--- /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;
+
+/**
+ * contains unassociated trees and a number of analysis sets
+ *
+ *
+ * @version $Revision$ $Date$
+ */
+public class VAMSAS extends org.vamsas.client.Vobject
+implements java.io.Serializable
+{
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Primary Key for vamsas object referencing
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _modifiable
+ */
+ private java.lang.String _modifiable;
+
+ /**
+ * Field _treeList
+ */
+ private java.util.Vector _treeList;
+
+ /**
+ * Field _dataSetList
+ */
+ private java.util.Vector _dataSetList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public VAMSAS()
+ {
+ super();
+ _treeList = new Vector();
+ _dataSetList = new Vector();
+ } //-- org.vamsas.objects.core.VAMSAS()
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method addDataSet
+ *
+ *
+ *
+ * @param vDataSet
+ */
+ public void addDataSet(org.vamsas.objects.core.DataSet vDataSet)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _dataSetList.addElement(vDataSet);
+ } //-- void addDataSet(org.vamsas.objects.core.DataSet)
+
+ /**
+ * Method addDataSet
+ *
+ *
+ *
+ * @param index
+ * @param vDataSet
+ */
+ public void addDataSet(int index, org.vamsas.objects.core.DataSet vDataSet)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ _dataSetList.insertElementAt(vDataSet, index);
+ } //-- void addDataSet(int, org.vamsas.objects.core.DataSet)
+
+ /**
+ * 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 enumerateDataSet
+ *
+ *
+ *
+ * @return Enumeration
+ */
+ public java.util.Enumeration enumerateDataSet()
+ {
+ return _dataSetList.elements();
+ } //-- java.util.Enumeration enumerateDataSet()
+
+ /**
+ * 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._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._modifiable != null) {
+ if (temp._modifiable == null) return false;
+ else if (!(this._modifiable.equals(temp._modifiable)))
+ return false;
+ }
+ else if (temp._modifiable != 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._dataSetList != null) {
+ if (temp._dataSetList == null) return false;
+ else if (!(this._dataSetList.equals(temp._dataSetList)))
+ return false;
+ }
+ else if (temp._dataSetList != null)
+ return false;
+ return true;
+ }
+ return false;
+ } //-- boolean equals(java.lang.Object)
+
+ /**
+ * Method getDataSet
+ *
+ *
+ *
+ * @param index
+ * @return DataSet
+ */
+ public org.vamsas.objects.core.DataSet getDataSet(int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _dataSetList.size())) {
+ throw new IndexOutOfBoundsException("getDataSet: Index value '"+index+"' not in range [0.."+_dataSetList.size()+ "]");
+ }
+
+ return (org.vamsas.objects.core.DataSet) _dataSetList.elementAt(index);
+ } //-- org.vamsas.objects.core.DataSet getDataSet(int)
+
+ /**
+ * Method getDataSet
+ *
+ *
+ *
+ * @return DataSet
+ */
+ public org.vamsas.objects.core.DataSet[] getDataSet()
+ {
+ 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.DataSet) _dataSetList.elementAt(index);
+ }
+ return mArray;
+ } //-- org.vamsas.objects.core.DataSet[] getDataSet()
+
+ /**
+ * Method getDataSetCount
+ *
+ *
+ *
+ * @return int
+ */
+ public int getDataSetCount()
+ {
+ return _dataSetList.size();
+ } //-- int getDataSetCount()
+
+ /**
+ * 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 'modifiable'.
+ *
+ * @return String
+ * @return the value of field 'modifiable'.
+ */
+ public java.lang.String getModifiable()
+ {
+ return this._modifiable;
+ } //-- java.lang.String getModifiable()
+
+ /**
+ * 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 removeAllDataSet
+ *
+ */
+ public void removeAllDataSet()
+ {
+ _dataSetList.removeAllElements();
+ } //-- void removeAllDataSet()
+
+ /**
+ * Method removeAllTree
+ *
+ */
+ public void removeAllTree()
+ {
+ _treeList.removeAllElements();
+ } //-- void removeAllTree()
+
+ /**
+ * Method removeDataSet
+ *
+ *
+ *
+ * @param index
+ * @return DataSet
+ */
+ public org.vamsas.objects.core.DataSet removeDataSet(int index)
+ {
+ 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 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 setDataSet
+ *
+ *
+ *
+ * @param index
+ * @param vDataSet
+ */
+ public void setDataSet(int index, org.vamsas.objects.core.DataSet vDataSet)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ //-- check bounds for index
+ if ((index < 0) || (index > _dataSetList.size())) {
+ throw new IndexOutOfBoundsException("setDataSet: Index value '"+index+"' not in range [0.."+_dataSetList.size()+ "]");
+ }
+ _dataSetList.setElementAt(vDataSet, index);
+ } //-- void setDataSet(int, org.vamsas.objects.core.DataSet)
+
+ /**
+ * Method setDataSet
+ *
+ *
+ *
+ * @param dataSetArray
+ */
+ public void setDataSet(org.vamsas.objects.core.DataSet[] dataSetArray)
+ {
+ //-- copy array
+ _dataSetList.removeAllElements();
+ for (int i = 0; i < dataSetArray.length; i++) {
+ _dataSetList.addElement(dataSetArray[i]);
+ }
+ } //-- void setDataSet(org.vamsas.objects.core.DataSet)
+
+ /**
+ * 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 'modifiable'.
+ *
+ * @param modifiable the value of field 'modifiable'.
+ */
+ public void setModifiable(java.lang.String modifiable)
+ {
+ this._modifiable = modifiable;
+ } //-- void setModifiable(java.lang.String)
+
+ /**
+ * 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 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 / blobdiff