private java.lang.String _id;
/**
- * Field _dendroList
+ * Field _treeList
*/
- private java.util.Vector _dendroList;
+ private java.util.Vector _treeList;
/**
- * Field _sequenceSetList
+ * Field _dataSetList
*/
- private java.util.Vector _sequenceSetList;
+ private java.util.Vector _dataSetList;
//----------------/
public VAMSAS()
{
super();
- _dendroList = new Vector();
- _sequenceSetList = new Vector();
+ _treeList = new Vector();
+ _dataSetList = new Vector();
} //-- org.vamsas.objects.core.VAMSAS()
//-----------/
/**
- * Method addDendro
+ * Method addDataSet
*
*
*
- * @param vDendro
+ * @param vDataSet
*/
- public void addDendro(org.vamsas.objects.core.Dendro vDendro)
+ public void addDataSet(org.vamsas.objects.core.DataSet vDataSet)
throws java.lang.IndexOutOfBoundsException
{
- _dendroList.addElement(vDendro);
- } //-- void addDendro(org.vamsas.objects.core.Dendro)
+ _dataSetList.addElement(vDataSet);
+ } //-- void addDataSet(org.vamsas.objects.core.DataSet)
/**
- * Method addDendro
+ * Method addDataSet
*
*
*
* @param index
- * @param vDendro
+ * @param vDataSet
*/
- public void addDendro(int index, org.vamsas.objects.core.Dendro vDendro)
+ public void addDataSet(int index, org.vamsas.objects.core.DataSet vDataSet)
throws java.lang.IndexOutOfBoundsException
{
- _dendroList.insertElementAt(vDendro, index);
- } //-- void addDendro(int, org.vamsas.objects.core.Dendro)
+ _dataSetList.insertElementAt(vDataSet, index);
+ } //-- void addDataSet(int, org.vamsas.objects.core.DataSet)
/**
- * Method addSequenceSet
+ * Method addTree
*
*
*
- * @param vSequenceSet
+ * @param vTree
*/
- public void addSequenceSet(org.vamsas.objects.core.SequenceSet vSequenceSet)
+ public void addTree(org.vamsas.objects.core.Tree vTree)
throws java.lang.IndexOutOfBoundsException
{
- _sequenceSetList.addElement(vSequenceSet);
- } //-- void addSequenceSet(org.vamsas.objects.core.SequenceSet)
+ _treeList.addElement(vTree);
+ } //-- void addTree(org.vamsas.objects.core.Tree)
/**
- * Method addSequenceSet
+ * Method addTree
*
*
*
* @param index
- * @param vSequenceSet
+ * @param vTree
*/
- public void addSequenceSet(int index, org.vamsas.objects.core.SequenceSet vSequenceSet)
+ public void addTree(int index, org.vamsas.objects.core.Tree vTree)
throws java.lang.IndexOutOfBoundsException
{
- _sequenceSetList.insertElementAt(vSequenceSet, index);
- } //-- void addSequenceSet(int, org.vamsas.objects.core.SequenceSet)
+ _treeList.insertElementAt(vTree, index);
+ } //-- void addTree(int, org.vamsas.objects.core.Tree)
/**
- * Method enumerateDendro
+ * Method enumerateDataSet
*
*
*
* @return Enumeration
*/
- public java.util.Enumeration enumerateDendro()
+ public java.util.Enumeration enumerateDataSet()
{
- return _dendroList.elements();
- } //-- java.util.Enumeration enumerateDendro()
+ return _dataSetList.elements();
+ } //-- java.util.Enumeration enumerateDataSet()
/**
- * Method enumerateSequenceSet
+ * Method enumerateTree
*
*
*
* @return Enumeration
*/
- public java.util.Enumeration enumerateSequenceSet()
+ public java.util.Enumeration enumerateTree()
{
- return _sequenceSetList.elements();
- } //-- java.util.Enumeration enumerateSequenceSet()
+ return _treeList.elements();
+ } //-- java.util.Enumeration enumerateTree()
/**
* Note: hashCode() has not been overriden
}
else if (temp._id != null)
return false;
- if (this._dendroList != null) {
- if (temp._dendroList == null) return false;
- else if (!(this._dendroList.equals(temp._dendroList)))
+ if (this._treeList != null) {
+ if (temp._treeList == null) return false;
+ else if (!(this._treeList.equals(temp._treeList)))
return false;
}
- else if (temp._dendroList != null)
+ else if (temp._treeList != null)
return false;
- if (this._sequenceSetList != null) {
- if (temp._sequenceSetList == null) return false;
- else if (!(this._sequenceSetList.equals(temp._sequenceSetList)))
+ if (this._dataSetList != null) {
+ if (temp._dataSetList == null) return false;
+ else if (!(this._dataSetList.equals(temp._dataSetList)))
return false;
}
- else if (temp._sequenceSetList != null)
+ else if (temp._dataSetList != null)
return false;
return true;
}
} //-- boolean equals(java.lang.Object)
/**
- * Method getDendro
+ * Method getDataSet
*
*
*
* @param index
- * @return Dendro
+ * @return DataSet
*/
- public org.vamsas.objects.core.Dendro getDendro(int index)
+ public org.vamsas.objects.core.DataSet getDataSet(int index)
throws java.lang.IndexOutOfBoundsException
{
//-- check bounds for index
- if ((index < 0) || (index > _dendroList.size())) {
- throw new IndexOutOfBoundsException("getDendro: Index value '"+index+"' not in range [0.."+_dendroList.size()+ "]");
+ if ((index < 0) || (index > _dataSetList.size())) {
+ throw new IndexOutOfBoundsException("getDataSet: Index value '"+index+"' not in range [0.."+_dataSetList.size()+ "]");
}
- return (org.vamsas.objects.core.Dendro) _dendroList.elementAt(index);
- } //-- org.vamsas.objects.core.Dendro getDendro(int)
+ return (org.vamsas.objects.core.DataSet) _dataSetList.elementAt(index);
+ } //-- org.vamsas.objects.core.DataSet getDataSet(int)
/**
- * Method getDendro
+ * Method getDataSet
*
*
*
- * @return Dendro
+ * @return DataSet
*/
- public org.vamsas.objects.core.Dendro[] getDendro()
+ public org.vamsas.objects.core.DataSet[] getDataSet()
{
- int size = _dendroList.size();
- org.vamsas.objects.core.Dendro[] mArray = new org.vamsas.objects.core.Dendro[size];
+ int size = _dataSetList.size();
+ org.vamsas.objects.core.DataSet[] mArray = new org.vamsas.objects.core.DataSet[size];
for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.Dendro) _dendroList.elementAt(index);
+ mArray[index] = (org.vamsas.objects.core.DataSet) _dataSetList.elementAt(index);
}
return mArray;
- } //-- org.vamsas.objects.core.Dendro[] getDendro()
+ } //-- org.vamsas.objects.core.DataSet[] getDataSet()
/**
- * Method getDendroCount
+ * Method getDataSetCount
*
*
*
* @return int
*/
- public int getDendroCount()
+ public int getDataSetCount()
{
- return _dendroList.size();
- } //-- int getDendroCount()
+ return _dataSetList.size();
+ } //-- int getDataSetCount()
/**
* Returns the value of field 'id'.
} //-- java.lang.String getId()
/**
- * Method getSequenceSet
+ * Method getTree
*
*
*
* @param index
- * @return SequenceSet
+ * @return Tree
*/
- public org.vamsas.objects.core.SequenceSet getSequenceSet(int index)
+ public org.vamsas.objects.core.Tree getTree(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()+ "]");
+ if ((index < 0) || (index > _treeList.size())) {
+ throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
}
- return (org.vamsas.objects.core.SequenceSet) _sequenceSetList.elementAt(index);
- } //-- org.vamsas.objects.core.SequenceSet getSequenceSet(int)
+ return (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
+ } //-- org.vamsas.objects.core.Tree getTree(int)
/**
- * Method getSequenceSet
+ * Method getTree
*
*
*
- * @return SequenceSet
+ * @return Tree
*/
- public org.vamsas.objects.core.SequenceSet[] getSequenceSet()
+ public org.vamsas.objects.core.Tree[] getTree()
{
- int size = _sequenceSetList.size();
- org.vamsas.objects.core.SequenceSet[] mArray = new org.vamsas.objects.core.SequenceSet[size];
+ 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.SequenceSet) _sequenceSetList.elementAt(index);
+ mArray[index] = (org.vamsas.objects.core.Tree) _treeList.elementAt(index);
}
return mArray;
- } //-- org.vamsas.objects.core.SequenceSet[] getSequenceSet()
+ } //-- org.vamsas.objects.core.Tree[] getTree()
/**
- * Method getSequenceSetCount
+ * Method getTreeCount
*
*
*
* @return int
*/
- public int getSequenceSetCount()
+ public int getTreeCount()
{
- return _sequenceSetList.size();
- } //-- int getSequenceSetCount()
+ return _treeList.size();
+ } //-- int getTreeCount()
/**
* Method isValid
} //-- void marshal(org.xml.sax.ContentHandler)
/**
- * Method removeAllDendro
+ * Method removeAllDataSet
*
*/
- public void removeAllDendro()
+ public void removeAllDataSet()
{
- _dendroList.removeAllElements();
- } //-- void removeAllDendro()
+ _dataSetList.removeAllElements();
+ } //-- void removeAllDataSet()
/**
- * Method removeAllSequenceSet
+ * Method removeAllTree
*
*/
- public void removeAllSequenceSet()
+ public void removeAllTree()
{
- _sequenceSetList.removeAllElements();
- } //-- void removeAllSequenceSet()
+ _treeList.removeAllElements();
+ } //-- void removeAllTree()
/**
- * Method removeDendro
+ * Method removeDataSet
*
*
*
* @param index
- * @return Dendro
+ * @return DataSet
*/
- public org.vamsas.objects.core.Dendro removeDendro(int index)
+ public org.vamsas.objects.core.DataSet removeDataSet(int index)
{
- java.lang.Object obj = _dendroList.elementAt(index);
- _dendroList.removeElementAt(index);
- return (org.vamsas.objects.core.Dendro) obj;
- } //-- org.vamsas.objects.core.Dendro removeDendro(int)
+ java.lang.Object obj = _dataSetList.elementAt(index);
+ _dataSetList.removeElementAt(index);
+ return (org.vamsas.objects.core.DataSet) obj;
+ } //-- org.vamsas.objects.core.DataSet removeDataSet(int)
/**
- * Method removeSequenceSet
+ * Method removeTree
*
*
*
* @param index
- * @return SequenceSet
+ * @return Tree
*/
- public org.vamsas.objects.core.SequenceSet removeSequenceSet(int index)
+ public org.vamsas.objects.core.Tree removeTree(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)
+ 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 setDendro
+ * Method setDataSet
*
*
*
* @param index
- * @param vDendro
+ * @param vDataSet
*/
- public void setDendro(int index, org.vamsas.objects.core.Dendro vDendro)
+ public void setDataSet(int index, org.vamsas.objects.core.DataSet vDataSet)
throws java.lang.IndexOutOfBoundsException
{
//-- check bounds for index
- if ((index < 0) || (index > _dendroList.size())) {
- throw new IndexOutOfBoundsException("setDendro: Index value '"+index+"' not in range [0.."+_dendroList.size()+ "]");
+ if ((index < 0) || (index > _dataSetList.size())) {
+ throw new IndexOutOfBoundsException("setDataSet: Index value '"+index+"' not in range [0.."+_dataSetList.size()+ "]");
}
- _dendroList.setElementAt(vDendro, index);
- } //-- void setDendro(int, org.vamsas.objects.core.Dendro)
+ _dataSetList.setElementAt(vDataSet, index);
+ } //-- void setDataSet(int, org.vamsas.objects.core.DataSet)
/**
- * Method setDendro
+ * Method setDataSet
*
*
*
- * @param dendroArray
+ * @param dataSetArray
*/
- public void setDendro(org.vamsas.objects.core.Dendro[] dendroArray)
+ public void setDataSet(org.vamsas.objects.core.DataSet[] dataSetArray)
{
//-- copy array
- _dendroList.removeAllElements();
- for (int i = 0; i < dendroArray.length; i++) {
- _dendroList.addElement(dendroArray[i]);
+ _dataSetList.removeAllElements();
+ for (int i = 0; i < dataSetArray.length; i++) {
+ _dataSetList.addElement(dataSetArray[i]);
}
- } //-- void setDendro(org.vamsas.objects.core.Dendro)
+ } //-- void setDataSet(org.vamsas.objects.core.DataSet)
/**
* Sets the value of field 'id'.
} //-- void setId(java.lang.String)
/**
- * Method setSequenceSet
+ * Method setTree
*
*
*
* @param index
- * @param vSequenceSet
+ * @param vTree
*/
- public void setSequenceSet(int index, org.vamsas.objects.core.SequenceSet vSequenceSet)
+ public void setTree(int index, org.vamsas.objects.core.Tree vTree)
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()+ "]");
+ if ((index < 0) || (index > _treeList.size())) {
+ throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");
}
- _sequenceSetList.setElementAt(vSequenceSet, index);
- } //-- void setSequenceSet(int, org.vamsas.objects.core.SequenceSet)
+ _treeList.setElementAt(vTree, index);
+ } //-- void setTree(int, org.vamsas.objects.core.Tree)
/**
- * Method setSequenceSet
+ * Method setTree
*
*
*
- * @param sequenceSetArray
+ * @param treeArray
*/
- public void setSequenceSet(org.vamsas.objects.core.SequenceSet[] sequenceSetArray)
+ public void setTree(org.vamsas.objects.core.Tree[] treeArray)
{
//-- copy array
- _sequenceSetList.removeAllElements();
- for (int i = 0; i < sequenceSetArray.length; i++) {
- _sequenceSetList.addElement(sequenceSetArray[i]);
+ _treeList.removeAllElements();
+ for (int i = 0; i < treeArray.length; i++) {
+ _treeList.addElement(treeArray[i]);
}
- } //-- void setSequenceSet(org.vamsas.objects.core.SequenceSet)
+ } //-- void setTree(org.vamsas.objects.core.Tree)
/**
* Method unmarshal
git://source.jalview.org / vamsas.git / blobdiff