import org.xml.sax.ContentHandler;
/**
- * Class SequenceSet.
+ * Class DataSet.
*
* @version $Revision$ $Date$
*/
-public class SequenceSet extends org.vamsas.client.object
+public class DataSet extends org.vamsas.client.object
implements java.io.Serializable
{
private java.util.Vector _sequenceList;
/**
- * Field _sequenceSetAnnotationsList
+ * Field _dataSetAnnotationsList
*/
- private java.util.Vector _sequenceSetAnnotationsList;
+ private java.util.Vector _dataSetAnnotationsList;
/**
* Field _alignmentList
//- Constructors -/
//----------------/
- public SequenceSet()
+ public DataSet()
{
super();
_sequenceList = new Vector();
- _sequenceSetAnnotationsList = new Vector();
+ _dataSetAnnotationsList = new Vector();
_alignmentList = new Vector();
_treeList = new Vector();
_provenanceList = new Vector();
- } //-- org.vamsas.objects.core.SequenceSet()
+ } //-- org.vamsas.objects.core.DataSet()
//-----------/
} //-- 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 addProvenance
*
*
} //-- 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 addTree
*
*
} //-- java.util.Enumeration enumerateAlignment()
/**
- * Method enumerateProvenance
+ * Method enumerateDataSetAnnotations
*
*
*
* @return Enumeration
*/
- public java.util.Enumeration enumerateProvenance()
+ public java.util.Enumeration enumerateDataSetAnnotations()
{
- return _provenanceList.elements();
- } //-- java.util.Enumeration enumerateProvenance()
+ return _dataSetAnnotationsList.elements();
+ } //-- java.util.Enumeration enumerateDataSetAnnotations()
/**
- * Method enumerateSequence
+ * Method enumerateProvenance
*
*
*
* @return Enumeration
*/
- public java.util.Enumeration enumerateSequence()
+ public java.util.Enumeration enumerateProvenance()
{
- return _sequenceList.elements();
- } //-- java.util.Enumeration enumerateSequence()
+ return _provenanceList.elements();
+ } //-- java.util.Enumeration enumerateProvenance()
/**
- * Method enumerateSequenceSetAnnotations
+ * Method enumerateSequence
*
*
*
* @return Enumeration
*/
- public java.util.Enumeration enumerateSequenceSetAnnotations()
+ public java.util.Enumeration enumerateSequence()
{
- return _sequenceSetAnnotationsList.elements();
- } //-- java.util.Enumeration enumerateSequenceSetAnnotations()
+ return _sequenceList.elements();
+ } //-- java.util.Enumeration enumerateSequence()
/**
* Method enumerateTree
if (super.equals(obj)==false)
return false;
- if (obj instanceof SequenceSet) {
+ if (obj instanceof DataSet) {
- SequenceSet temp = (SequenceSet)obj;
+ DataSet temp = (DataSet)obj;
if (this._id != null) {
if (temp._id == null) return false;
else if (!(this._id.equals(temp._id)))
}
else if (temp._sequenceList != null)
return false;
- if (this._sequenceSetAnnotationsList != null) {
- if (temp._sequenceSetAnnotationsList == null) return false;
- else if (!(this._sequenceSetAnnotationsList.equals(temp._sequenceSetAnnotationsList)))
+ if (this._dataSetAnnotationsList != null) {
+ if (temp._dataSetAnnotationsList == null) return false;
+ else if (!(this._dataSetAnnotationsList.equals(temp._dataSetAnnotationsList)))
return false;
}
- else if (temp._sequenceSetAnnotationsList != null)
+ else if (temp._dataSetAnnotationsList != null)
return false;
if (this._alignmentList != null) {
if (temp._alignmentList == null) return false;
} //-- 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'.
*
* @return String
} //-- 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()
-
- /**
* Method getTree
*
*
} //-- void removeAllAlignment()
/**
+ * Method removeAllDataSetAnnotations
+ *
+ */
+ public void removeAllDataSetAnnotations()
+ {
+ _dataSetAnnotationsList.removeAllElements();
+ } //-- void removeAllDataSetAnnotations()
+
+ /**
* Method removeAllProvenance
*
*/
} //-- void removeAllSequence()
/**
- * Method removeAllSequenceSetAnnotations
+ * Method removeAllTree
*
*/
- public void removeAllSequenceSetAnnotations()
+ public void removeAllTree()
{
- _sequenceSetAnnotationsList.removeAllElements();
- } //-- void removeAllSequenceSetAnnotations()
+ _treeList.removeAllElements();
+ } //-- void removeAllTree()
/**
- * Method removeAllTree
+ * Method removeDataSetAnnotations
*
+ *
+ *
+ * @param index
+ * @return DataSetAnnotations
*/
- public void removeAllTree()
+ public org.vamsas.objects.core.DataSetAnnotations removeDataSetAnnotations(int index)
{
- _treeList.removeAllElements();
- } //-- void removeAllTree()
+ 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 removeProvenance
} //-- 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)
-
- /**
* Method removeTree
*
*
} //-- 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'.
*
* @param id the value of field 'id'.
} //-- 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)
-
- /**
* Method setTree
*
*
*
*
* @param reader
- * @return SequenceSet
+ * @return DataSet
*/
- public static org.vamsas.objects.core.SequenceSet unmarshal(java.io.Reader reader)
+ 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.SequenceSet) Unmarshaller.unmarshal(org.vamsas.objects.core.SequenceSet.class, reader);
- } //-- org.vamsas.objects.core.SequenceSet unmarshal(java.io.Reader)
+ 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
git://source.jalview.org / vamsas.git / blobdiff