+++ /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 Alignment.
- *
- * @version $Revision$ $Date$
- */
-public class Alignment extends org.vamsas.client.Vobject
-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;
-
- /**
- * Primary Key for vamsas object referencing
- *
- */
- private java.lang.String _id;
-
- /**
- * Field _modifiable
- */
- private java.lang.String _modifiable;
-
- /**
- * This is annotation over the coordinate frame
- * defined by all the columns in the alignment.
- *
- */
- private java.util.Vector _alignmentAnnotationList;
-
- /**
- * Field _treeList
- */
- private java.util.Vector _treeList;
-
- /**
- * Field _alignmentSequenceList
- */
- private java.util.Vector _alignmentSequenceList;
-
- /**
- * typical properties may be additional
- * alignment score objects
- */
- private java.util.Vector _propertyList;
-
- /**
- * Field _provenance
- */
- private org.vamsas.objects.core.Provenance _provenance;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Alignment()
- {
- super();
- _alignmentAnnotationList = new Vector();
- _treeList = new Vector();
- _alignmentSequenceList = new Vector();
- _propertyList = new Vector();
- } //-- org.vamsas.objects.core.Alignment()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addAlignmentAnnotation
- *
- *
- *
- * @param vAlignmentAnnotation
- */
- public void addAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
- throws java.lang.IndexOutOfBoundsException
- {
- _alignmentAnnotationList.addElement(vAlignmentAnnotation);
- } //-- void addAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation)
-
- /**
- * Method addAlignmentAnnotation
- *
- *
- *
- * @param index
- * @param vAlignmentAnnotation
- */
- public void addAlignmentAnnotation(int index, org.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
- throws java.lang.IndexOutOfBoundsException
- {
- _alignmentAnnotationList.insertElementAt(vAlignmentAnnotation, index);
- } //-- void addAlignmentAnnotation(int, org.vamsas.objects.core.AlignmentAnnotation)
-
- /**
- * 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 addProperty
- *
- *
- *
- * @param vProperty
- */
- public void addProperty(org.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- _propertyList.addElement(vProperty);
- } //-- void addProperty(org.vamsas.objects.core.Property)
-
- /**
- * Method addProperty
- *
- *
- *
- * @param index
- * @param vProperty
- */
- public void addProperty(int index, org.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- _propertyList.insertElementAt(vProperty, index);
- } //-- void addProperty(int, org.vamsas.objects.core.Property)
-
- /**
- * 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 deleteAligned
- *
- */
- public void deleteAligned()
- {
- this._has_aligned= false;
- } //-- void deleteAligned()
-
- /**
- * Method enumerateAlignmentAnnotation
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateAlignmentAnnotation()
- {
- return _alignmentAnnotationList.elements();
- } //-- java.util.Enumeration enumerateAlignmentAnnotation()
-
- /**
- * Method enumerateAlignmentSequence
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateAlignmentSequence()
- {
- return _alignmentSequenceList.elements();
- } //-- java.util.Enumeration enumerateAlignmentSequence()
-
- /**
- * Method enumerateProperty
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateProperty()
- {
- return _propertyList.elements();
- } //-- java.util.Enumeration enumerateProperty()
-
- /**
- * 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._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._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._alignmentAnnotationList != null) {
- if (temp._alignmentAnnotationList == null) return false;
- else if (!(this._alignmentAnnotationList.equals(temp._alignmentAnnotationList)))
- return false;
- }
- else if (temp._alignmentAnnotationList != 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._propertyList != null) {
- if (temp._propertyList == null) return false;
- else if (!(this._propertyList.equals(temp._propertyList)))
- return false;
- }
- else if (temp._propertyList != 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 getAlignmentAnnotation
- *
- *
- *
- * @param index
- * @return AlignmentAnnotation
- */
- public org.vamsas.objects.core.AlignmentAnnotation getAlignmentAnnotation(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _alignmentAnnotationList.size())) {
- throw new IndexOutOfBoundsException("getAlignmentAnnotation: Index value '"+index+"' not in range [0.."+_alignmentAnnotationList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.AlignmentAnnotation) _alignmentAnnotationList.elementAt(index);
- } //-- org.vamsas.objects.core.AlignmentAnnotation getAlignmentAnnotation(int)
-
- /**
- * Method getAlignmentAnnotation
- *
- *
- *
- * @return AlignmentAnnotation
- */
- public org.vamsas.objects.core.AlignmentAnnotation[] getAlignmentAnnotation()
- {
- int size = _alignmentAnnotationList.size();
- org.vamsas.objects.core.AlignmentAnnotation[] mArray = new org.vamsas.objects.core.AlignmentAnnotation[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.AlignmentAnnotation) _alignmentAnnotationList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.AlignmentAnnotation[] getAlignmentAnnotation()
-
- /**
- * Method getAlignmentAnnotationCount
- *
- *
- *
- * @return int
- */
- public int getAlignmentAnnotationCount()
- {
- return _alignmentAnnotationList.size();
- } //-- int getAlignmentAnnotationCount()
-
- /**
- * 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 '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 '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 getProperty
- *
- *
- *
- * @param index
- * @return Property
- */
- public org.vamsas.objects.core.Property getProperty(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _propertyList.size())) {
- throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
- }
-
- return (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
- } //-- org.vamsas.objects.core.Property getProperty(int)
-
- /**
- * Method getProperty
- *
- *
- *
- * @return Property
- */
- public org.vamsas.objects.core.Property[] getProperty()
- {
- int size = _propertyList.size();
- org.vamsas.objects.core.Property[] mArray = new org.vamsas.objects.core.Property[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (org.vamsas.objects.core.Property) _propertyList.elementAt(index);
- }
- return mArray;
- } //-- org.vamsas.objects.core.Property[] getProperty()
-
- /**
- * Method getPropertyCount
- *
- *
- *
- * @return int
- */
- public int getPropertyCount()
- {
- return _propertyList.size();
- } //-- int getPropertyCount()
-
- /**
- * 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 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 removeAlignmentAnnotation
- *
- *
- *
- * @param index
- * @return AlignmentAnnotation
- */
- public org.vamsas.objects.core.AlignmentAnnotation removeAlignmentAnnotation(int index)
- {
- java.lang.Object obj = _alignmentAnnotationList.elementAt(index);
- _alignmentAnnotationList.removeElementAt(index);
- return (org.vamsas.objects.core.AlignmentAnnotation) obj;
- } //-- org.vamsas.objects.core.AlignmentAnnotation removeAlignmentAnnotation(int)
-
- /**
- * 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 removeAllAlignmentAnnotation
- *
- */
- public void removeAllAlignmentAnnotation()
- {
- _alignmentAnnotationList.removeAllElements();
- } //-- void removeAllAlignmentAnnotation()
-
- /**
- * Method removeAllAlignmentSequence
- *
- */
- public void removeAllAlignmentSequence()
- {
- _alignmentSequenceList.removeAllElements();
- } //-- void removeAllAlignmentSequence()
-
- /**
- * Method removeAllProperty
- *
- */
- public void removeAllProperty()
- {
- _propertyList.removeAllElements();
- } //-- void removeAllProperty()
-
- /**
- * Method removeAllTree
- *
- */
- public void removeAllTree()
- {
- _treeList.removeAllElements();
- } //-- void removeAllTree()
-
- /**
- * Method removeProperty
- *
- *
- *
- * @param index
- * @return Property
- */
- public org.vamsas.objects.core.Property removeProperty(int index)
- {
- java.lang.Object obj = _propertyList.elementAt(index);
- _propertyList.removeElementAt(index);
- return (org.vamsas.objects.core.Property) obj;
- } //-- org.vamsas.objects.core.Property removeProperty(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)
-
- /**
- * 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 setAlignmentAnnotation
- *
- *
- *
- * @param index
- * @param vAlignmentAnnotation
- */
- public void setAlignmentAnnotation(int index, org.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _alignmentAnnotationList.size())) {
- throw new IndexOutOfBoundsException("setAlignmentAnnotation: Index value '"+index+"' not in range [0.."+_alignmentAnnotationList.size()+ "]");
- }
- _alignmentAnnotationList.setElementAt(vAlignmentAnnotation, index);
- } //-- void setAlignmentAnnotation(int, org.vamsas.objects.core.AlignmentAnnotation)
-
- /**
- * Method setAlignmentAnnotation
- *
- *
- *
- * @param alignmentAnnotationArray
- */
- public void setAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation[] alignmentAnnotationArray)
- {
- //-- copy array
- _alignmentAnnotationList.removeAllElements();
- for (int i = 0; i < alignmentAnnotationArray.length; i++) {
- _alignmentAnnotationList.addElement(alignmentAnnotationArray[i]);
- }
- } //-- void setAlignmentAnnotation(org.vamsas.objects.core.AlignmentAnnotation)
-
- /**
- * 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 '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 '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 setProperty
- *
- *
- *
- * @param index
- * @param vProperty
- */
- public void setProperty(int index, org.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _propertyList.size())) {
- throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
- }
- _propertyList.setElementAt(vProperty, index);
- } //-- void setProperty(int, org.vamsas.objects.core.Property)
-
- /**
- * Method setProperty
- *
- *
- *
- * @param propertyArray
- */
- public void setProperty(org.vamsas.objects.core.Property[] propertyArray)
- {
- //-- copy array
- _propertyList.removeAllElements();
- for (int i = 0; i < propertyArray.length; i++) {
- _propertyList.addElement(propertyArray[i]);
- }
- } //-- void setProperty(org.vamsas.objects.core.Property)
-
- /**
- * 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()
-
-}
git://source.jalview.org / vamsas.git / blobdiff