+++ /dev/null
-/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package org.vamsas.objects.core;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * Class DataSet.
- *
- * @version $Revision$ $Date$
- */
-public class DataSet extends org.vamsas.client.Vobject
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Primary Key for vamsas object referencing
- */
- private java.lang.String _id;
-
- /**
- * Field _sequenceList
- */
- private java.util.Vector _sequenceList;
-
- /**
- * Field _dataSetAnnotationsList
- */
- private java.util.Vector _dataSetAnnotationsList;
-
- /**
- * Field _alignmentList
- */
- private java.util.Vector _alignmentList;
-
- /**
- * Field _treeList
- */
- private java.util.Vector _treeList;
-
- /**
- * Field _provenance
- */
- private org.vamsas.objects.core.Provenance _provenance;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public DataSet()
- {
- super();
- _sequenceList = new Vector();
- _dataSetAnnotationsList = new Vector();
- _alignmentList = new Vector();
- _treeList = new Vector();
- } //-- org.vamsas.objects.core.DataSet()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addAlignment
- *
- *
- *
- * @param vAlignment
- */
- public void addAlignment(org.vamsas.objects.core.Alignment vAlignment)
- throws java.lang.IndexOutOfBoundsException
- {
- _alignmentList.addElement(vAlignment);
- } //-- void addAlignment(org.vamsas.objects.core.Alignment)
-
- /**
- * Method addAlignment
- *
- *
- *
- * @param index
- * @param vAlignment
- */
- public void addAlignment(int index, org.vamsas.objects.core.Alignment vAlignment)
- throws java.lang.IndexOutOfBoundsException
- {
- _alignmentList.insertElementAt(vAlignment, index);
- } //-- void addAlignment(int, org.vamsas.objects.core.Alignment)
-
- /**
- * Method addDataSetAnnotations
- *
- *
- *
- * @param vDataSetAnnotations
- */
- public void addDataSetAnnotations(org.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations)
- throws java.lang.IndexOutOfBoundsException
- {
- _dataSetAnnotationsList.addElement(vDataSetAnnotations);
- } //-- void addDataSetAnnotations(org.vamsas.objects.core.DataSetAnnotations)
-
- /**
- * Method addDataSetAnnotations
- *
- *
- *
- * @param index
- * @param vDataSetAnnotations
- */
- public void addDataSetAnnotations(int index, org.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations)
- throws java.lang.IndexOutOfBoundsException
- {
- _dataSetAnnotationsList.insertElementAt(vDataSetAnnotations, index);
- } //-- void addDataSetAnnotations(int, org.vamsas.objects.core.DataSetAnnotations)
-
- /**
- * Method addSequence
- *
- *
- *
- * @param vSequence
- */
- public void addSequence(org.vamsas.objects.core.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException
- {
- _sequenceList.addElement(vSequence);
- } //-- void addSequence(org.vamsas.objects.core.Sequence)
-
- /**
- * Method addSequence
- *
- *
- *
- * @param index
- * @param vSequence
- */
- public void addSequence(int index, org.vamsas.objects.core.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException
- {
- _sequenceList.insertElementAt(vSequence, index);
- } //-- void addSequence(int, org.vamsas.objects.core.Sequence)
-
- /**
- * Method addTree
- *
- *
- *
- * @param vTree
- */
- public void addTree(org.vamsas.objects.core.Tree vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- _treeList.addElement(vTree);
- } //-- void addTree(org.vamsas.objects.core.Tree)
-
- /**
- * Method addTree
- *
- *
- *
- * @param index
- * @param vTree
- */
- public void addTree(int index, org.vamsas.objects.core.Tree vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- _treeList.insertElementAt(vTree, index);
- } //-- void addTree(int, org.vamsas.objects.core.Tree)
-
- /**
- * Method enumerateAlignment
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateAlignment()
- {
- return _alignmentList.elements();
- } //-- java.util.Enumeration enumerateAlignment()
-
- /**
- * Method enumerateDataSetAnnotations
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateDataSetAnnotations()
- {
- return _dataSetAnnotationsList.elements();
- } //-- java.util.Enumeration enumerateDataSetAnnotations()
-
- /**
- * Method enumerateSequence
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateSequence()
- {
- return _sequenceList.elements();
- } //-- java.util.Enumeration enumerateSequence()
-
- /**
- * Method enumerateTree
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateTree()
- {
- return _treeList.elements();
- } //-- java.util.Enumeration enumerateTree()
-
- /**
- * Note: hashCode() has not been overriden
- *
- * @param obj
- * @return boolean
- */
- public boolean equals(java.lang.Object obj)
- {
- if ( this == obj )
- return true;
-
- if (super.equals(obj)==false)
- return false;
-
- if (obj instanceof DataSet) {
-
- DataSet temp = (DataSet)obj;
- if (this._id != null) {
- if (temp._id == null) return false;
- else if (!(this._id.equals(temp._id)))
- return false;
- }
- else if (temp._id != null)
- return false;
- if (this._sequenceList != null) {
- if (temp._sequenceList == null) return false;
- else if (!(this._sequenceList.equals(temp._sequenceList)))
- return false;
- }
- else if (temp._sequenceList != null)
- return false;
- if (this._dataSetAnnotationsList != null) {
- if (temp._dataSetAnnotationsList == null) return false;
- else if (!(this._dataSetAnnotationsList.equals(temp._dataSetAnnotationsList)))
- return false;
- }
- else if (temp._dataSetAnnotationsList != null)
- return false;
- if (this._alignmentList != null) {
- if (temp._alignmentList == null) return false;
- else if (!(this._alignmentList.equals(temp._alignmentList)))
- return false;
- }
- else if (temp._alignmentList != null)
- return false;
- if (this._treeList != null) {
- if (temp._treeList == null) return false;
- else if (!(this._treeList.equals(temp._treeList)))
- return false;
- }
- else if (temp._treeList != null)
- return false;
- if (this._provenance != null) {
- if (temp._provenance == null) return false;
- else if (!(this._provenance.equals(temp._provenance)))
- return false;
- }
- else if (temp._provenance != null)
- return false;
- return true;
- }
- return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Method getAlignment
- *
- *
- *
- * @param index
- * @return Alignment
- */
- public org.vamsas.objects.core.Alignment getAlignment(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _alignmentList.size())) {
- throw new IndexOutOfBoundsException("getAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.Alignment) _alignmentList.elementAt(index);
- } //-- org.vamsas.objects.core.Alignment getAlignment(int)
-
- /**
- * Method getAlignment
- *
- *
- *
- * @return Alignment
- */
- public org.vamsas.objects.core.Alignment[] getAlignment()
- {
- int size = _alignmentList.size();
- org.vamsas.objects.core.Alignment[] mArray = new org.vamsas.objects.core.Alignment[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.Alignment) _alignmentList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.Alignment[] getAlignment()
-
- /**
- * Method getAlignmentCount
- *
- *
- *
- * @return int
- */
- public int getAlignmentCount()
- {
- return _alignmentList.size();
- } //-- int getAlignmentCount()
-
- /**
- * Method getDataSetAnnotations
- *
- *
- *
- * @param index
- * @return DataSetAnnotations
- */
- public org.vamsas.objects.core.DataSetAnnotations getDataSetAnnotations(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _dataSetAnnotationsList.size())) {
- throw new IndexOutOfBoundsException("getDataSetAnnotations: Index value '"+index+"' not in range [0.."+_dataSetAnnotationsList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.DataSetAnnotations) _dataSetAnnotationsList.elementAt(index);
- } //-- org.vamsas.objects.core.DataSetAnnotations getDataSetAnnotations(int)
-
- /**
- * Method getDataSetAnnotations
- *
- *
- *
- * @return DataSetAnnotations
- */
- public org.vamsas.objects.core.DataSetAnnotations[] getDataSetAnnotations()
- {
- int size = _dataSetAnnotationsList.size();
- org.vamsas.objects.core.DataSetAnnotations[] mArray = new org.vamsas.objects.core.DataSetAnnotations[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.DataSetAnnotations) _dataSetAnnotationsList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.DataSetAnnotations[] getDataSetAnnotations()
-
- /**
- * Method getDataSetAnnotationsCount
- *
- *
- *
- * @return int
- */
- public int getDataSetAnnotationsCount()
- {
- return _dataSetAnnotationsList.size();
- } //-- int getDataSetAnnotationsCount()
-
- /**
- * Returns the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- * @return String
- * @return the value of field 'id'.
- */
- public java.lang.String getId()
- {
- return this._id;
- } //-- java.lang.String getId()
-
- /**
- * Returns the value of field 'provenance'.
- *
- * @return Provenance
- * @return the value of field 'provenance'.
- */
- public org.vamsas.objects.core.Provenance getProvenance()
- {
- return this._provenance;
- } //-- org.vamsas.objects.core.Provenance getProvenance()
-
- /**
- * Method getSequence
- *
- *
- *
- * @param index
- * @return Sequence
- */
- public org.vamsas.objects.core.Sequence getSequence(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _sequenceList.size())) {
- throw new IndexOutOfBoundsException("getSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.Sequence) _sequenceList.elementAt(index);
- } //-- org.vamsas.objects.core.Sequence getSequence(int)
-
- /**
- * Method getSequence
- *
- *
- *
- * @return Sequence
- */
- public org.vamsas.objects.core.Sequence[] getSequence()
- {
- int size = _sequenceList.size();
- org.vamsas.objects.core.Sequence[] mArray = new org.vamsas.objects.core.Sequence[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.Sequence) _sequenceList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.Sequence[] getSequence()
-
- /**
- * Method getSequenceCount
- *
- *
- *
- * @return int
- */
- public int getSequenceCount()
- {
- return _sequenceList.size();
- } //-- int getSequenceCount()
-
- /**
- * Method getTree
- *
- *
- *
- * @param index
- * @return Tree
- */
- public org.vamsas.objects.core.Tree getTree(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _treeList.size())) {
- throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
- } //-- org.vamsas.objects.core.Tree getTree(int)
-
- /**
- * Method getTree
- *
- *
- *
- * @return Tree
- */
- public org.vamsas.objects.core.Tree[] getTree()
- {
- int size = _treeList.size();
- org.vamsas.objects.core.Tree[] mArray = new org.vamsas.objects.core.Tree[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.Tree[] getTree()
-
- /**
- * Method getTreeCount
- *
- *
- *
- * @return int
- */
- public int getTreeCount()
- {
- return _treeList.size();
- } //-- int getTreeCount()
-
- /**
- * Method isValid
- *
- *
- *
- * @return boolean
- */
- public boolean isValid()
- {
- try {
- validate();
- }
- catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- } //-- boolean isValid()
-
- /**
- * Method marshal
- *
- *
- *
- * @param out
- */
- public void marshal(java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
- Marshaller.marshal(this, out);
- } //-- void marshal(java.io.Writer)
-
- /**
- * Method marshal
- *
- *
- *
- * @param handler
- */
- public void marshal(org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
- Marshaller.marshal(this, handler);
- } //-- void marshal(org.xml.sax.ContentHandler)
-
- /**
- * Method removeAlignment
- *
- *
- *
- * @param index
- * @return Alignment
- */
- public org.vamsas.objects.core.Alignment removeAlignment(int index)
- {
- java.lang.Object obj = _alignmentList.elementAt(index);
- _alignmentList.removeElementAt(index);
- return (org.vamsas.objects.core.Alignment) obj;
- } //-- org.vamsas.objects.core.Alignment removeAlignment(int)
-
- /**
- * Method removeAllAlignment
- *
- */
- public void removeAllAlignment()
- {
- _alignmentList.removeAllElements();
- } //-- void removeAllAlignment()
-
- /**
- * Method removeAllDataSetAnnotations
- *
- */
- public void removeAllDataSetAnnotations()
- {
- _dataSetAnnotationsList.removeAllElements();
- } //-- void removeAllDataSetAnnotations()
-
- /**
- * Method removeAllSequence
- *
- */
- public void removeAllSequence()
- {
- _sequenceList.removeAllElements();
- } //-- void removeAllSequence()
-
- /**
- * Method removeAllTree
- *
- */
- public void removeAllTree()
- {
- _treeList.removeAllElements();
- } //-- void removeAllTree()
-
- /**
- * Method removeDataSetAnnotations
- *
- *
- *
- * @param index
- * @return DataSetAnnotations
- */
- public org.vamsas.objects.core.DataSetAnnotations removeDataSetAnnotations(int index)
- {
- java.lang.Object obj = _dataSetAnnotationsList.elementAt(index);
- _dataSetAnnotationsList.removeElementAt(index);
- return (org.vamsas.objects.core.DataSetAnnotations) obj;
- } //-- org.vamsas.objects.core.DataSetAnnotations removeDataSetAnnotations(int)
-
- /**
- * Method removeSequence
- *
- *
- *
- * @param index
- * @return Sequence
- */
- public org.vamsas.objects.core.Sequence removeSequence(int index)
- {
- java.lang.Object obj = _sequenceList.elementAt(index);
- _sequenceList.removeElementAt(index);
- return (org.vamsas.objects.core.Sequence) obj;
- } //-- org.vamsas.objects.core.Sequence removeSequence(int)
-
- /**
- * Method removeTree
- *
- *
- *
- * @param index
- * @return Tree
- */
- public org.vamsas.objects.core.Tree removeTree(int index)
- {
- java.lang.Object obj = _treeList.elementAt(index);
- _treeList.removeElementAt(index);
- return (org.vamsas.objects.core.Tree) obj;
- } //-- org.vamsas.objects.core.Tree removeTree(int)
-
- /**
- * Method setAlignment
- *
- *
- *
- * @param index
- * @param vAlignment
- */
- public void setAlignment(int index, org.vamsas.objects.core.Alignment vAlignment)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _alignmentList.size())) {
- throw new IndexOutOfBoundsException("setAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]");
- }
- _alignmentList.setElementAt(vAlignment, index);
- } //-- void setAlignment(int, org.vamsas.objects.core.Alignment)
-
- /**
- * Method setAlignment
- *
- *
- *
- * @param alignmentArray
- */
- public void setAlignment(org.vamsas.objects.core.Alignment[] alignmentArray)
- {
- //-- copy array
- _alignmentList.removeAllElements();
- for (int i = 0; i < alignmentArray.length; i++) {
- _alignmentList.addElement(alignmentArray[i]);
- }
- } //-- void setAlignment(org.vamsas.objects.core.Alignment)
-
- /**
- * Method setDataSetAnnotations
- *
- *
- *
- * @param index
- * @param vDataSetAnnotations
- */
- public void setDataSetAnnotations(int index, org.vamsas.objects.core.DataSetAnnotations vDataSetAnnotations)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _dataSetAnnotationsList.size())) {
- throw new IndexOutOfBoundsException("setDataSetAnnotations: Index value '"+index+"' not in range [0.."+_dataSetAnnotationsList.size()+ "]");
- }
- _dataSetAnnotationsList.setElementAt(vDataSetAnnotations, index);
- } //-- void setDataSetAnnotations(int, org.vamsas.objects.core.DataSetAnnotations)
-
- /**
- * Method setDataSetAnnotations
- *
- *
- *
- * @param dataSetAnnotationsArray
- */
- public void setDataSetAnnotations(org.vamsas.objects.core.DataSetAnnotations[] dataSetAnnotationsArray)
- {
- //-- copy array
- _dataSetAnnotationsList.removeAllElements();
- for (int i = 0; i < dataSetAnnotationsArray.length; i++) {
- _dataSetAnnotationsList.addElement(dataSetAnnotationsArray[i]);
- }
- } //-- void setDataSetAnnotations(org.vamsas.objects.core.DataSetAnnotations)
-
- /**
- * Sets the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- * @param id the value of field 'id'.
- */
- public void setId(java.lang.String id)
- {
- this._id = id;
- } //-- void setId(java.lang.String)
-
- /**
- * Sets the value of field 'provenance'.
- *
- * @param provenance the value of field 'provenance'.
- */
- public void setProvenance(org.vamsas.objects.core.Provenance provenance)
- {
- this._provenance = provenance;
- } //-- void setProvenance(org.vamsas.objects.core.Provenance)
-
- /**
- * Method setSequence
- *
- *
- *
- * @param index
- * @param vSequence
- */
- public void setSequence(int index, org.vamsas.objects.core.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _sequenceList.size())) {
- throw new IndexOutOfBoundsException("setSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]");
- }
- _sequenceList.setElementAt(vSequence, index);
- } //-- void setSequence(int, org.vamsas.objects.core.Sequence)
-
- /**
- * Method setSequence
- *
- *
- *
- * @param sequenceArray
- */
- public void setSequence(org.vamsas.objects.core.Sequence[] sequenceArray)
- {
- //-- copy array
- _sequenceList.removeAllElements();
- for (int i = 0; i < sequenceArray.length; i++) {
- _sequenceList.addElement(sequenceArray[i]);
- }
- } //-- void setSequence(org.vamsas.objects.core.Sequence)
-
- /**
- * Method setTree
- *
- *
- *
- * @param index
- * @param vTree
- */
- public void setTree(int index, org.vamsas.objects.core.Tree vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _treeList.size())) {
- throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
- }
- _treeList.setElementAt(vTree, index);
- } //-- void setTree(int, org.vamsas.objects.core.Tree)
-
- /**
- * Method setTree
- *
- *
- *
- * @param treeArray
- */
- public void setTree(org.vamsas.objects.core.Tree[] treeArray)
- {
- //-- copy array
- _treeList.removeAllElements();
- for (int i = 0; i < treeArray.length; i++) {
- _treeList.addElement(treeArray[i]);
- }
- } //-- void setTree(org.vamsas.objects.core.Tree)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return DataSet
- */
- public static org.vamsas.objects.core.DataSet unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (org.vamsas.objects.core.DataSet) Unmarshaller.unmarshal(org.vamsas.objects.core.DataSet.class, reader);
- } //-- org.vamsas.objects.core.DataSet unmarshal(java.io.Reader)
-
- /**
- * Method validate
- *
- */
- public void validate()
- throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- } //-- void validate()
-
-}
git://source.jalview.org / vamsas.git / blobdiff