentSequence)obj;
+ if (this._id != null) {
+ if (temp._id == null) return false;
+ else if (!(this._id.equals(temp._id)))
+ return false;
+ }
+ else if (temp._id != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return Object
+ * @return the value of field 'id'.
+ */
+ public java.lang.Object getId()
+ {
+ return this._id;
+ } //-- java.lang.Object getId()
+
+ /**
+ * Method isValid
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean isValid()
+ {
+ try {
+ validate();
+ }
+ catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ } //-- boolean isValid()
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param out
+ */
+ public void marshal(java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, out);
+ } //-- void marshal(java.io.Writer)
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param handler
+ */
+ public void marshal(org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, handler);
+ } //-- void marshal(org.xml.sax.ContentHandler)
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(java.lang.Object id)
+ {
+ this._id = id;
+ } //-- void setId(java.lang.Object)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return SequenceType
+ */
+ public static org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.AlignmentSequence) Unmarshaller.unmarshal(org.vamsas.objects.core.AlignmentSequence.class, reader);
+ } //-- org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * 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.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 AnnotationElement.
+ *
+ * @version $Revision$ $Date$
+ */
+public class AnnotationElement extends org.vamsas.client.object
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _position
+ */
+ private int _position;
+
+ /**
+ * keeps track of state for field: _position
+ */
+ private boolean _has_position;
+
+ /**
+ * Field _displayCharacter
+ */
+ private java.lang.String _displayCharacter;
+
+ /**
+ * Field _description
+ */
+ private java.lang.String _description;
+
+ /**
+ * Field _secondaryStructure
+ */
+ private java.lang.String _secondaryStructure;
+
+ /**
+ * Field _value
+ */
+ private float _value;
+
+ /**
+ * keeps track of state for field: _value
+ */
+ private boolean _has_value;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public AnnotationElement()
+ {
+ super();
+ } //-- org.vamsas.objects.core.AnnotationElement()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method deletePosition
+ *
+ */
+ public void deletePosition()
+ {
+ this._has_position= false;
+ } //-- void deletePosition()
+
+ /**
+ * Method deleteValue
+ *
+ */
+ public void deleteValue()
+ {
+ this._has_value= false;
+ } //-- void deleteValue()
+
+ /**
+ * Note: hashCode() has not been overriden
+ *
+ * @param obj
+ * @return boolean
+ */
+ public boolean equals(java.lang.Object obj)
+ {
+ if ( this == obj )
+ return true;
+
+ if (super.equals(obj)==false)
+ return false;
+
+ if (obj instanceof AnnotationElement) {
+
+ AnnotationElement temp = (AnnotationElement)obj;
+ if (this._position != temp._position)
+ return false;
+ if (this._has_position != temp._has_position)
+ return false;
+ if (this._displayCharacter != null) {
+ if (temp._displayCharacter == null) return false;
+ else if (!(this._displayCharacter.equals(temp._displayCharacter)))
+ return false;
+ }
+ else if (temp._displayCharacter != null)
+ return false;
+ if (this._description != null) {
+ if (temp._description == null) return false;
+ else if (!(this._description.equals(temp._description)))
+ return false;
+ }
+ else if (temp._description != null)
+ return false;
+ if (this._secondaryStructure != null) {
+ if (temp._secondaryStructure == null) return false;
+ else if (!(this._secondaryStructure.equals(temp._secondaryStructure)))
+ return false;
+ }
+ else if (temp._secondaryStructure != null)
+ return false;
+ if (this._value != temp._value)
+ return false;
+ if (this._has_value != temp._has_value)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Returns the value of field 'description'.
+ *
+ * @return String
+ * @return the value of field 'description'.
+ */
+ public java.lang.String getDescription()
+ {
+ return this._description;
+ } //-- java.lang.String getDescription()
+
+ /**
+ * Returns the value of field 'displayCharacter'.
+ *
+ * @return String
+ * @return the value of field 'displayCharacter'.
+ */
+ public java.lang.String getDisplayCharacter()
+ {
+ return this._displayCharacter;
+ } //-- java.lang.String getDisplayCharacter()
+
+ /**
+ * Returns the value of field 'position'.
+ *
+ * @return int
+ * @return the value of field 'position'.
+ */
+ public int getPosition()
+ {
+ return this._position;
+ } //-- int getPosition()
+
+ /**
+ * Returns the value of field 'secondaryStructure'.
+ *
+ * @return String
+ * @return the value of field 'secondaryStructure'.
+ */
+ public java.lang.String getSecondaryStructure()
+ {
+ return this._secondaryStructure;
+ } //-- java.lang.String getSecondaryStructure()
+
+ /**
+ * Returns the value of field 'value'.
+ *
+ * @return float
+ * @return the value of field 'value'.
+ */
+ public float getValue()
+ {
+ return this._value;
+ } //-- float getValue()
+
+ /**
+ * Method hasPosition
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasPosition()
+ {
+ return this._has_position;
+ } //-- boolean hasPosition()
+
+ /**
+ * Method hasValue
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasValue()
+ {
+ return this._has_value;
+ } //-- boolean hasValue()
+
+ /**
+ * Method isValid
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean isValid()
+ {
+ try {
+ validate();
+ }
+ catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ } //-- boolean isValid()
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param out
+ */
+ public void marshal(java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, out);
+ } //-- void marshal(java.io.Writer)
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param handler
+ */
+ public void marshal(org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, handler);
+ } //-- void marshal(org.xml.sax.ContentHandler)
+
+ /**
+ * Sets the value of field 'description'.
+ *
+ * @param description the value of field 'description'.
+ */
+ public void setDescription(java.lang.String description)
+ {
+ this._description = description;
+ } //-- void setDescription(java.lang.String)
+
+ /**
+ * Sets the value of field 'displayCharacter'.
+ *
+ * @param displayCharacter the value of field 'displayCharacter'
+ */
+ public void setDisplayCharacter(java.lang.String displayCharacter)
+ {
+ this._displayCharacter = displayCharacter;
+ } //-- void setDisplayCharacter(java.lang.String)
+
+ /**
+ * Sets the value of field 'position'.
+ *
+ * @param position the value of field 'position'.
+ */
+ public void setPosition(int position)
+ {
+ this._position = position;
+ this._has_position = true;
+ } //-- void setPosition(int)
+
+ /**
+ * Sets the value of field 'secondaryStructure'.
+ *
+ * @param secondaryStructure the value of field
+ * 'secondaryStructure'.
+ */
+ public void setSecondaryStructure(java.lang.String secondaryStructure)
+ {
+ this._secondaryStructure = secondaryStructure;
+ } //-- void setSecondaryStructure(java.lang.String)
+
+ /**
+ * Sets the value of field 'value'.
+ *
+ * @param value the value of field 'value'.
+ */
+ public void setValue(float value)
+ {
+ this._value = value;
+ this._has_value = true;
+ } //-- void setValue(float)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return AnnotationElement
+ */
+ public static org.vamsas.objects.core.AnnotationElement unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.AnnotationElement) Unmarshaller.unmarshal(org.vamsas.objects.core.AnnotationElement.class, reader);
+ } //-- org.vamsas.objects.core.AnnotationElement unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Application.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Application extends org.vamsas.client.object
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _version
+ */
+ private java.lang.Object _version;
+
+ /**
+ * Field _name
+ */
+ private java.lang.Object _name;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Application()
+ {
+ super();
+ } //-- org.vamsas.objects.core.Application()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Note: hashCode() has not been overriden
+ *
+ * @param obj
+ * @return boolean
+ */
+ public boolean equals(java.lang.Object obj)
+ {
+ if ( this == obj )
+ return true;
+
+ if (super.equals(obj)==false)
+ return false;
+
+ if (obj instanceof Application) {
+
+ Application temp = (Application)obj;
+ if (this._version != null) {
+ if (temp._version == null) return false;
+ else if (!(this._version.equals(temp._version)))
+ return false;
+ }
+ else if (temp._version != null)
+ return false;
+ if (this._name != null) {
+ if (temp._name == null) return false;
+ else if (!(this._name.equals(temp._name)))
+ return false;
+ }
+ else if (temp._name != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return Object
+ * @return the value of field 'name'.
+ */
+ public java.lang.Object getName()
+ {
+ return this._name;
+ } //-- java.lang.Object getName()
+
+ /**
+ * Returns the value of field 'version'.
+ *
+ * @return Object
+ * @return the value of field 'version'.
+ */
+ public java.lang.Object getVersion()
+ {
+ return this._version;
+ } //-- java.lang.Object getVersion()
+
+ /**
+ * Method isValid
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean isValid()
+ {
+ try {
+ validate();
+ }
+ catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ } //-- boolean isValid()
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param out
+ */
+ public void marshal(java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, out);
+ } //-- void marshal(java.io.Writer)
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param handler
+ */
+ public void marshal(org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, handler);
+ } //-- void marshal(org.xml.sax.ContentHandler)
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name the value of field 'name'.
+ */
+ public void setName(java.lang.Object name)
+ {
+ this._name = name;
+ } //-- void setName(java.lang.Object)
+
+ /**
+ * Sets the value of field 'version'.
+ *
+ * @param version the value of field 'version'.
+ */
+ public void setVersion(java.lang.Object version)
+ {
+ this._version = version;
+ } //-- void setVersion(java.lang.Object)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return Application
+ */
+ public static org.vamsas.objects.core.Application unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.Application) Unmarshaller.unmarshal(org.vamsas.objects.core.Application.class, reader);
+ } //-- org.vamsas.objects.core.Application unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * 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.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 ApplicationData.
+ *
+ * @version $Revision$ $Date$
+ */
+public class ApplicationData extends org.vamsas.client.object
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _application
+ */
+ private org.vamsas.objects.core.Application _application;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public ApplicationData()
+ {
+ super();
+ } //-- org.vamsas.objects.core.ApplicationData()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Note: hashCode() has not been overriden
+ *
+ * @param obj
+ * @return boolean
+ */
+ public boolean equals(java.lang.Object obj)
+ {
+ if ( this == obj )
+ return true;
+
+ if (super.equals(obj)==false)
+ return false;
+
+ if (obj instanceof ApplicationData) {
+
+ ApplicationData temp = (ApplicationData)obj;
+ if (this._application != null) {
+ if (temp._application == null) return false;
+ else if (!(this._application.equals(temp._application)))
+ return false;
+ }
+ else if (temp._application != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Returns the value of field 'application'.
+ *
+ * @return Application
+ * @return the value of field 'application'.
+ */
+ public org.vamsas.objects.core.Application getApplication()
+ {
+ return this._application;
+ } //-- org.vamsas.objects.core.Application getApplication()
+
+ /**
+ * Method isValid
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean isValid()
+ {
+ try {
+ validate();
+ }
+ catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ } //-- boolean isValid()
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param out
+ */
+ public void marshal(java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, out);
+ } //-- void marshal(java.io.Writer)
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param handler
+ */
+ public void marshal(org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, handler);
+ } //-- void marshal(org.xml.sax.ContentHandler)
+
+ /**
+ * Sets the value of field 'application'.
+ *
+ * @param application the value of field 'application'.
+ */
+ public void setApplication(org.vamsas.objects.core.Application application)
+ {
+ this._application = application;
+ } //-- void setApplication(org.vamsas.objects.core.Application)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return ApplicationData
+ */
+ public static org.vamsas.objects.core.ApplicationData unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.ApplicationData) Unmarshaller.unmarshal(org.vamsas.objects.core.ApplicationData.class, reader);
+ } //-- org.vamsas.objects.core.ApplicationData unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * 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.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 DbRef.
+ *
+ * @version $Revision$ $Date$
+ */
+public class DbRef extends org.vamsas.client.object
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _source
+ */
+ private java.lang.Object _source;
+
+ /**
+ * Field _version
+ */
+ private java.lang.Object _version;
+
+ /**
+ * Field _accessionId
+ */
+ private java.lang.Object _accessionId;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public DbRef()
+ {
+ super();
+ } //-- org.vamsas.objects.core.DbRef()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Note: hashCode() has not been overriden
+ *
+ * @param obj
+ * @return boolean
+ */
+ public boolean equals(java.lang.Object obj)
+ {
+ if ( this == obj )
+ return true;
+
+ if (super.equals(obj)==false)
+ return false;
+
+ if (obj instanceof DbRef) {
+
+ DbRef temp = (DbRef)obj;
+ if (this._source != null) {
+ if (temp._source == null) return false;
+ else if (!(this._source.equals(temp._source)))
+ return false;
+ }
+ else if (temp._source != null)
+ return false;
+ if (this._version != null) {
+ if (temp._version == null) return false;
+ else if (!(this._version.equals(temp._version)))
+ return false;
+ }
+ else if (temp._version != null)
+ return false;
+ if (this._accessionId != null) {
+ if (temp._accessionId == null) return false;
+ else if (!(this._accessionId.equals(temp._accessionId)))
+ return false;
+ }
+ else if (temp._accessionId != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Returns the value of field 'accessionId'.
+ *
+ * @return Object
+ * @return the value of field 'accessionId'.
+ */
+ public java.lang.Object getAccessionId()
+ {
+ return this._accessionId;
+ } //-- java.lang.Object getAccessionId()
+
+ /**
+ * Returns the value of field 'source'.
+ *
+ * @return Object
+ * @return the value of field 'source'.
+ */
+ public java.lang.Object getSource()
+ {
+ return this._source;
+ } //-- java.lang.Object getSource()
+
+ /**
+ * Returns the value of field 'version'.
+ *
+ * @return Object
+ * @return the value of field 'version'.
+ */
+ public java.lang.Object getVersion()
+ {
+ return this._version;
+ } //-- java.lang.Object getVersion()
+
+ /**
+ * Method isValid
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean isValid()
+ {
+ try {
+ validate();
+ }
+ catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ } //-- boolean isValid()
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param out
+ */
+ public void marshal(java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, out);
+ } //-- void marshal(java.io.Writer)
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param handler
+ */
+ public void marshal(org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, handler);
+ } //-- void marshal(org.xml.sax.ContentHandler)
+
+ /**
+ * Sets the value of field 'accessionId'.
+ *
+ * @param accessionId the value of field 'accessionId'.
+ */
+ public void setAccessionId(java.lang.Object accessionId)
+ {
+ this._accessionId = accessionId;
+ } //-- void setAccessionId(java.lang.Object)
+
+ /**
+ * Sets the value of field 'source'.
+ *
+ * @param source the value of field 'source'.
+ */
+ public void setSource(java.lang.Object source)
+ {
+ this._source = source;
+ } //-- void setSource(java.lang.Object)
+
+ /**
+ * Sets the value of field 'version'.
+ *
+ * @param version the value of field 'version'.
+ */
+ public void setVersion(java.lang.Object version)
+ {
+ this._version = version;
+ } //-- void setVersion(java.lang.Object)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return DbRef
+ */
+ public static org.vamsas.objects.core.DbRef unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.DbRef) Unmarshaller.unmarshal(org.vamsas.objects.core.DbRef.class, reader);
+ } //-- org.vamsas.objects.core.DbRef unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Entry.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Entry extends org.vamsas.client.object
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _user
+ */
+ private java.lang.String _user;
+
+ /**
+ * Field _action
+ */
+ private java.lang.String _action;
+
+ /**
+ * Field _date
+ */
+ private org.exolab.castor.types.Date _date;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Entry()
+ {
+ super();
+ } //-- org.vamsas.objects.core.Entry()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Note: hashCode() has not been overriden
+ *
+ * @param obj
+ * @return boolean
+ */
+ public boolean equals(java.lang.Object obj)
+ {
+ if ( this == obj )
+ return true;
+
+ if (super.equals(obj)==false)
+ return false;
+
+ if (obj instanceof Entry) {
+
+ Entry temp = (Entry)obj;
+ if (this._user != null) {
+ if (temp._user == null) return false;
+ else if (!(this._user.equals(temp._user)))
+ return false;
+ }
+ else if (temp._user != null)
+ return false;
+ if (this._action != null) {
+ if (temp._action == null) return false;
+ else if (!(this._action.equals(temp._action)))
+ return false;
+ }
+ else if (temp._action != null)
+ return false;
+ if (this._date != null) {
+ if (temp._date == null) return false;
+ else if (!(this._date.equals(temp._date)))
+ return false;
+ }
+ else if (temp._date != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Returns the value of field 'action'.
+ *
+ * @return String
+ * @return the value of field 'action'.
+ */
+ public java.lang.String getAction()
+ {
+ return this._action;
+ } //-- java.lang.String getAction()
+
+ /**
+ * Returns the value of field 'date'.
+ *
+ * @return Date
+ * @return the value of field 'date'.
+ */
+ public org.exolab.castor.types.Date getDate()
+ {
+ return this._date;
+ } //-- org.exolab.castor.types.Date getDate()
+
+ /**
+ * Returns the value of field 'user'.
+ *
+ * @return String
+ * @return the value of field 'user'.
+ */
+ public java.lang.String getUser()
+ {
+ return this._user;
+ } //-- java.lang.String getUser()
+
+ /**
+ * Method isValid
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean isValid()
+ {
+ try {
+ validate();
+ }
+ catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ } //-- boolean isValid()
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param out
+ */
+ public void marshal(java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, out);
+ } //-- void marshal(java.io.Writer)
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param handler
+ */
+ public void marshal(org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, handler);
+ } //-- void marshal(org.xml.sax.ContentHandler)
+
+ /**
+ * Sets the value of field 'action'.
+ *
+ * @param action the value of field 'action'.
+ */
+ public void setAction(java.lang.String action)
+ {
+ this._action = action;
+ } //-- void setAction(java.lang.String)
+
+ /**
+ * Sets the value of field 'date'.
+ *
+ * @param date the value of field 'date'.
+ */
+ public void setDate(org.exolab.castor.types.Date date)
+ {
+ this._date = date;
+ } //-- void setDate(org.exolab.castor.types.Date)
+
+ /**
+ * Sets the value of field 'user'.
+ *
+ * @param user the value of field 'user'.
+ */
+ public void setUser(java.lang.String user)
+ {
+ this._user = user;
+ } //-- void setUser(java.lang.String)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return Entry
+ */
+ public static org.vamsas.objects.core.Entry unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.Entry) Unmarshaller.unmarshal(org.vamsas.objects.core.Entry.class, reader);
+ } //-- org.vamsas.objects.core.Entry unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class LockFile.
+ *
+ * @version $Revision$ $Date$
+ */
+public class LockFile extends org.vamsas.client.object
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * internal content storage
+ */
+ private java.lang.String _content = "";
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public LockFile()
+ {
+ super();
+ setContent("");
+ } //-- org.vamsas.objects.core.LockFile()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Note: hashCode() has not been overriden
+ *
+ * @param obj
+ * @return boolean
+ */
+ public boolean equals(java.lang.Object obj)
+ {
+ if ( this == obj )
+ return true;
+
+ if (super.equals(obj)==false)
+ return false;
+
+ if (obj instanceof LockFile) {
+
+ LockFile temp = (LockFile)obj;
+ if (this._content != null) {
+ if (temp._content == null) return false;
+ else if (!(this._content.equals(temp._content)))
+ return false;
+ }
+ else if (temp._content != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Returns the value of field 'content'. The field 'content'
+ * has the following description: internal content storage
+ *
+ * @return String
+ * @return the value of field 'content'.
+ */
+ public java.lang.String getContent()
+ {
+ return this._content;
+ } //-- java.lang.String getContent()
+
+ /**
+ * Method isValid
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean isValid()
+ {
+ try {
+ validate();
+ }
+ catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ } //-- boolean isValid()
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param out
+ */
+ public void marshal(java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, out);
+ } //-- void marshal(java.io.Writer)
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param handler
+ */
+ public void marshal(org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, handler);
+ } //-- void marshal(org.xml.sax.ContentHandler)
+
+ /**
+ * Sets the value of field 'content'. The field 'content' has
+ * the following description: internal content storage
+ *
+ * @param content the value of field 'content'.
+ */
+ public void setContent(java.lang.String content)
+ {
+ this._content = content;
+ } //-- void setContent(java.lang.String)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return LockFile
+ */
+ public static org.vamsas.objects.core.LockFile unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.LockFile) Unmarshaller.unmarshal(org.vamsas.objects.core.LockFile.class, reader);
+ } //-- org.vamsas.objects.core.LockFile unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Provenance.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Provenance extends org.vamsas.client.object
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _items
+ */
+ private java.util.Vector _items;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Provenance()
+ {
+ super();
+ _items = new Vector();
+ } //-- org.vamsas.objects.core.Provenance()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addProvenanceItem
+ *
+ *
+ *
+ * @param vProvenanceItem
+ */
+ public void addProvenanceItem(org.vamsas.objects.core.ProvenanceItem vProvenanceItem)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _items.addElement(vProvenanceItem);
+ } //-- void addProvenanceItem(org.vamsas.objects.core.ProvenanceItem)
+
+ /**
+ * Method addProvenanceItem
+ *
+ *
+ *
+ * @param index
+ * @param vProvenanceItem
+ */
+ public void addProvenanceItem(int index, org.vamsas.objects.core.ProvenanceItem vProvenanceItem)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _items.insertElementAt(vProvenanceItem, index);
+ } //-- void addProvenanceItem(int, org.vamsas.objects.core.ProvenanceItem)
+
+ /**
+ * Method enumerateProvenanceItem
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateProvenanceItem()
+ {
+ return _items.elements();
+ } //-- java.util.Enumeration enumerateProvenanceItem()
+
+ /**
+ * Note: hashCode() has not been overriden
+ *
+ * @param obj
+ * @return boolean
+ */
+ public boolean equals(java.lang.Object obj)
+ {
+ if ( this == obj )
+ return true;
+
+ if (super.equals(obj)==false)
+ return false;
+
+ if (obj instanceof Provenance) {
+
+ Provenance temp = (Provenance)obj;
+ if (this._items != null) {
+ if (temp._items == null) return false;
+ else if (!(this._items.equals(temp._items)))
+ return false;
+ }
+ else if (temp._items != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Method getProvenanceItem
+ *
+ *
+ *
+ * @param index
+ * @return ProvenanceItem
+ */
+ public org.vamsas.objects.core.ProvenanceItem getProvenanceItem(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _items.size())) {
+ throw new IndexOutOfBoundsException("getProvenanceItem: Index value '"+index+"' not in range [0.."+_items.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.ProvenanceItem) _items.elementAt(index);
+ } //-- org.vamsas.objects.core.ProvenanceItem getProvenanceItem(int)
+
+ /**
+ * Method getProvenanceItem
+ *
+ *
+ *
+ * @return ProvenanceItem
+ */
+ public org.vamsas.objects.core.ProvenanceItem[] getProvenanceItem()
+ {
+ int size = _items.size();
+ org.vamsas.objects.core.ProvenanceItem[] mArray = new org.vamsas.objects.core.ProvenanceItem[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.ProvenanceItem) _items.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.ProvenanceItem[] getProvenanceItem()
+
+ /**
+ * Method getProvenanceItemCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getProvenanceItemCount()
+ {
+ return _items.size();
+ } //-- int getProvenanceItemCount()
+
+ /**
+ * Method isValid
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean isValid()
+ {
+ try {
+ validate();
+ }
+ catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ } //-- boolean isValid()
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param out
+ */
+ public void marshal(java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, out);
+ } //-- void marshal(java.io.Writer)
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param handler
+ */
+ public void marshal(org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, handler);
+ } //-- void marshal(org.xml.sax.ContentHandler)
+
+ /**
+ * Method removeAllProvenanceItem
+ *
+ */
+ public void removeAllProvenanceItem()
+ {
+ _items.removeAllElements();
+ } //-- void removeAllProvenanceItem()
+
+ /**
+ * Method removeProvenanceItem
+ *
+ *
+ *
+ * @param index
+ * @return ProvenanceItem
+ */
+ public org.vamsas.objects.core.ProvenanceItem removeProvenanceItem(int index)
+ {
+ java.lang.Object obj = _items.elementAt(index);
+ _items.removeElementAt(index);
+ return (org.vamsas.objects.core.ProvenanceItem) obj;
+ } //-- org.vamsas.objects.core.ProvenanceItem removeProvenanceItem(int)
+
+ /**
+ * Method setProvenanceItem
+ *
+ *
+ *
+ * @param index
+ * @param vProvenanceItem
+ */
+ public void setProvenanceItem(int index, org.vamsas.objects.core.ProvenanceItem vProvenanceItem)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _items.size())) {
+ throw new IndexOutOfBoundsException("setProvenanceItem: Index value '"+index+"' not in range [0.."+_items.size()+ "]");
+ }
+ _items.setElementAt(vProvenanceItem, index);
+ } //-- void setProvenanceItem(int, org.vamsas.objects.core.ProvenanceItem)
+
+ /**
+ * Method setProvenanceItem
+ *
+ *
+ *
+ * @param provenanceItemArray
+ */
+ public void setProvenanceItem(org.vamsas.objects.core.ProvenanceItem[] provenanceItemArray)
+ {
+ //-- copy array
+ _items.removeAllElements();
+ for (int i = 0; i < provenanceItemArray.length; i++) {
+ _items.addElement(provenanceItemArray[i]);
+ }
+ } //-- void setProvenanceItem(org.vamsas.objects.core.ProvenanceItem)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return Provenance
+ */
+ public static org.vamsas.objects.core.Provenance unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.Provenance) Unmarshaller.unmarshal(org.vamsas.objects.core.Provenance.class, reader);
+ } //-- org.vamsas.objects.core.Provenance unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.Serializable;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class ProvenanceItem.
+ *
+ * @version $Revision$ $Date$
+ */
+public class ProvenanceItem implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _entry
+ */
+ private org.vamsas.objects.core.Entry _entry;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public ProvenanceItem()
+ {
+ super();
+ } //-- org.vamsas.objects.core.ProvenanceItem()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Returns the value of field 'entry'.
+ *
+ * @return Entry
+ * @return the value of field 'entry'.
+ */
+ public org.vamsas.objects.core.Entry getEntry()
+ {
+ return this._entry;
+ } //-- org.vamsas.objects.core.Entry getEntry()
+
+ /**
+ * Sets the value of field 'entry'.
+ *
+ * @param entry the value of field 'entry'.
+ */
+ public void setEntry(org.vamsas.objects.core.Entry entry)
+ {
+ this._entry = entry;
+ } //-- void setEntry(org.vamsas.objects.core.Entry)
+
+}
--- /dev/null
+/*
+ * 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.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 Sequence.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Sequence extends org.vamsas.objects.core.SequenceType
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _dictionary
+ */
+ private java.lang.String _dictionary;
+
+ /**
+ * Field _id
+ */
+ private java.lang.String _id;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Sequence()
+ {
+ super();
+ } //-- org.vamsas.objects.core.Sequence()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Note: hashCode() has not been overriden
+ *
+ * @param obj
+ * @return boolean
+ */
+ public boolean equals(java.lang.Object obj)
+ {
+ if ( this == obj )
+ return true;
+
+ if (super.equals(obj)==false)
+ return false;
+
+ if (obj instanceof Sequence) {
+
+ Sequence temp = (Sequence)obj;
+ if (this._dictionary != null) {
+ if (temp._dictionary == null) return false;
+ else if (!(this._dictionary.equals(temp._dictionary)))
+ return false;
+ }
+ else if (temp._dictionary != null)
+ return false;
+ if (this._id != null) {
+ if (temp._id == null) return false;
+ else if (!(this._id.equals(temp._id)))
+ return false;
+ }
+ else if (temp._id != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Returns the value of field 'dictionary'.
+ *
+ * @return String
+ * @return the value of field 'dictionary'.
+ */
+ public java.lang.String getDictionary()
+ {
+ return this._dictionary;
+ } //-- java.lang.String getDictionary()
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return String
+ * @return the value of field 'id'.
+ */
+ public java.lang.String getId()
+ {
+ return this._id;
+ } //-- java.lang.String getId()
+
+ /**
+ * Method isValid
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean isValid()
+ {
+ try {
+ validate();
+ }
+ catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ } //-- boolean isValid()
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param out
+ */
+ public void marshal(java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, out);
+ } //-- void marshal(java.io.Writer)
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param handler
+ */
+ public void marshal(org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, handler);
+ } //-- void marshal(org.xml.sax.ContentHandler)
+
+ /**
+ * Sets the value of field 'dictionary'.
+ *
+ * @param dictionary the value of field 'dictionary'.
+ */
+ public void setDictionary(java.lang.String dictionary)
+ {
+ this._dictionary = dictionary;
+ } //-- void setDictionary(java.lang.String)
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(java.lang.String id)
+ {
+ this._id = id;
+ } //-- void setId(java.lang.String)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return SequenceType
+ */
+ public static org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.Sequence) Unmarshaller.unmarshal(org.vamsas.objects.core.Sequence.class, reader);
+ } //-- org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class 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.objects.core.Tree _tree;
+
+ /**
+ * Field _provenance
+ */
+ private org.vamsas.objects.core.Provenance _provenance;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public SequenceSet()
+ {
+ super();
+ _sequenceList = new Vector();
+ _sequenceSetAnnotationsList = new Vector();
+ _alignmentList = new Vector();
+ } //-- org.vamsas.objects.core.SequenceSet()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addAlignment
+ *
+ *
+ *
+ * @param vAlignment
+ */
+ public void addAlignment(org.vamsas.objects.core.Alignment vAlignment)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _alignmentList.addElement(vAlignment);
+ } //-- void addAlignment(org.vamsas.objects.core.Alignment)
+
+ /**
+ * Method addAlignment
+ *
+ *
+ *
+ * @param index
+ * @param vAlignment
+ */
+ public void addAlignment(int index, org.vamsas.objects.core.Alignment vAlignment)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _alignmentList.insertElementAt(vAlignment, index);
+ } //-- void addAlignment(int, org.vamsas.objects.core.Alignment)
+
+ /**
+ * Method addSequence
+ *
+ *
+ *
+ * @param vSequence
+ */
+ public void addSequence(org.vamsas.objects.core.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _sequenceList.addElement(vSequence);
+ } //-- void addSequence(org.vamsas.objects.core.Sequence)
+
+ /**
+ * Method addSequence
+ *
+ *
+ *
+ * @param index
+ * @param vSequence
+ */
+ public void addSequence(int index, org.vamsas.objects.core.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _sequenceList.insertElementAt(vSequence, index);
+ } //-- void addSequence(int, org.vamsas.objects.core.Sequence)
+
+ /**
+ * Method addSequenceSetAnnotations
+ *
+ *
+ *
+ * @param vSequenceSetAnnotations
+ */
+ public void addSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations vSequenceSetAnnotations)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _sequenceSetAnnotationsList.addElement(vSequenceSetAnnotations);
+ } //-- void addSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations)
+
+ /**
+ * Method addSequenceSetAnnotations
+ *
+ *
+ *
+ * @param index
+ * @param vSequenceSetAnnotations
+ */
+ public void addSequenceSetAnnotations(int index, org.vamsas.objects.core.SequenceSetAnnotations vSequenceSetAnnotations)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _sequenceSetAnnotationsList.insertElementAt(vSequenceSetAnnotations, index);
+ } //-- void addSequenceSetAnnotations(int, org.vamsas.objects.core.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.objects.core.Alignment getAlignment(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _alignmentList.size())) {
+ throw new IndexOutOfBoundsException("getAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.Alignment) _alignmentList.elementAt(index);
+ } //-- org.vamsas.objects.core.Alignment getAlignment(int)
+
+ /**
+ * Method getAlignment
+ *
+ *
+ *
+ * @return Alignment
+ */
+ public org.vamsas.objects.core.Alignment[] getAlignment()
+ {
+ int size = _alignmentList.size();
+ org.vamsas.objects.core.Alignment[] mArray = new org.vamsas.objects.core.Alignment[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.Alignment) _alignmentList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.Alignment[] getAlignment()
+
+ /**
+ * Method getAlignmentCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getAlignmentCount()
+ {
+ return _alignmentList.size();
+ } //-- int getAlignmentCount()
+
+ /**
+ * 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.objects.core.Provenance getProvenance()
+ {
+ return this._provenance;
+ } //-- org.vamsas.objects.core.Provenance getProvenance()
+
+ /**
+ * Method getSequence
+ *
+ *
+ *
+ * @param index
+ * @return Sequence
+ */
+ public org.vamsas.objects.core.Sequence getSequence(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _sequenceList.size())) {
+ throw new IndexOutOfBoundsException("getSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.Sequence) _sequenceList.elementAt(index);
+ } //-- org.vamsas.objects.core.Sequence getSequence(int)
+
+ /**
+ * Method getSequence
+ *
+ *
+ *
+ * @return Sequence
+ */
+ public org.vamsas.objects.core.Sequence[] getSequence()
+ {
+ int size = _sequenceList.size();
+ org.vamsas.objects.core.Sequence[] mArray = new org.vamsas.objects.core.Sequence[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.Sequence) _sequenceList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.Sequence[] getSequence()
+
+ /**
+ * Method getSequenceCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getSequenceCount()
+ {
+ return _sequenceList.size();
+ } //-- int getSequenceCount()
+
+ /**
+ * Method getSequenceSetAnnotations
+ *
+ *
+ *
+ * @param index
+ * @return SequenceSetAnnotations
+ */
+ public org.vamsas.objects.core.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.objects.core.SequenceSetAnnotations) _sequenceSetAnnotationsList.elementAt(index);
+ } //-- org.vamsas.objects.core.SequenceSetAnnotations getSequenceSetAnnotations(int)
+
+ /**
+ * Method getSequenceSetAnnotations
+ *
+ *
+ *
+ * @return SequenceSetAnnotations
+ */
+ public org.vamsas.objects.core.SequenceSetAnnotations[] getSequenceSetAnnotations()
+ {
+ int size = _sequenceSetAnnotationsList.size();
+ org.vamsas.objects.core.SequenceSetAnnotations[] mArray = new org.vamsas.objects.core.SequenceSetAnnotations[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.SequenceSetAnnotations) _sequenceSetAnnotationsList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.SequenceSetAnnotations[] getSequenceSetAnnotations()
+
+ /**
+ * 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.objects.core.Tree getTree()
+ {
+ return this._tree;
+ } //-- org.vamsas.objects.core.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.objects.core.Alignment removeAlignment(int index)
+ {
+ java.lang.Object obj = _alignmentList.elementAt(index);
+ _alignmentList.removeElementAt(index);
+ return (org.vamsas.objects.core.Alignment) obj;
+ } //-- org.vamsas.objects.core.Alignment removeAlignment(int)
+
+ /**
+ * Method removeAllAlignment
+ *
+ */
+ public void removeAllAlignment()
+ {
+ _alignmentList.removeAllElements();
+ } //-- void removeAllAlignment()
+
+ /**
+ * Method 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.objects.core.Sequence removeSequence(int index)
+ {
+ java.lang.Object obj = _sequenceList.elementAt(index);
+ _sequenceList.removeElementAt(index);
+ return (org.vamsas.objects.core.Sequence) obj;
+ } //-- org.vamsas.objects.core.Sequence removeSequence(int)
+
+ /**
+ * Method removeSequenceSetAnnotations
+ *
+ *
+ *
+ * @param index
+ * @return SequenceSetAnnotations
+ */
+ public org.vamsas.objects.core.SequenceSetAnnotations removeSequenceSetAnnotations(int index)
+ {
+ java.lang.Object obj = _sequenceSetAnnotationsList.elementAt(index);
+ _sequenceSetAnnotationsList.removeElementAt(index);
+ return (org.vamsas.objects.core.SequenceSetAnnotations) obj;
+ } //-- org.vamsas.objects.core.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.objects.core.Alignment vAlignment)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _alignmentList.size())) {
+ throw new IndexOutOfBoundsException("setAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]");
+ }
+ _alignmentList.setElementAt(vAlignment, index);
+ } //-- void setAlignment(int, org.vamsas.objects.core.Alignment)
+
+ /**
+ * Method setAlignment
+ *
+ *
+ *
+ * @param alignmentArray
+ */
+ public void setAlignment(org.vamsas.objects.core.Alignment[] alignmentArray)
+ {
+ //-- copy array
+ _alignmentList.removeAllElements();
+ for (int i = 0; i < alignmentArray.length; i++) {
+ _alignmentList.addElement(alignmentArray[i]);
+ }
+ } //-- void setAlignment(org.vamsas.objects.core.Alignment)
+
+ /**
+ * 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.objects.core.Provenance provenance)
+ {
+ this._provenance = provenance;
+ } //-- void setProvenance(org.vamsas.objects.core.Provenance)
+
+ /**
+ * Method setSequence
+ *
+ *
+ *
+ * @param index
+ * @param vSequence
+ */
+ public void setSequence(int index, org.vamsas.objects.core.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _sequenceList.size())) {
+ throw new IndexOutOfBoundsException("setSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]");
+ }
+ _sequenceList.setElementAt(vSequence, index);
+ } //-- void setSequence(int, org.vamsas.objects.core.Sequence)
+
+ /**
+ * Method setSequence
+ *
+ *
+ *
+ * @param sequenceArray
+ */
+ public void setSequence(org.vamsas.objects.core.Sequence[] sequenceArray)
+ {
+ //-- copy array
+ _sequenceList.removeAllElements();
+ for (int i = 0; i < sequenceArray.length; i++) {
+ _sequenceList.addElement(sequenceArray[i]);
+ }
+ } //-- void setSequence(org.vamsas.objects.core.Sequence)
+
+ /**
+ * Method setSequenceSetAnnotations
+ *
+ *
+ *
+ * @param index
+ * @param vSequenceSetAnnotations
+ */
+ public void setSequenceSetAnnotations(int index, org.vamsas.objects.core.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.objects.core.SequenceSetAnnotations)
+
+ /**
+ * Method setSequenceSetAnnotations
+ *
+ *
+ *
+ * @param sequenceSetAnnotationsArray
+ */
+ public void setSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations[] sequenceSetAnnotationsArray)
+ {
+ //-- copy array
+ _sequenceSetAnnotationsList.removeAllElements();
+ for (int i = 0; i < sequenceSetAnnotationsArray.length; i++) {
+ _sequenceSetAnnotationsList.addElement(sequenceSetAnnotationsArray[i]);
+ }
+ } //-- void setSequenceSetAnnotations(org.vamsas.objects.core.SequenceSetAnnotations)
+
+ /**
+ * Sets the value of field 'tree'.
+ *
+ * @param tree the value of field 'tree'.
+ */
+ public void setTree(org.vamsas.objects.core.Tree tree)
+ {
+ this._tree = tree;
+ } //-- void setTree(org.vamsas.objects.core.Tree)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return SequenceSet
+ */
+ public static org.vamsas.objects.core.SequenceSet unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.SequenceSet) Unmarshaller.unmarshal(org.vamsas.objects.core.SequenceSet.class, reader);
+ } //-- org.vamsas.objects.core.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()
+
+}
--- /dev/null
+/*
+ * 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.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 SequenceSetAnnotations.
+ *
+ * @version $Revision$ $Date$
+ */
+public class SequenceSetAnnotations extends org.vamsas.client.object
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _type
+ */
+ private java.lang.String _type;
+
+ /**
+ * Field _end
+ */
+ private java.lang.String _end;
+
+ /**
+ * Field _begin
+ */
+ private java.lang.String _begin;
+
+ /**
+ * Field _seqRef
+ */
+ private java.lang.Object _seqRef;
+
+ /**
+ * Field _description
+ */
+ private java.lang.String _description;
+
+ /**
+ * Field _status
+ */
+ private java.lang.String _status;
+
+ /**
+ * Field _annotationElementList
+ */
+ private java.util.Vector _annotationElementList;
+
+ /**
+ * Field _provenance
+ */
+ private org.vamsas.objects.core.Provenance _provenance;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public SequenceSetAnnotations()
+ {
+ super();
+ _annotationElementList = new Vector();
+ } //-- org.vamsas.objects.core.SequenceSetAnnotations()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addAnnotationElement
+ *
+ *
+ *
+ * @param vAnnotationElement
+ */
+ public void addAnnotationElement(org.vamsas.objects.core.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _annotationElementList.addElement(vAnnotationElement);
+ } //-- void addAnnotationElement(org.vamsas.objects.core.AnnotationElement)
+
+ /**
+ * Method addAnnotationElement
+ *
+ *
+ *
+ * @param index
+ * @param vAnnotationElement
+ */
+ public void addAnnotationElement(int index, org.vamsas.objects.core.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _annotationElementList.insertElementAt(vAnnotationElement, index);
+ } //-- void addAnnotationElement(int, org.vamsas.objects.core.AnnotationElement)
+
+ /**
+ * Method enumerateAnnotationElement
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateAnnotationElement()
+ {
+ return _annotationElementList.elements();
+ } //-- java.util.Enumeration enumerateAnnotationElement()
+
+ /**
+ * Note: hashCode() has not been overriden
+ *
+ * @param obj
+ * @return boolean
+ */
+ public boolean equals(java.lang.Object obj)
+ {
+ if ( this == obj )
+ return true;
+
+ if (super.equals(obj)==false)
+ return false;
+
+ if (obj instanceof SequenceSetAnnotations) {
+
+ SequenceSetAnnotations temp = (SequenceSetAnnotations)obj;
+ if (this._type != null) {
+ if (temp._type == null) return false;
+ else if (!(this._type.equals(temp._type)))
+ return false;
+ }
+ else if (temp._type != null)
+ return false;
+ if (this._end != null) {
+ if (temp._end == null) return false;
+ else if (!(this._end.equals(temp._end)))
+ return false;
+ }
+ else if (temp._end != null)
+ return false;
+ if (this._begin != null) {
+ if (temp._begin == null) return false;
+ else if (!(this._begin.equals(temp._begin)))
+ return false;
+ }
+ else if (temp._begin != null)
+ return false;
+ if (this._seqRef != null) {
+ if (temp._seqRef == null) return false;
+ else if (!(this._seqRef.equals(temp._seqRef)))
+ return false;
+ }
+ else if (temp._seqRef != null)
+ return false;
+ if (this._description != null) {
+ if (temp._description == null) return false;
+ else if (!(this._description.equals(temp._description)))
+ return false;
+ }
+ else if (temp._description != null)
+ return false;
+ if (this._status != null) {
+ if (temp._status == null) return false;
+ else if (!(this._status.equals(temp._status)))
+ return false;
+ }
+ else if (temp._status != null)
+ return false;
+ if (this._annotationElementList != null) {
+ if (temp._annotationElementList == null) return false;
+ else if (!(this._annotationElementList.equals(temp._annotationElementList)))
+ return false;
+ }
+ else if (temp._annotationElementList != null)
+ return false;
+ if (this._provenance != null) {
+ if (temp._provenance == null) return false;
+ else if (!(this._provenance.equals(temp._provenance)))
+ return false;
+ }
+ else if (temp._provenance != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Method getAnnotationElement
+ *
+ *
+ *
+ * @param index
+ * @return AnnotationElement
+ */
+ public org.vamsas.objects.core.AnnotationElement getAnnotationElement(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _annotationElementList.size())) {
+ throw new IndexOutOfBoundsException("getAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index);
+ } //-- org.vamsas.objects.core.AnnotationElement getAnnotationElement(int)
+
+ /**
+ * Method getAnnotationElement
+ *
+ *
+ *
+ * @return AnnotationElement
+ */
+ public org.vamsas.objects.core.AnnotationElement[] getAnnotationElement()
+ {
+ int size = _annotationElementList.size();
+ org.vamsas.objects.core.AnnotationElement[] mArray = new org.vamsas.objects.core.AnnotationElement[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.AnnotationElement[] getAnnotationElement()
+
+ /**
+ * Method getAnnotationElementCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getAnnotationElementCount()
+ {
+ return _annotationElementList.size();
+ } //-- int getAnnotationElementCount()
+
+ /**
+ * Returns the value of field 'begin'.
+ *
+ * @return String
+ * @return the value of field 'begin'.
+ */
+ public java.lang.String getBegin()
+ {
+ return this._begin;
+ } //-- java.lang.String getBegin()
+
+ /**
+ * Returns the value of field 'description'.
+ *
+ * @return String
+ * @return the value of field 'description'.
+ */
+ public java.lang.String getDescription()
+ {
+ return this._description;
+ } //-- java.lang.String getDescription()
+
+ /**
+ * Returns the value of field 'end'.
+ *
+ * @return String
+ * @return the value of field 'end'.
+ */
+ public java.lang.String getEnd()
+ {
+ return this._end;
+ } //-- java.lang.String getEnd()
+
+ /**
+ * Returns the value of field 'provenance'.
+ *
+ * @return Provenance
+ * @return the value of field 'provenance'.
+ */
+ public org.vamsas.objects.core.Provenance getProvenance()
+ {
+ return this._provenance;
+ } //-- org.vamsas.objects.core.Provenance getProvenance()
+
+ /**
+ * Returns the value of field 'seqRef'.
+ *
+ * @return Object
+ * @return the value of field 'seqRef'.
+ */
+ public java.lang.Object getSeqRef()
+ {
+ return this._seqRef;
+ } //-- java.lang.Object getSeqRef()
+
+ /**
+ * Returns the value of field 'status'.
+ *
+ * @return String
+ * @return the value of field 'status'.
+ */
+ public java.lang.String getStatus()
+ {
+ return this._status;
+ } //-- java.lang.String getStatus()
+
+ /**
+ * Returns the value of field 'type'.
+ *
+ * @return String
+ * @return the value of field 'type'.
+ */
+ public java.lang.String getType()
+ {
+ return this._type;
+ } //-- java.lang.String getType()
+
+ /**
+ * Method isValid
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean isValid()
+ {
+ try {
+ validate();
+ }
+ catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ } //-- boolean isValid()
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param out
+ */
+ public void marshal(java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, out);
+ } //-- void marshal(java.io.Writer)
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param handler
+ */
+ public void marshal(org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, handler);
+ } //-- void marshal(org.xml.sax.ContentHandler)
+
+ /**
+ * Method removeAllAnnotationElement
+ *
+ */
+ public void removeAllAnnotationElement()
+ {
+ _annotationElementList.removeAllElements();
+ } //-- void removeAllAnnotationElement()
+
+ /**
+ * Method removeAnnotationElement
+ *
+ *
+ *
+ * @param index
+ * @return AnnotationElement
+ */
+ public org.vamsas.objects.core.AnnotationElement removeAnnotationElement(int index)
+ {
+ java.lang.Object obj = _annotationElementList.elementAt(index);
+ _annotationElementList.removeElementAt(index);
+ return (org.vamsas.objects.core.AnnotationElement) obj;
+ } //-- org.vamsas.objects.core.AnnotationElement removeAnnotationElement(int)
+
+ /**
+ * Method setAnnotationElement
+ *
+ *
+ *
+ * @param index
+ * @param vAnnotationElement
+ */
+ public void setAnnotationElement(int index, org.vamsas.objects.core.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _annotationElementList.size())) {
+ throw new IndexOutOfBoundsException("setAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]");
+ }
+ _annotationElementList.setElementAt(vAnnotationElement, index);
+ } //-- void setAnnotationElement(int, org.vamsas.objects.core.AnnotationElement)
+
+ /**
+ * Method setAnnotationElement
+ *
+ *
+ *
+ * @param annotationElementArray
+ */
+ public void setAnnotationElement(org.vamsas.objects.core.AnnotationElement[] annotationElementArray)
+ {
+ //-- copy array
+ _annotationElementList.removeAllElements();
+ for (int i = 0; i < annotationElementArray.length; i++) {
+ _annotationElementList.addElement(annotationElementArray[i]);
+ }
+ } //-- void setAnnotationElement(org.vamsas.objects.core.AnnotationElement)
+
+ /**
+ * Sets the value of field 'begin'.
+ *
+ * @param begin the value of field 'begin'.
+ */
+ public void setBegin(java.lang.String begin)
+ {
+ this._begin = begin;
+ } //-- void setBegin(java.lang.String)
+
+ /**
+ * Sets the value of field 'description'.
+ *
+ * @param description the value of field 'description'.
+ */
+ public void setDescription(java.lang.String description)
+ {
+ this._description = description;
+ } //-- void setDescription(java.lang.String)
+
+ /**
+ * Sets the value of field 'end'.
+ *
+ * @param end the value of field 'end'.
+ */
+ public void setEnd(java.lang.String end)
+ {
+ this._end = end;
+ } //-- void setEnd(java.lang.String)
+
+ /**
+ * Sets the value of field 'provenance'.
+ *
+ * @param provenance the value of field 'provenance'.
+ */
+ public void setProvenance(org.vamsas.objects.core.Provenance provenance)
+ {
+ this._provenance = provenance;
+ } //-- void setProvenance(org.vamsas.objects.core.Provenance)
+
+ /**
+ * Sets the value of field 'seqRef'.
+ *
+ * @param seqRef the value of field 'seqRef'.
+ */
+ public void setSeqRef(java.lang.Object seqRef)
+ {
+ this._seqRef = seqRef;
+ } //-- void setSeqRef(java.lang.Object)
+
+ /**
+ * Sets the value of field 'status'.
+ *
+ * @param status the value of field 'status'.
+ */
+ public void setStatus(java.lang.String status)
+ {
+ this._status = status;
+ } //-- void setStatus(java.lang.String)
+
+ /**
+ * Sets the value of field 'type'.
+ *
+ * @param type the value of field 'type'.
+ */
+ public void setType(java.lang.String type)
+ {
+ this._type = type;
+ } //-- void setType(java.lang.String)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return SequenceSetAnnotations
+ */
+ public static org.vamsas.objects.core.SequenceSetAnnotations unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.SequenceSetAnnotations) Unmarshaller.unmarshal(org.vamsas.objects.core.SequenceSetAnnotations.class, reader);
+ } //-- org.vamsas.objects.core.SequenceSetAnnotations unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * 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.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 $Revision$ $Date$
+ */
+public class SequenceType extends org.vamsas.client.object
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _start
+ */
+ private int _start;
+
+ /**
+ * keeps track of state for field: _start
+ */
+ private boolean _has_start;
+
+ /**
+ * Field _end
+ */
+ private int _end;
+
+ /**
+ * keeps track of state for field: _end
+ */
+ private boolean _has_end;
+
+ /**
+ * Field _sequence
+ */
+ private java.lang.String _sequence;
+
+ /**
+ * Field _name
+ */
+ private java.lang.String _name;
+
+ /**
+ * Field _dbRefList
+ */
+ private java.util.Vector _dbRefList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public SequenceType()
+ {
+ super();
+ _dbRefList = new Vector();
+ } //-- org.vamsas.objects.core.SequenceType()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addDbRef
+ *
+ *
+ *
+ * @param vDbRef
+ */
+ public void addDbRef(org.vamsas.objects.core.DbRef vDbRef)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _dbRefList.addElement(vDbRef);
+ } //-- void addDbRef(org.vamsas.objects.core.DbRef)
+
+ /**
+ * Method addDbRef
+ *
+ *
+ *
+ * @param index
+ * @param vDbRef
+ */
+ public void addDbRef(int index, org.vamsas.objects.core.DbRef vDbRef)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _dbRefList.insertElementAt(vDbRef, index);
+ } //-- void addDbRef(int, org.vamsas.objects.core.DbRef)
+
+ /**
+ * Method deleteEnd
+ *
+ */
+ public void deleteEnd()
+ {
+ this._has_end= false;
+ } //-- void deleteEnd()
+
+ /**
+ * Method deleteStart
+ *
+ */
+ public void deleteStart()
+ {
+ this._has_start= false;
+ } //-- void deleteStart()
+
+ /**
+ * Method enumerateDbRef
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateDbRef()
+ {
+ return _dbRefList.elements();
+ } //-- java.util.Enumeration enumerateDbRef()
+
+ /**
+ * Note: hashCode() has not been overriden
+ *
+ * @param obj
+ * @return boolean
+ */
+ public boolean equals(java.lang.Object obj)
+ {
+ if ( this == obj )
+ return true;
+
+ if (super.equals(obj)==false)
+ return false;
+
+ if (obj instanceof SequenceType) {
+
+ SequenceType temp = (SequenceType)obj;
+ if (this._start != temp._start)
+ return false;
+ if (this._has_start != temp._has_start)
+ return false;
+ if (this._end != temp._end)
+ return false;
+ if (this._has_end != temp._has_end)
+ return false;
+ if (this._sequence != null) {
+ if (temp._sequence == null) return false;
+ else if (!(this._sequence.equals(temp._sequence)))
+ return false;
+ }
+ else if (temp._sequence != null)
+ return false;
+ if (this._name != null) {
+ if (temp._name == null) return false;
+ else if (!(this._name.equals(temp._name)))
+ return false;
+ }
+ else if (temp._name != null)
+ return false;
+ if (this._dbRefList != null) {
+ if (temp._dbRefList == null) return false;
+ else if (!(this._dbRefList.equals(temp._dbRefList)))
+ return false;
+ }
+ else if (temp._dbRefList != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Method getDbRef
+ *
+ *
+ *
+ * @param index
+ * @return DbRef
+ */
+ public org.vamsas.objects.core.DbRef getDbRef(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _dbRefList.size())) {
+ throw new IndexOutOfBoundsException("getDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.DbRef) _dbRefList.elementAt(index);
+ } //-- org.vamsas.objects.core.DbRef getDbRef(int)
+
+ /**
+ * Method getDbRef
+ *
+ *
+ *
+ * @return DbRef
+ */
+ public org.vamsas.objects.core.DbRef[] getDbRef()
+ {
+ int size = _dbRefList.size();
+ org.vamsas.objects.core.DbRef[] mArray = new org.vamsas.objects.core.DbRef[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.DbRef) _dbRefList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.DbRef[] getDbRef()
+
+ /**
+ * Method getDbRefCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getDbRefCount()
+ {
+ return _dbRefList.size();
+ } //-- int getDbRefCount()
+
+ /**
+ * Returns the value of field 'end'.
+ *
+ * @return int
+ * @return the value of field 'end'.
+ */
+ public int getEnd()
+ {
+ return this._end;
+ } //-- int getEnd()
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return String
+ * @return the value of field 'name'.
+ */
+ public java.lang.String getName()
+ {
+ return this._name;
+ } //-- java.lang.String getName()
+
+ /**
+ * Returns the value of field 'sequence'.
+ *
+ * @return String
+ * @return the value of field 'sequence'.
+ */
+ public java.lang.String getSequence()
+ {
+ return this._sequence;
+ } //-- java.lang.String getSequence()
+
+ /**
+ * Returns the value of field 'start'.
+ *
+ * @return int
+ * @return the value of field 'start'.
+ */
+ public int getStart()
+ {
+ return this._start;
+ } //-- int getStart()
+
+ /**
+ * Method hasEnd
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasEnd()
+ {
+ return this._has_end;
+ } //-- boolean hasEnd()
+
+ /**
+ * Method hasStart
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean hasStart()
+ {
+ return this._has_start;
+ } //-- boolean hasStart()
+
+ /**
+ * Method isValid
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean isValid()
+ {
+ try {
+ validate();
+ }
+ catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ } //-- boolean isValid()
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param out
+ */
+ public void marshal(java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, out);
+ } //-- void marshal(java.io.Writer)
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param handler
+ */
+ public void marshal(org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, handler);
+ } //-- void marshal(org.xml.sax.ContentHandler)
+
+ /**
+ * Method removeAllDbRef
+ *
+ */
+ public void removeAllDbRef()
+ {
+ _dbRefList.removeAllElements();
+ } //-- void removeAllDbRef()
+
+ /**
+ * Method removeDbRef
+ *
+ *
+ *
+ * @param index
+ * @return DbRef
+ */
+ public org.vamsas.objects.core.DbRef removeDbRef(int index)
+ {
+ java.lang.Object obj = _dbRefList.elementAt(index);
+ _dbRefList.removeElementAt(index);
+ return (org.vamsas.objects.core.DbRef) obj;
+ } //-- org.vamsas.objects.core.DbRef removeDbRef(int)
+
+ /**
+ * Method setDbRef
+ *
+ *
+ *
+ * @param index
+ * @param vDbRef
+ */
+ public void setDbRef(int index, org.vamsas.objects.core.DbRef vDbRef)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _dbRefList.size())) {
+ throw new IndexOutOfBoundsException("setDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]");
+ }
+ _dbRefList.setElementAt(vDbRef, index);
+ } //-- void setDbRef(int, org.vamsas.objects.core.DbRef)
+
+ /**
+ * Method setDbRef
+ *
+ *
+ *
+ * @param dbRefArray
+ */
+ public void setDbRef(org.vamsas.objects.core.DbRef[] dbRefArray)
+ {
+ //-- copy array
+ _dbRefList.removeAllElements();
+ for (int i = 0; i < dbRefArray.length; i++) {
+ _dbRefList.addElement(dbRefArray[i]);
+ }
+ } //-- void setDbRef(org.vamsas.objects.core.DbRef)
+
+ /**
+ * Sets the value of field 'end'.
+ *
+ * @param end the value of field 'end'.
+ */
+ public void setEnd(int end)
+ {
+ this._end = end;
+ this._has_end = true;
+ } //-- void setEnd(int)
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name the value of field 'name'.
+ */
+ public void setName(java.lang.String name)
+ {
+ this._name = name;
+ } //-- void setName(java.lang.String)
+
+ /**
+ * Sets the value of field 'sequence'.
+ *
+ * @param sequence the value of field 'sequence'.
+ */
+ public void setSequence(java.lang.String sequence)
+ {
+ this._sequence = sequence;
+ } //-- void setSequence(java.lang.String)
+
+ /**
+ * Sets the value of field 'start'.
+ *
+ * @param start the value of field 'start'.
+ */
+ public void setStart(int start)
+ {
+ this._start = start;
+ this._has_start = true;
+ } //-- void setStart(int)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return SequenceType
+ */
+ public static org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.SequenceType) Unmarshaller.unmarshal(org.vamsas.objects.core.SequenceType.class, reader);
+ } //-- org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Tree.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Tree extends org.vamsas.client.object
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _provenance
+ */
+ private org.vamsas.objects.core.Provenance _provenance;
+
+ /**
+ * Field _newickFormat
+ */
+ private java.lang.String _newickFormat;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Tree()
+ {
+ super();
+ } //-- org.vamsas.objects.core.Tree()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Note: hashCode() has not been overriden
+ *
+ * @param obj
+ * @return boolean
+ */
+ public boolean equals(java.lang.Object obj)
+ {
+ if ( this == obj )
+ return true;
+
+ if (super.equals(obj)==false)
+ return false;
+
+ if (obj instanceof Tree) {
+
+ Tree temp = (Tree)obj;
+ if (this._provenance != null) {
+ if (temp._provenance == null) return false;
+ else if (!(this._provenance.equals(temp._provenance)))
+ return false;
+ }
+ else if (temp._provenance != null)
+ return false;
+ if (this._newickFormat != null) {
+ if (temp._newickFormat == null) return false;
+ else if (!(this._newickFormat.equals(temp._newickFormat)))
+ return false;
+ }
+ else if (temp._newickFormat != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Returns the value of field 'newickFormat'.
+ *
+ * @return String
+ * @return the value of field 'newickFormat'.
+ */
+ public java.lang.String getNewickFormat()
+ {
+ return this._newickFormat;
+ } //-- java.lang.String getNewickFormat()
+
+ /**
+ * Returns the value of field 'provenance'.
+ *
+ * @return Provenance
+ * @return the value of field 'provenance'.
+ */
+ public org.vamsas.objects.core.Provenance getProvenance()
+ {
+ return this._provenance;
+ } //-- org.vamsas.objects.core.Provenance getProvenance()
+
+ /**
+ * Method isValid
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean isValid()
+ {
+ try {
+ validate();
+ }
+ catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ } //-- boolean isValid()
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param out
+ */
+ public void marshal(java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, out);
+ } //-- void marshal(java.io.Writer)
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param handler
+ */
+ public void marshal(org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, handler);
+ } //-- void marshal(org.xml.sax.ContentHandler)
+
+ /**
+ * Sets the value of field 'newickFormat'.
+ *
+ * @param newickFormat the value of field 'newickFormat'.
+ */
+ public void setNewickFormat(java.lang.String newickFormat)
+ {
+ this._newickFormat = newickFormat;
+ } //-- void setNewickFormat(java.lang.String)
+
+ /**
+ * Sets the value of field 'provenance'.
+ *
+ * @param provenance the value of field 'provenance'.
+ */
+ public void setProvenance(org.vamsas.objects.core.Provenance provenance)
+ {
+ this._provenance = provenance;
+ } //-- void setProvenance(org.vamsas.objects.core.Provenance)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return Tree
+ */
+ public static org.vamsas.objects.core.Tree unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.Tree) Unmarshaller.unmarshal(org.vamsas.objects.core.Tree.class, reader);
+ } //-- org.vamsas.objects.core.Tree unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class VAMSAS.
+ *
+ * @version $Revision$ $Date$
+ */
+public class VAMSAS extends org.vamsas.client.object
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _treeList
+ */
+ private java.util.Vector _treeList;
+
+ /**
+ * Field _sequenceSetList
+ */
+ private java.util.Vector _sequenceSetList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public VAMSAS()
+ {
+ super();
+ _treeList = new Vector();
+ _sequenceSetList = new Vector();
+ } //-- org.vamsas.objects.core.VAMSAS()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addSequenceSet
+ *
+ *
+ *
+ * @param vSequenceSet
+ */
+ public void addSequenceSet(org.vamsas.objects.core.SequenceSet vSequenceSet)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _sequenceSetList.addElement(vSequenceSet);
+ } //-- void addSequenceSet(org.vamsas.objects.core.SequenceSet)
+
+ /**
+ * Method addSequenceSet
+ *
+ *
+ *
+ * @param index
+ * @param vSequenceSet
+ */
+ public void addSequenceSet(int index, org.vamsas.objects.core.SequenceSet vSequenceSet)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _sequenceSetList.insertElementAt(vSequenceSet, index);
+ } //-- void addSequenceSet(int, org.vamsas.objects.core.SequenceSet)
+
+ /**
+ * Method addTree
+ *
+ *
+ *
+ * @param vTree
+ */
+ public void addTree(java.lang.String vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _treeList.addElement(vTree);
+ } //-- void addTree(java.lang.String)
+
+ /**
+ * Method addTree
+ *
+ *
+ *
+ * @param index
+ * @param vTree
+ */
+ public void addTree(int index, java.lang.String vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _treeList.insertElementAt(vTree, index);
+ } //-- void addTree(int, java.lang.String)
+
+ /**
+ * Method enumerateSequenceSet
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateSequenceSet()
+ {
+ return _sequenceSetList.elements();
+ } //-- java.util.Enumeration enumerateSequenceSet()
+
+ /**
+ * Method enumerateTree
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateTree()
+ {
+ return _treeList.elements();
+ } //-- java.util.Enumeration enumerateTree()
+
+ /**
+ * Note: hashCode() has not been overriden
+ *
+ * @param obj
+ * @return boolean
+ */
+ public boolean equals(java.lang.Object obj)
+ {
+ if ( this == obj )
+ return true;
+
+ if (super.equals(obj)==false)
+ return false;
+
+ if (obj instanceof VAMSAS) {
+
+ VAMSAS temp = (VAMSAS)obj;
+ if (this._treeList != null) {
+ if (temp._treeList == null) return false;
+ else if (!(this._treeList.equals(temp._treeList)))
+ return false;
+ }
+ else if (temp._treeList != null)
+ return false;
+ if (this._sequenceSetList != null) {
+ if (temp._sequenceSetList == null) return false;
+ else if (!(this._sequenceSetList.equals(temp._sequenceSetList)))
+ return false;
+ }
+ else if (temp._sequenceSetList != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Method getSequenceSet
+ *
+ *
+ *
+ * @param index
+ * @return SequenceSet
+ */
+ public org.vamsas.objects.core.SequenceSet getSequenceSet(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _sequenceSetList.size())) {
+ throw new IndexOutOfBoundsException("getSequenceSet: Index value '"+index+"' not in range [0.."+_sequenceSetList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.SequenceSet) _sequenceSetList.elementAt(index);
+ } //-- org.vamsas.objects.core.SequenceSet getSequenceSet(int)
+
+ /**
+ * Method getSequenceSet
+ *
+ *
+ *
+ * @return SequenceSet
+ */
+ public org.vamsas.objects.core.SequenceSet[] getSequenceSet()
+ {
+ int size = _sequenceSetList.size();
+ org.vamsas.objects.core.SequenceSet[] mArray = new org.vamsas.objects.core.SequenceSet[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (org.vamsas.objects.core.SequenceSet) _sequenceSetList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.SequenceSet[] getSequenceSet()
+
+ /**
+ * Method getSequenceSetCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getSequenceSetCount()
+ {
+ return _sequenceSetList.size();
+ } //-- int getSequenceSetCount()
+
+ /**
+ * Method getTree
+ *
+ *
+ *
+ * @param index
+ * @return String
+ */
+ public java.lang.String getTree(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _treeList.size())) {
+ throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
+ }
+
+ return (String)_treeList.elementAt(index);
+ } //-- java.lang.String getTree(int)
+
+ /**
+ * Method getTree
+ *
+ *
+ *
+ * @return String
+ */
+ public java.lang.String[] getTree()
+ {
+ int size = _treeList.size();
+ java.lang.String[] mArray = new java.lang.String[size];
+ for (int index = 0; index < size; index++) {
+ mArray[index] = (String)_treeList.elementAt(index);
+ }
+ return mArray;
+ } //-- java.lang.String[] getTree()
+
+ /**
+ * Method getTreeCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getTreeCount()
+ {
+ return _treeList.size();
+ } //-- int getTreeCount()
+
+ /**
+ * Method isValid
+ *
+ *
+ *
+ * @return boolean
+ */
+ public boolean isValid()
+ {
+ try {
+ validate();
+ }
+ catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ } //-- boolean isValid()
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param out
+ */
+ public void marshal(java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, out);
+ } //-- void marshal(java.io.Writer)
+
+ /**
+ * Method marshal
+ *
+ *
+ *
+ * @param handler
+ */
+ public void marshal(org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+
+ Marshaller.marshal(this, handler);
+ } //-- void marshal(org.xml.sax.ContentHandler)
+
+ /**
+ * Method removeAllSequenceSet
+ *
+ */
+ public void removeAllSequenceSet()
+ {
+ _sequenceSetList.removeAllElements();
+ } //-- void removeAllSequenceSet()
+
+ /**
+ * Method removeAllTree
+ *
+ */
+ public void removeAllTree()
+ {
+ _treeList.removeAllElements();
+ } //-- void removeAllTree()
+
+ /**
+ * Method removeSequenceSet
+ *
+ *
+ *
+ * @param index
+ * @return SequenceSet
+ */
+ public org.vamsas.objects.core.SequenceSet removeSequenceSet(int index)
+ {
+ java.lang.Object obj = _sequenceSetList.elementAt(index);
+ _sequenceSetList.removeElementAt(index);
+ return (org.vamsas.objects.core.SequenceSet) obj;
+ } //-- org.vamsas.objects.core.SequenceSet removeSequenceSet(int)
+
+ /**
+ * Method removeTree
+ *
+ *
+ *
+ * @param index
+ * @return String
+ */
+ public java.lang.String removeTree(int index)
+ {
+ java.lang.Object obj = _treeList.elementAt(index);
+ _treeList.removeElementAt(index);
+ return (String)obj;
+ } //-- java.lang.String removeTree(int)
+
+ /**
+ * Method setSequenceSet
+ *
+ *
+ *
+ * @param index
+ * @param vSequenceSet
+ */
+ public void setSequenceSet(int index, org.vamsas.objects.core.SequenceSet vSequenceSet)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _sequenceSetList.size())) {
+ throw new IndexOutOfBoundsException("setSequenceSet: Index value '"+index+"' not in range [0.."+_sequenceSetList.size()+ "]");
+ }
+ _sequenceSetList.setElementAt(vSequenceSet, index);
+ } //-- void setSequenceSet(int, org.vamsas.objects.core.SequenceSet)
+
+ /**
+ * Method setSequenceSet
+ *
+ *
+ *
+ * @param sequenceSetArray
+ */
+ public void setSequenceSet(org.vamsas.objects.core.SequenceSet[] sequenceSetArray)
+ {
+ //-- copy array
+ _sequenceSetList.removeAllElements();
+ for (int i = 0; i < sequenceSetArray.length; i++) {
+ _sequenceSetList.addElement(sequenceSetArray[i]);
+ }
+ } //-- void setSequenceSet(org.vamsas.objects.core.SequenceSet)
+
+ /**
+ * Method setTree
+ *
+ *
+ *
+ * @param index
+ * @param vTree
+ */
+ public void setTree(int index, java.lang.String vTree)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _treeList.size())) {
+ throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
+ }
+ _treeList.setElementAt(vTree, index);
+ } //-- void setTree(int, java.lang.String)
+
+ /**
+ * Method setTree
+ *
+ *
+ *
+ * @param treeArray
+ */
+ public void setTree(java.lang.String[] treeArray)
+ {
+ //-- copy array
+ _treeList.removeAllElements();
+ for (int i = 0; i < treeArray.length; i++) {
+ _treeList.addElement(treeArray[i]);
+ }
+ } //-- void setTree(java.lang.String)
+
+ /**
+ * Method unmarshal
+ *
+ *
+ *
+ * @param reader
+ * @return VAMSAS
+ */
+ public static org.vamsas.objects.core.VAMSAS unmarshal(java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+ {
+ return (org.vamsas.objects.core.VAMSAS) Unmarshaller.unmarshal(org.vamsas.objects.core.VAMSAS.class, reader);
+ } //-- org.vamsas.objects.core.VAMSAS unmarshal(java.io.Reader)
+
+ /**
+ * Method validate
+ *
+ */
+ public void validate()
+ throws org.exolab.castor.xml.ValidationException
+ {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ } //-- void validate()
+
+}
git://source.jalview.org / vamsas.git / commitdiff