/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * This file is part of the Vamsas Client version 0.1.
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite,
+ * Andrew Waterhouse and Dominik Lindner.
+ *
+ * Earlier versions have also been incorporated into Jalview version 2.4
+ * since 2008, and TOPALi version 2 since 2007.
+ *
+ * The Vamsas Client is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * The Vamsas Client is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the Vamsas Client. If not, see <http://www.gnu.org/licenses/>.
*/
-
package uk.ac.vamsas.objects.core;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import org.exolab.castor.xml.Marshaller;
/**
* Class Alignment.
*
- * @version $Revision$ $Date$
+ * @version $Revision$ $Date: 2007-06-28 14:51:44 +0100 (Thu, 28 Jun 2007)
+ * $
*/
-public class Alignment extends uk.ac.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 uk.ac.vamsas.objects.core.Provenance _provenance;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Alignment() {
- super();
- this._alignmentAnnotationList = new java.util.Vector();
- this._treeList = new java.util.Vector();
- this._alignmentSequenceList = new java.util.Vector();
- this._propertyList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @param vAlignmentAnnotation
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addAlignmentAnnotation(
- final uk.ac.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
- throws java.lang.IndexOutOfBoundsException {
- this._alignmentAnnotationList.addElement(vAlignmentAnnotation);
- }
-
- /**
- *
- *
- * @param index
- * @param vAlignmentAnnotation
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addAlignmentAnnotation(
- final int index,
- final uk.ac.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
- throws java.lang.IndexOutOfBoundsException {
- this._alignmentAnnotationList.add(index, vAlignmentAnnotation);
- }
-
- /**
- *
- *
- * @param vAlignmentSequence
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addAlignmentSequence(
- final uk.ac.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
- throws java.lang.IndexOutOfBoundsException {
- this._alignmentSequenceList.addElement(vAlignmentSequence);
- }
-
- /**
- *
- *
- * @param index
- * @param vAlignmentSequence
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addAlignmentSequence(
- final int index,
- final uk.ac.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
- throws java.lang.IndexOutOfBoundsException {
- this._alignmentSequenceList.add(index, vAlignmentSequence);
- }
-
- /**
- *
- *
- * @param vProperty
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addProperty(
- final uk.ac.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException {
- this._propertyList.addElement(vProperty);
- }
-
- /**
- *
- *
- * @param index
- * @param vProperty
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addProperty(
- final int index,
- final uk.ac.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException {
- this._propertyList.add(index, vProperty);
- }
-
- /**
- *
- *
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addTree(
- final uk.ac.vamsas.objects.core.Tree vTree)
- throws java.lang.IndexOutOfBoundsException {
- this._treeList.addElement(vTree);
- }
-
- /**
- *
- *
- * @param index
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void addTree(
- final int index,
- final uk.ac.vamsas.objects.core.Tree vTree)
- throws java.lang.IndexOutOfBoundsException {
- this._treeList.add(index, vTree);
- }
-
- /**
- */
- public void deleteAligned(
- ) {
- this._has_aligned= false;
- }
-
- /**
- * Method enumerateAlignmentAnnotation.
- *
- * @return an Enumeration over all
- * uk.ac.vamsas.objects.core.AlignmentAnnotation elements
- */
- public java.util.Enumeration enumerateAlignmentAnnotation(
- ) {
- return this._alignmentAnnotationList.elements();
- }
-
- /**
- * Method enumerateAlignmentSequence.
- *
- * @return an Enumeration over all
- * uk.ac.vamsas.objects.core.AlignmentSequence elements
- */
- public java.util.Enumeration enumerateAlignmentSequence(
- ) {
- return this._alignmentSequenceList.elements();
- }
-
- /**
- * Method enumerateProperty.
- *
- * @return an Enumeration over all
- * uk.ac.vamsas.objects.core.Property elements
- */
- public java.util.Enumeration enumerateProperty(
- ) {
- return this._propertyList.elements();
- }
-
- /**
- * Method enumerateTree.
- *
- * @return an Enumeration over all
- * uk.ac.vamsas.objects.core.Tree elements
- */
- public java.util.Enumeration enumerateTree(
- ) {
- return this._treeList.elements();
- }
-
- /**
- * Overrides the java.lang.Object.equals method.
- *
- * @param obj
- * @return true if the objects are equal.
- */
- public boolean equals(
- final java.lang.Object obj) {
- if ( this == obj )
- return true;
-
- if (super.equals(obj)==false)
+public class Alignment extends uk.ac.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 uk.ac.vamsas.objects.core.Provenance _provenance;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Alignment() {
+ super();
+ this._alignmentAnnotationList = new java.util.Vector();
+ this._treeList = new java.util.Vector();
+ this._alignmentSequenceList = new java.util.Vector();
+ this._propertyList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vAlignmentAnnotation
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAlignmentAnnotation(
+ final uk.ac.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
+ throws java.lang.IndexOutOfBoundsException {
+ this._alignmentAnnotationList.addElement(vAlignmentAnnotation);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlignmentAnnotation
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAlignmentAnnotation(final int index,
+ final uk.ac.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
+ throws java.lang.IndexOutOfBoundsException {
+ this._alignmentAnnotationList.add(index, vAlignmentAnnotation);
+ }
+
+ /**
+ *
+ *
+ * @param vAlignmentSequence
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAlignmentSequence(
+ final uk.ac.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
+ throws java.lang.IndexOutOfBoundsException {
+ this._alignmentSequenceList.addElement(vAlignmentSequence);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlignmentSequence
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAlignmentSequence(final int index,
+ final uk.ac.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
+ throws java.lang.IndexOutOfBoundsException {
+ this._alignmentSequenceList.add(index, vAlignmentSequence);
+ }
+
+ /**
+ *
+ *
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addProperty(final uk.ac.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException {
+ this._propertyList.addElement(vProperty);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addProperty(final int index,
+ final uk.ac.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException {
+ this._propertyList.add(index, vProperty);
+ }
+
+ /**
+ *
+ *
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addTree(final uk.ac.vamsas.objects.core.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ this._treeList.addElement(vTree);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addTree(final int index,
+ final uk.ac.vamsas.objects.core.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ this._treeList.add(index, vTree);
+ }
+
+ /**
+ */
+ public void deleteAligned() {
+ this._has_aligned = false;
+ }
+
+ /**
+ * Method enumerateAlignmentAnnotation.
+ *
+ * @return an Enumeration over all
+ * uk.ac.vamsas.objects.core.AlignmentAnnotation elements
+ */
+ public java.util.Enumeration enumerateAlignmentAnnotation() {
+ return this._alignmentAnnotationList.elements();
+ }
+
+ /**
+ * Method enumerateAlignmentSequence.
+ *
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.AlignmentSequence
+ * elements
+ */
+ public java.util.Enumeration enumerateAlignmentSequence() {
+ return this._alignmentSequenceList.elements();
+ }
+
+ /**
+ * Method enumerateProperty.
+ *
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.Property elements
+ */
+ public java.util.Enumeration enumerateProperty() {
+ return this._propertyList.elements();
+ }
+
+ /**
+ * Method enumerateTree.
+ *
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.Tree elements
+ */
+ public java.util.Enumeration enumerateTree() {
+ return this._treeList.elements();
+ }
+
+ /**
+ * Overrides the java.lang.Object.equals method.
+ *
+ * @param obj
+ * @return true if the objects are equal.
+ */
+ public boolean equals(final java.lang.Object obj) {
+ if (this == obj)
+ return true;
+
+ if (super.equals(obj) == false)
+ return false;
+
+ if (obj instanceof Alignment) {
+
+ Alignment temp = (Alignment) obj;
+ boolean thcycle;
+ boolean tmcycle;
+ if (this._gapChar != null) {
+ if (temp._gapChar == null)
+ return false;
+ if (this._gapChar != temp._gapChar) {
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._gapChar);
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._gapChar);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._gapChar);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._gapChar);
+ }
+ ;
return false;
-
- if (obj instanceof Alignment) {
-
- Alignment temp = (Alignment)obj;
- boolean thcycle;
- boolean tmcycle;
- if (this._gapChar != null) {
- if (temp._gapChar == null) return false;
- if (this._gapChar != temp._gapChar) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._gapChar);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._gapChar);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._gapChar); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._gapChar); };
- return false;
- }
- if (!thcycle) {
- if (!this._gapChar.equals(temp._gapChar)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._gapChar);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._gapChar);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._gapChar);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._gapChar);
- }
- }
- } 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;
- if (this._id != temp._id) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._id);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._id);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._id); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._id); };
- return false;
- }
- if (!thcycle) {
- if (!this._id.equals(temp._id)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
- }
- }
- } else if (temp._id != null)
- return false;
- if (this._modifiable != null) {
- if (temp._modifiable == null) return false;
- if (this._modifiable != temp._modifiable) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._modifiable);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._modifiable);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable); };
- return false;
- }
- if (!thcycle) {
- if (!this._modifiable.equals(temp._modifiable)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
- }
- }
- } else if (temp._modifiable != null)
- return false;
- if (this._alignmentAnnotationList != null) {
- if (temp._alignmentAnnotationList == null) return false;
- if (this._alignmentAnnotationList != temp._alignmentAnnotationList) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._alignmentAnnotationList);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._alignmentAnnotationList);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._alignmentAnnotationList); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._alignmentAnnotationList); };
- return false;
- }
- if (!thcycle) {
- if (!this._alignmentAnnotationList.equals(temp._alignmentAnnotationList)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._alignmentAnnotationList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._alignmentAnnotationList);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._alignmentAnnotationList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._alignmentAnnotationList);
- }
- }
- } else if (temp._alignmentAnnotationList != null)
- return false;
- if (this._treeList != null) {
- if (temp._treeList == null) return false;
- if (this._treeList != temp._treeList) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._treeList);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._treeList);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList); };
- return false;
- }
- if (!thcycle) {
- if (!this._treeList.equals(temp._treeList)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
- }
- }
- } else if (temp._treeList != null)
- return false;
- if (this._alignmentSequenceList != null) {
- if (temp._alignmentSequenceList == null) return false;
- if (this._alignmentSequenceList != temp._alignmentSequenceList) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._alignmentSequenceList);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._alignmentSequenceList);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._alignmentSequenceList); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._alignmentSequenceList); };
- return false;
- }
- if (!thcycle) {
- if (!this._alignmentSequenceList.equals(temp._alignmentSequenceList)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._alignmentSequenceList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._alignmentSequenceList);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._alignmentSequenceList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._alignmentSequenceList);
- }
- }
- } else if (temp._alignmentSequenceList != null)
- return false;
- if (this._propertyList != null) {
- if (temp._propertyList == null) return false;
- if (this._propertyList != temp._propertyList) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._propertyList);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._propertyList);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList); };
- return false;
- }
- if (!thcycle) {
- if (!this._propertyList.equals(temp._propertyList)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
- }
- }
- } else if (temp._propertyList != null)
- return false;
- if (this._provenance != null) {
- if (temp._provenance == null) return false;
- if (this._provenance != temp._provenance) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._provenance);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._provenance);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance); };
- return false;
- }
- if (!thcycle) {
- if (!this._provenance.equals(temp._provenance)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
- }
- }
- } else if (temp._provenance != null)
- return false;
- return true;
+ }
+ if (!thcycle) {
+ if (!this._gapChar.equals(temp._gapChar)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._gapChar);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._gapChar);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._gapChar);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._gapChar);
+ }
}
+ } else if (temp._gapChar != null)
return false;
- }
-
- /**
- * Returns the value of field 'aligned'.
- *
- * @return the value of field 'Aligned'.
- */
- public boolean getAligned(
- ) {
- return this._aligned;
- }
-
- /**
- * Method getAlignmentAnnotation.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * uk.ac.vamsas.objects.core.AlignmentAnnotation at the given
- * index
- */
- public uk.ac.vamsas.objects.core.AlignmentAnnotation getAlignmentAnnotation(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._alignmentAnnotationList.size()) {
- throw new IndexOutOfBoundsException("getAlignmentAnnotation: Index value '" + index + "' not in range [0.." + (this._alignmentAnnotationList.size() - 1) + "]");
- }
-
- return (uk.ac.vamsas.objects.core.AlignmentAnnotation) _alignmentAnnotationList.get(index);
- }
-
- /**
- * Method getAlignmentAnnotation.Returns the contents of the
- * collection in an Array. <p>Note: Just in case the
- * collection contents are changing in another thread, we pass
- * a 0-length Array of the correct type into the API call.
- * This way we <i>know</i> that the Array returned is of
- * exactly the correct length.
- *
- * @return this collection as an Array
- */
- public uk.ac.vamsas.objects.core.AlignmentAnnotation[] getAlignmentAnnotation(
- ) {
- uk.ac.vamsas.objects.core.AlignmentAnnotation[] array = new uk.ac.vamsas.objects.core.AlignmentAnnotation[0];
- return (uk.ac.vamsas.objects.core.AlignmentAnnotation[]) this._alignmentAnnotationList.toArray(array);
- }
-
- /**
- * Method getAlignmentAnnotationAsReference.Returns a reference
- * to '_alignmentAnnotationList'. No type checking is performed
- * on any modifications to the Vector.
- *
- * @return a reference to the Vector backing this class
- */
- public java.util.Vector getAlignmentAnnotationAsReference(
- ) {
- return this._alignmentAnnotationList;
- }
-
- /**
- * Method getAlignmentAnnotationCount.
- *
- * @return the size of this collection
- */
- public int getAlignmentAnnotationCount(
- ) {
- return this._alignmentAnnotationList.size();
- }
-
- /**
- * Method getAlignmentSequence.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the
- * uk.ac.vamsas.objects.core.AlignmentSequence at the given inde
- */
- public uk.ac.vamsas.objects.core.AlignmentSequence getAlignmentSequence(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._alignmentSequenceList.size()) {
- throw new IndexOutOfBoundsException("getAlignmentSequence: Index value '" + index + "' not in range [0.." + (this._alignmentSequenceList.size() - 1) + "]");
- }
-
- return (uk.ac.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.get(index);
- }
-
- /**
- * Method getAlignmentSequence.Returns the contents of the
- * collection in an Array. <p>Note: Just in case the
- * collection contents are changing in another thread, we pass
- * a 0-length Array of the correct type into the API call.
- * This way we <i>know</i> that the Array returned is of
- * exactly the correct length.
- *
- * @return this collection as an Array
- */
- public uk.ac.vamsas.objects.core.AlignmentSequence[] getAlignmentSequence(
- ) {
- uk.ac.vamsas.objects.core.AlignmentSequence[] array = new uk.ac.vamsas.objects.core.AlignmentSequence[0];
- return (uk.ac.vamsas.objects.core.AlignmentSequence[]) this._alignmentSequenceList.toArray(array);
- }
-
- /**
- * Method getAlignmentSequenceAsReference.Returns a reference
- * to '_alignmentSequenceList'. No type checking is performed
- * on any modifications to the Vector.
- *
- * @return a reference to the Vector backing this class
- */
- public java.util.Vector getAlignmentSequenceAsReference(
- ) {
- return this._alignmentSequenceList;
- }
-
- /**
- * Method getAlignmentSequenceCount.
- *
- * @return the size of this collection
- */
- public int getAlignmentSequenceCount(
- ) {
- return this._alignmentSequenceList.size();
- }
-
- /**
- * Returns the value of field 'gapChar'.
- *
- * @return the value of field 'GapChar'.
- */
- public java.lang.String getGapChar(
- ) {
- return this._gapChar;
- }
-
- /**
- * Returns the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- *
- * @return the value of field 'Id'.
- */
- public java.lang.String getId(
- ) {
- return this._id;
- }
-
- /**
- * Returns the value of field 'modifiable'.
- *
- * @return the value of field 'Modifiable'.
- */
- public java.lang.String getModifiable(
- ) {
- return this._modifiable;
- }
-
- /**
- * Method getProperty.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the uk.ac.vamsas.objects.core.Property
- * at the given index
- */
- public uk.ac.vamsas.objects.core.Property getProperty(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._propertyList.size()) {
- throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
- }
-
- return (uk.ac.vamsas.objects.core.Property) _propertyList.get(index);
- }
-
- /**
- * Method getProperty.Returns the contents of the collection in
- * an Array. <p>Note: Just in case the collection contents
- * are changing in another thread, we pass a 0-length Array of
- * the correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public uk.ac.vamsas.objects.core.Property[] getProperty(
- ) {
- uk.ac.vamsas.objects.core.Property[] array = new uk.ac.vamsas.objects.core.Property[0];
- return (uk.ac.vamsas.objects.core.Property[]) this._propertyList.toArray(array);
- }
-
- /**
- * Method getPropertyAsReference.Returns a reference to
- * '_propertyList'. No type checking is performed on any
- * modifications to the Vector.
- *
- * @return a reference to the Vector backing this class
- */
- public java.util.Vector getPropertyAsReference(
- ) {
- return this._propertyList;
- }
-
- /**
- * Method getPropertyCount.
- *
- * @return the size of this collection
- */
- public int getPropertyCount(
- ) {
- return this._propertyList.size();
- }
-
- /**
- * Returns the value of field 'provenance'.
- *
- * @return the value of field 'Provenance'.
- */
- public uk.ac.vamsas.objects.core.Provenance getProvenance(
- ) {
- return this._provenance;
- }
-
- /**
- * Method getTree.
- *
- * @param index
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- * @return the value of the uk.ac.vamsas.objects.core.Tree at
- * the given index
- */
- public uk.ac.vamsas.objects.core.Tree getTree(
- final int index)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._treeList.size()) {
- throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
- }
-
- return (uk.ac.vamsas.objects.core.Tree) _treeList.get(index);
- }
-
- /**
- * Method getTree.Returns the contents of the collection in an
- * Array. <p>Note: Just in case the collection contents are
- * changing in another thread, we pass a 0-length Array of the
- * correct type into the API call. This way we <i>know</i>
- * that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public uk.ac.vamsas.objects.core.Tree[] getTree(
- ) {
- uk.ac.vamsas.objects.core.Tree[] array = new uk.ac.vamsas.objects.core.Tree[0];
- return (uk.ac.vamsas.objects.core.Tree[]) this._treeList.toArray(array);
- }
-
- /**
- * Method getTreeAsReference.Returns a reference to
- * '_treeList'. No type checking is performed on any
- * modifications to the Vector.
- *
- * @return a reference to the Vector backing this class
- */
- public java.util.Vector getTreeAsReference(
- ) {
- return this._treeList;
- }
-
- /**
- * Method getTreeCount.
- *
- * @return the size of this collection
- */
- public int getTreeCount(
- ) {
- return this._treeList.size();
- }
-
- /**
- * Method hasAligned.
- *
- * @return true if at least one Aligned has been added
- */
- public boolean hasAligned(
- ) {
- return this._has_aligned;
- }
-
- /**
- * Overrides the java.lang.Object.hashCode method.
- * <p>
- * The following steps came from <b>Effective Java Programming
- * Language Guide</b> by Joshua Bloch, Chapter 3
- *
- * @return a hash code value for the object.
- */
- public int hashCode(
- ) {
- int result = super.hashCode();
-
- long tmp;
- if (_gapChar != null
- && !org.castor.util.CycleBreaker.startingToCycle(_gapChar)) {
- result = 37 * result + _gapChar.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_gapChar);
- }
- result = 37 * result + (_aligned?0:1);
- if (_id != null
- && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
- result = 37 * result + _id.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_id);
- }
- if (_modifiable != null
- && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) {
- result = 37 * result + _modifiable.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable);
- }
- if (_alignmentAnnotationList != null
- && !org.castor.util.CycleBreaker.startingToCycle(_alignmentAnnotationList)) {
- result = 37 * result + _alignmentAnnotationList.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_alignmentAnnotationList);
- }
- if (_treeList != null
- && !org.castor.util.CycleBreaker.startingToCycle(_treeList)) {
- result = 37 * result + _treeList.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_treeList);
- }
- if (_alignmentSequenceList != null
- && !org.castor.util.CycleBreaker.startingToCycle(_alignmentSequenceList)) {
- result = 37 * result + _alignmentSequenceList.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_alignmentSequenceList);
- }
- if (_propertyList != null
- && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) {
- result = 37 * result + _propertyList.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList);
- }
- if (_provenance != null
- && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {
- result = 37 * result + _provenance.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_provenance);
- }
-
- return result;
- }
-
- /**
- * Returns the value of field 'aligned'.
- *
- * @return the value of field 'Aligned'.
- */
- public boolean isAligned(
- ) {
- return this._aligned;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid(
- ) {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
+ 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;
+ if (this._id != temp._id) {
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
+ ;
return false;
+ }
+ if (!thcycle) {
+ if (!this._id.equals(temp._id)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
}
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void marshal(
- final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException if an IOException occurs during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- */
- public void marshal(
- final org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Method removeAlignmentAnnotation.
- *
- * @param vAlignmentAnnotation
- * @return true if the object was removed from the collection.
- */
- public boolean removeAlignmentAnnotation(
- final uk.ac.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation) {
- boolean removed = _alignmentAnnotationList.remove(vAlignmentAnnotation);
- return removed;
- }
-
- /**
- * Method removeAlignmentAnnotationAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public uk.ac.vamsas.objects.core.AlignmentAnnotation removeAlignmentAnnotationAt(
- final int index) {
- java.lang.Object obj = this._alignmentAnnotationList.remove(index);
- return (uk.ac.vamsas.objects.core.AlignmentAnnotation) obj;
- }
-
- /**
- * Method removeAlignmentSequence.
- *
- * @param vAlignmentSequence
- * @return true if the object was removed from the collection.
- */
- public boolean removeAlignmentSequence(
- final uk.ac.vamsas.objects.core.AlignmentSequence vAlignmentSequence) {
- boolean removed = _alignmentSequenceList.remove(vAlignmentSequence);
- return removed;
- }
-
- /**
- * Method removeAlignmentSequenceAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public uk.ac.vamsas.objects.core.AlignmentSequence removeAlignmentSequenceAt(
- final int index) {
- java.lang.Object obj = this._alignmentSequenceList.remove(index);
- return (uk.ac.vamsas.objects.core.AlignmentSequence) obj;
- }
-
- /**
- */
- public void removeAllAlignmentAnnotation(
- ) {
- this._alignmentAnnotationList.clear();
- }
-
- /**
- */
- public void removeAllAlignmentSequence(
- ) {
- this._alignmentSequenceList.clear();
- }
-
- /**
- */
- public void removeAllProperty(
- ) {
- this._propertyList.clear();
- }
-
- /**
- */
- public void removeAllTree(
- ) {
- this._treeList.clear();
- }
-
- /**
- * Method removeProperty.
- *
- * @param vProperty
- * @return true if the object was removed from the collection.
- */
- public boolean removeProperty(
- final uk.ac.vamsas.objects.core.Property vProperty) {
- boolean removed = _propertyList.remove(vProperty);
- return removed;
- }
-
- /**
- * Method removePropertyAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public uk.ac.vamsas.objects.core.Property removePropertyAt(
- final int index) {
- java.lang.Object obj = this._propertyList.remove(index);
- return (uk.ac.vamsas.objects.core.Property) obj;
- }
-
- /**
- * Method removeTree.
- *
- * @param vTree
- * @return true if the object was removed from the collection.
- */
- public boolean removeTree(
- final uk.ac.vamsas.objects.core.Tree vTree) {
- boolean removed = _treeList.remove(vTree);
- return removed;
- }
-
- /**
- * Method removeTreeAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public uk.ac.vamsas.objects.core.Tree removeTreeAt(
- final int index) {
- java.lang.Object obj = this._treeList.remove(index);
- return (uk.ac.vamsas.objects.core.Tree) obj;
- }
-
- /**
- * Sets the value of field 'aligned'.
- *
- * @param aligned the value of field 'aligned'.
- */
- public void setAligned(
- final boolean aligned) {
- this._aligned = aligned;
- this._has_aligned = true;
- }
-
- /**
- *
- *
- * @param index
- * @param vAlignmentAnnotation
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setAlignmentAnnotation(
- final int index,
- final uk.ac.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._alignmentAnnotationList.size()) {
- throw new IndexOutOfBoundsException("setAlignmentAnnotation: Index value '" + index + "' not in range [0.." + (this._alignmentAnnotationList.size() - 1) + "]");
- }
-
- this._alignmentAnnotationList.set(index, vAlignmentAnnotation);
- }
-
- /**
- *
- *
- * @param vAlignmentAnnotationArray
- */
- public void setAlignmentAnnotation(
- final uk.ac.vamsas.objects.core.AlignmentAnnotation[] vAlignmentAnnotationArray) {
- //-- copy array
- _alignmentAnnotationList.clear();
-
- for (int i = 0; i < vAlignmentAnnotationArray.length; i++) {
- this._alignmentAnnotationList.add(vAlignmentAnnotationArray[i]);
- }
- }
-
- /**
- * Sets the value of '_alignmentAnnotationList' by copying the
- * given Vector. All elements will be checked for type safety.
- *
- * @param vAlignmentAnnotationList the Vector to copy.
- */
- public void setAlignmentAnnotation(
- final java.util.Vector vAlignmentAnnotationList) {
- // copy vector
- this._alignmentAnnotationList.clear();
-
- this._alignmentAnnotationList.addAll(vAlignmentAnnotationList);
- }
-
- /**
- * Sets the value of '_alignmentAnnotationList' by setting it
- * to the given Vector. No type checking is performed.
- * @deprecated
- *
- * @param alignmentAnnotationVector the Vector to set.
- */
- public void setAlignmentAnnotationAsReference(
- final java.util.Vector alignmentAnnotationVector) {
- this._alignmentAnnotationList = alignmentAnnotationVector;
- }
-
- /**
- *
- *
- * @param index
- * @param vAlignmentSequence
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setAlignmentSequence(
- final int index,
- final uk.ac.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._alignmentSequenceList.size()) {
- throw new IndexOutOfBoundsException("setAlignmentSequence: Index value '" + index + "' not in range [0.." + (this._alignmentSequenceList.size() - 1) + "]");
+ } else if (temp._id != null)
+ return false;
+ if (this._modifiable != null) {
+ if (temp._modifiable == null)
+ return false;
+ if (this._modifiable != temp._modifiable) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._modifiable);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._modifiable);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._modifiable.equals(temp._modifiable)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._modifiable);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._modifiable);
+ }
}
-
- this._alignmentSequenceList.set(index, vAlignmentSequence);
- }
-
- /**
- *
- *
- * @param vAlignmentSequenceArray
- */
- public void setAlignmentSequence(
- final uk.ac.vamsas.objects.core.AlignmentSequence[] vAlignmentSequenceArray) {
- //-- copy array
- _alignmentSequenceList.clear();
-
- for (int i = 0; i < vAlignmentSequenceArray.length; i++) {
- this._alignmentSequenceList.add(vAlignmentSequenceArray[i]);
+ } else if (temp._modifiable != null)
+ return false;
+ if (this._alignmentAnnotationList != null) {
+ if (temp._alignmentAnnotationList == null)
+ return false;
+ if (this._alignmentAnnotationList != temp._alignmentAnnotationList) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._alignmentAnnotationList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._alignmentAnnotationList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._alignmentAnnotationList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._alignmentAnnotationList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._alignmentAnnotationList
+ .equals(temp._alignmentAnnotationList)) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._alignmentAnnotationList);
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._alignmentAnnotationList);
+ return false;
+ }
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._alignmentAnnotationList);
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._alignmentAnnotationList);
+ }
}
- }
-
- /**
- * Sets the value of '_alignmentSequenceList' by copying the
- * given Vector. All elements will be checked for type safety.
- *
- * @param vAlignmentSequenceList the Vector to copy.
- */
- public void setAlignmentSequence(
- final java.util.Vector vAlignmentSequenceList) {
- // copy vector
- this._alignmentSequenceList.clear();
-
- this._alignmentSequenceList.addAll(vAlignmentSequenceList);
- }
-
- /**
- * Sets the value of '_alignmentSequenceList' by setting it to
- * the given Vector. No type checking is performed.
- * @deprecated
- *
- * @param alignmentSequenceVector the Vector to set.
- */
- public void setAlignmentSequenceAsReference(
- final java.util.Vector alignmentSequenceVector) {
- this._alignmentSequenceList = alignmentSequenceVector;
- }
-
- /**
- * Sets the value of field 'gapChar'.
- *
- * @param gapChar the value of field 'gapChar'.
- */
- public void setGapChar(
- final java.lang.String gapChar) {
- this._gapChar = gapChar;
- }
-
- /**
- * 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(
- final java.lang.String id) {
- this._id = id;
- }
-
- /**
- * Sets the value of field 'modifiable'.
- *
- * @param modifiable the value of field 'modifiable'.
- */
- public void setModifiable(
- final java.lang.String modifiable) {
- this._modifiable = modifiable;
- }
-
- /**
- *
- *
- * @param index
- * @param vProperty
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setProperty(
- final int index,
- final uk.ac.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._propertyList.size()) {
- throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
+ } else if (temp._alignmentAnnotationList != null)
+ return false;
+ if (this._treeList != null) {
+ if (temp._treeList == null)
+ return false;
+ if (this._treeList != temp._treeList) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._treeList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._treeList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._treeList.equals(temp._treeList)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._treeList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._treeList);
+ }
}
-
- this._propertyList.set(index, vProperty);
- }
-
- /**
- *
- *
- * @param vPropertyArray
- */
- public void setProperty(
- final uk.ac.vamsas.objects.core.Property[] vPropertyArray) {
- //-- copy array
- _propertyList.clear();
-
- for (int i = 0; i < vPropertyArray.length; i++) {
- this._propertyList.add(vPropertyArray[i]);
+ } else if (temp._treeList != null)
+ return false;
+ if (this._alignmentSequenceList != null) {
+ if (temp._alignmentSequenceList == null)
+ return false;
+ if (this._alignmentSequenceList != temp._alignmentSequenceList) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._alignmentSequenceList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._alignmentSequenceList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._alignmentSequenceList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._alignmentSequenceList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._alignmentSequenceList
+ .equals(temp._alignmentSequenceList)) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._alignmentSequenceList);
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._alignmentSequenceList);
+ return false;
+ }
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._alignmentSequenceList);
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._alignmentSequenceList);
+ }
}
- }
-
- /**
- * Sets the value of '_propertyList' by copying the given
- * Vector. All elements will be checked for type safety.
- *
- * @param vPropertyList the Vector to copy.
- */
- public void setProperty(
- final java.util.Vector vPropertyList) {
- // copy vector
- this._propertyList.clear();
-
- this._propertyList.addAll(vPropertyList);
- }
-
- /**
- * Sets the value of '_propertyList' by setting it to the given
- * Vector. No type checking is performed.
- * @deprecated
- *
- * @param propertyVector the Vector to set.
- */
- public void setPropertyAsReference(
- final java.util.Vector propertyVector) {
- this._propertyList = propertyVector;
- }
-
- /**
- * Sets the value of field 'provenance'.
- *
- * @param provenance the value of field 'provenance'.
- */
- public void setProvenance(
- final uk.ac.vamsas.objects.core.Provenance provenance) {
- this._provenance = provenance;
- }
-
- /**
- *
- *
- * @param index
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setTree(
- final int index,
- final uk.ac.vamsas.objects.core.Tree vTree)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._treeList.size()) {
- throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ } else if (temp._alignmentSequenceList != null)
+ return false;
+ if (this._propertyList != null) {
+ if (temp._propertyList == null)
+ return false;
+ if (this._propertyList != temp._propertyList) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._propertyList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._propertyList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._propertyList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._propertyList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._propertyList.equals(temp._propertyList)) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._propertyList);
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._propertyList);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._propertyList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._propertyList);
+ }
}
-
- this._treeList.set(index, vTree);
- }
-
- /**
- *
- *
- * @param vTreeArray
- */
- public void setTree(
- final uk.ac.vamsas.objects.core.Tree[] vTreeArray) {
- //-- copy array
- _treeList.clear();
-
- for (int i = 0; i < vTreeArray.length; i++) {
- this._treeList.add(vTreeArray[i]);
+ } else if (temp._propertyList != null)
+ return false;
+ if (this._provenance != null) {
+ if (temp._provenance == null)
+ return false;
+ if (this._provenance != temp._provenance) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._provenance);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._provenance);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._provenance.equals(temp._provenance)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._provenance);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._provenance);
+ }
}
- }
-
- /**
- * Sets the value of '_treeList' by copying the given Vector.
- * All elements will be checked for type safety.
- *
- * @param vTreeList the Vector to copy.
- */
- public void setTree(
- final java.util.Vector vTreeList) {
- // copy vector
- this._treeList.clear();
-
- this._treeList.addAll(vTreeList);
- }
-
- /**
- * Sets the value of '_treeList' by setting it to the given
- * Vector. No type checking is performed.
- * @deprecated
- *
- * @param treeVector the Vector to set.
- */
- public void setTreeAsReference(
- final java.util.Vector treeVector) {
- this._treeList = treeVector;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException if object is
- * null or if any SAXException is thrown during marshaling
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- * @return the unmarshaled uk.ac.vamsas.objects.core.Alignment
- */
- public static uk.ac.vamsas.objects.core.Alignment unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (uk.ac.vamsas.objects.core.Alignment) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Alignment.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException if this
- * object is an invalid instance according to the schema
- */
- public void validate(
- )
- throws org.exolab.castor.xml.ValidationException {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
+ } else if (temp._provenance != null)
+ return false;
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Returns the value of field 'aligned'.
+ *
+ * @return the value of field 'Aligned'.
+ */
+ public boolean getAligned() {
+ return this._aligned;
+ }
+
+ /**
+ * Method getAlignmentAnnotation.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the uk.ac.vamsas.objects.core.AlignmentAnnotation at
+ * the given index
+ */
+ public uk.ac.vamsas.objects.core.AlignmentAnnotation getAlignmentAnnotation(
+ final int index) throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._alignmentAnnotationList.size()) {
+ throw new IndexOutOfBoundsException(
+ "getAlignmentAnnotation: Index value '" + index
+ + "' not in range [0.."
+ + (this._alignmentAnnotationList.size() - 1) + "]");
+ }
+
+ return (uk.ac.vamsas.objects.core.AlignmentAnnotation) _alignmentAnnotationList
+ .get(index);
+ }
+
+ /**
+ * Method getAlignmentAnnotation.Returns the contents of the collection in an
+ * Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public uk.ac.vamsas.objects.core.AlignmentAnnotation[] getAlignmentAnnotation() {
+ uk.ac.vamsas.objects.core.AlignmentAnnotation[] array = new uk.ac.vamsas.objects.core.AlignmentAnnotation[0];
+ return (uk.ac.vamsas.objects.core.AlignmentAnnotation[]) this._alignmentAnnotationList
+ .toArray(array);
+ }
+
+ /**
+ * Method getAlignmentAnnotationAsReference.Returns a reference to
+ * '_alignmentAnnotationList'. No type checking is performed on any
+ * modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getAlignmentAnnotationAsReference() {
+ return this._alignmentAnnotationList;
+ }
+
+ /**
+ * Method getAlignmentAnnotationCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAlignmentAnnotationCount() {
+ return this._alignmentAnnotationList.size();
+ }
+
+ /**
+ * Method getAlignmentSequence.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the uk.ac.vamsas.objects.core.AlignmentSequence at the
+ * given inde
+ */
+ public uk.ac.vamsas.objects.core.AlignmentSequence getAlignmentSequence(
+ final int index) throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._alignmentSequenceList.size()) {
+ throw new IndexOutOfBoundsException("getAlignmentSequence: Index value '"
+ + index + "' not in range [0.."
+ + (this._alignmentSequenceList.size() - 1) + "]");
+ }
+
+ return (uk.ac.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList
+ .get(index);
+ }
+
+ /**
+ * Method getAlignmentSequence.Returns the contents of the collection in an
+ * Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public uk.ac.vamsas.objects.core.AlignmentSequence[] getAlignmentSequence() {
+ uk.ac.vamsas.objects.core.AlignmentSequence[] array = new uk.ac.vamsas.objects.core.AlignmentSequence[0];
+ return (uk.ac.vamsas.objects.core.AlignmentSequence[]) this._alignmentSequenceList
+ .toArray(array);
+ }
+
+ /**
+ * Method getAlignmentSequenceAsReference.Returns a reference to
+ * '_alignmentSequenceList'. No type checking is performed on any
+ * modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getAlignmentSequenceAsReference() {
+ return this._alignmentSequenceList;
+ }
+
+ /**
+ * Method getAlignmentSequenceCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAlignmentSequenceCount() {
+ return this._alignmentSequenceList.size();
+ }
+
+ /**
+ * Returns the value of field 'gapChar'.
+ *
+ * @return the value of field 'GapChar'.
+ */
+ public java.lang.String getGapChar() {
+ return this._gapChar;
+ }
+
+ /**
+ * Returns the value of field 'id'. The field 'id' has the following
+ * description: Primary Key for vamsas object referencing
+ *
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId() {
+ return this._id;
+ }
+
+ /**
+ * Returns the value of field 'modifiable'.
+ *
+ * @return the value of field 'Modifiable'.
+ */
+ public java.lang.String getModifiable() {
+ return this._modifiable;
+ }
+
+ /**
+ * Method getProperty.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the uk.ac.vamsas.objects.core.Property at the given
+ * index
+ */
+ public uk.ac.vamsas.objects.core.Property getProperty(final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._propertyList.size()) {
+ throw new IndexOutOfBoundsException("getProperty: Index value '" + index
+ + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
+ }
+
+ return (uk.ac.vamsas.objects.core.Property) _propertyList.get(index);
+ }
+
+ /**
+ * Method getProperty.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public uk.ac.vamsas.objects.core.Property[] getProperty() {
+ uk.ac.vamsas.objects.core.Property[] array = new uk.ac.vamsas.objects.core.Property[0];
+ return (uk.ac.vamsas.objects.core.Property[]) this._propertyList
+ .toArray(array);
+ }
+
+ /**
+ * Method getPropertyAsReference.Returns a reference to '_propertyList'. No
+ * type checking is performed on any modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getPropertyAsReference() {
+ return this._propertyList;
+ }
+
+ /**
+ * Method getPropertyCount.
+ *
+ * @return the size of this collection
+ */
+ public int getPropertyCount() {
+ return this._propertyList.size();
+ }
+
+ /**
+ * Returns the value of field 'provenance'.
+ *
+ * @return the value of field 'Provenance'.
+ */
+ public uk.ac.vamsas.objects.core.Provenance getProvenance() {
+ return this._provenance;
+ }
+
+ /**
+ * Method getTree.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ * @return the value of the uk.ac.vamsas.objects.core.Tree at the given index
+ */
+ public uk.ac.vamsas.objects.core.Tree getTree(final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size()) {
+ throw new IndexOutOfBoundsException("getTree: Index value '" + index
+ + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ return (uk.ac.vamsas.objects.core.Tree) _treeList.get(index);
+ }
+
+ /**
+ * Method getTree.Returns the contents of the collection in an Array.
+ * <p>
+ * Note: Just in case the collection contents are changing in another thread,
+ * we pass a 0-length Array of the correct type into the API call. This way we
+ * <i>know</i> that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public uk.ac.vamsas.objects.core.Tree[] getTree() {
+ uk.ac.vamsas.objects.core.Tree[] array = new uk.ac.vamsas.objects.core.Tree[0];
+ return (uk.ac.vamsas.objects.core.Tree[]) this._treeList.toArray(array);
+ }
+
+ /**
+ * Method getTreeAsReference.Returns a reference to '_treeList'. No type
+ * checking is performed on any modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getTreeAsReference() {
+ return this._treeList;
+ }
+
+ /**
+ * Method getTreeCount.
+ *
+ * @return the size of this collection
+ */
+ public int getTreeCount() {
+ return this._treeList.size();
+ }
+
+ /**
+ * Method hasAligned.
+ *
+ * @return true if at least one Aligned has been added
+ */
+ public boolean hasAligned() {
+ return this._has_aligned;
+ }
+
+ /**
+ * Overrides the java.lang.Object.hashCode method.
+ * <p>
+ * The following steps came from <b>Effective Java Programming Language
+ * Guide</b> by Joshua Bloch, Chapter 3
+ *
+ * @return a hash code value for the object.
+ */
+ public int hashCode() {
+ int result = super.hashCode();
+
+ long tmp;
+ if (_gapChar != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_gapChar)) {
+ result = 37 * result + _gapChar.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_gapChar);
+ }
+ result = 37 * result + (_aligned ? 0 : 1);
+ if (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
+ result = 37 * result + _id.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_id);
+ }
+ if (_modifiable != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_modifiable)) {
+ result = 37 * result + _modifiable.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_modifiable);
+ }
+ if (_alignmentAnnotationList != null
+ && !org.castor.util.CycleBreaker
+ .startingToCycle(_alignmentAnnotationList)) {
+ result = 37 * result + _alignmentAnnotationList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_alignmentAnnotationList);
+ }
+ if (_treeList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_treeList)) {
+ result = 37 * result + _treeList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_treeList);
+ }
+ if (_alignmentSequenceList != null
+ && !org.castor.util.CycleBreaker
+ .startingToCycle(_alignmentSequenceList)) {
+ result = 37 * result + _alignmentSequenceList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_alignmentSequenceList);
+ }
+ if (_propertyList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) {
+ result = 37 * result + _propertyList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList);
+ }
+ if (_provenance != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {
+ result = 37 * result + _provenance.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_provenance);
+ }
+
+ return result;
+ }
+
+ /**
+ * Returns the value of field 'aligned'.
+ *
+ * @return the value of field 'Aligned'.
+ */
+ public boolean isAligned() {
+ return this._aligned;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid() {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void marshal(final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException
+ * if an IOException occurs during marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ */
+ public void marshal(final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Method removeAlignmentAnnotation.
+ *
+ * @param vAlignmentAnnotation
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAlignmentAnnotation(
+ final uk.ac.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation) {
+ boolean removed = _alignmentAnnotationList.remove(vAlignmentAnnotation);
+ return removed;
+ }
+
+ /**
+ * Method removeAlignmentAnnotationAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.AlignmentAnnotation removeAlignmentAnnotationAt(
+ final int index) {
+ java.lang.Object obj = this._alignmentAnnotationList.remove(index);
+ return (uk.ac.vamsas.objects.core.AlignmentAnnotation) obj;
+ }
+
+ /**
+ * Method removeAlignmentSequence.
+ *
+ * @param vAlignmentSequence
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAlignmentSequence(
+ final uk.ac.vamsas.objects.core.AlignmentSequence vAlignmentSequence) {
+ boolean removed = _alignmentSequenceList.remove(vAlignmentSequence);
+ return removed;
+ }
+
+ /**
+ * Method removeAlignmentSequenceAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.AlignmentSequence removeAlignmentSequenceAt(
+ final int index) {
+ java.lang.Object obj = this._alignmentSequenceList.remove(index);
+ return (uk.ac.vamsas.objects.core.AlignmentSequence) obj;
+ }
+
+ /**
+ */
+ public void removeAllAlignmentAnnotation() {
+ this._alignmentAnnotationList.clear();
+ }
+
+ /**
+ */
+ public void removeAllAlignmentSequence() {
+ this._alignmentSequenceList.clear();
+ }
+
+ /**
+ */
+ public void removeAllProperty() {
+ this._propertyList.clear();
+ }
+
+ /**
+ */
+ public void removeAllTree() {
+ this._treeList.clear();
+ }
+
+ /**
+ * Method removeProperty.
+ *
+ * @param vProperty
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeProperty(
+ final uk.ac.vamsas.objects.core.Property vProperty) {
+ boolean removed = _propertyList.remove(vProperty);
+ return removed;
+ }
+
+ /**
+ * Method removePropertyAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.Property removePropertyAt(final int index) {
+ java.lang.Object obj = this._propertyList.remove(index);
+ return (uk.ac.vamsas.objects.core.Property) obj;
+ }
+
+ /**
+ * Method removeTree.
+ *
+ * @param vTree
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeTree(final uk.ac.vamsas.objects.core.Tree vTree) {
+ boolean removed = _treeList.remove(vTree);
+ return removed;
+ }
+
+ /**
+ * Method removeTreeAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.Tree removeTreeAt(final int index) {
+ java.lang.Object obj = this._treeList.remove(index);
+ return (uk.ac.vamsas.objects.core.Tree) obj;
+ }
+
+ /**
+ * Sets the value of field 'aligned'.
+ *
+ * @param aligned
+ * the value of field 'aligned'.
+ */
+ public void setAligned(final boolean aligned) {
+ this._aligned = aligned;
+ this._has_aligned = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlignmentAnnotation
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setAlignmentAnnotation(final int index,
+ final uk.ac.vamsas.objects.core.AlignmentAnnotation vAlignmentAnnotation)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._alignmentAnnotationList.size()) {
+ throw new IndexOutOfBoundsException(
+ "setAlignmentAnnotation: Index value '" + index
+ + "' not in range [0.."
+ + (this._alignmentAnnotationList.size() - 1) + "]");
+ }
+
+ this._alignmentAnnotationList.set(index, vAlignmentAnnotation);
+ }
+
+ /**
+ *
+ *
+ * @param vAlignmentAnnotationArray
+ */
+ public void setAlignmentAnnotation(
+ final uk.ac.vamsas.objects.core.AlignmentAnnotation[] vAlignmentAnnotationArray) {
+ // -- copy array
+ _alignmentAnnotationList.clear();
+
+ for (int i = 0; i < vAlignmentAnnotationArray.length; i++) {
+ this._alignmentAnnotationList.add(vAlignmentAnnotationArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_alignmentAnnotationList' by copying the given Vector.
+ * All elements will be checked for type safety.
+ *
+ * @param vAlignmentAnnotationList
+ * the Vector to copy.
+ */
+ public void setAlignmentAnnotation(
+ final java.util.Vector vAlignmentAnnotationList) {
+ // copy vector
+ this._alignmentAnnotationList.clear();
+
+ this._alignmentAnnotationList.addAll(vAlignmentAnnotationList);
+ }
+
+ /**
+ * Sets the value of '_alignmentAnnotationList' by setting it to the given
+ * Vector. No type checking is performed.
+ *
+ * @deprecated
+ *
+ * @param alignmentAnnotationVector
+ * the Vector to set.
+ */
+ public void setAlignmentAnnotationAsReference(
+ final java.util.Vector alignmentAnnotationVector) {
+ this._alignmentAnnotationList = alignmentAnnotationVector;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlignmentSequence
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setAlignmentSequence(final int index,
+ final uk.ac.vamsas.objects.core.AlignmentSequence vAlignmentSequence)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._alignmentSequenceList.size()) {
+ throw new IndexOutOfBoundsException("setAlignmentSequence: Index value '"
+ + index + "' not in range [0.."
+ + (this._alignmentSequenceList.size() - 1) + "]");
+ }
+
+ this._alignmentSequenceList.set(index, vAlignmentSequence);
+ }
+
+ /**
+ *
+ *
+ * @param vAlignmentSequenceArray
+ */
+ public void setAlignmentSequence(
+ final uk.ac.vamsas.objects.core.AlignmentSequence[] vAlignmentSequenceArray) {
+ // -- copy array
+ _alignmentSequenceList.clear();
+
+ for (int i = 0; i < vAlignmentSequenceArray.length; i++) {
+ this._alignmentSequenceList.add(vAlignmentSequenceArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_alignmentSequenceList' by copying the given Vector. All
+ * elements will be checked for type safety.
+ *
+ * @param vAlignmentSequenceList
+ * the Vector to copy.
+ */
+ public void setAlignmentSequence(final java.util.Vector vAlignmentSequenceList) {
+ // copy vector
+ this._alignmentSequenceList.clear();
+
+ this._alignmentSequenceList.addAll(vAlignmentSequenceList);
+ }
+
+ /**
+ * Sets the value of '_alignmentSequenceList' by setting it to the given
+ * Vector. No type checking is performed.
+ *
+ * @deprecated
+ *
+ * @param alignmentSequenceVector
+ * the Vector to set.
+ */
+ public void setAlignmentSequenceAsReference(
+ final java.util.Vector alignmentSequenceVector) {
+ this._alignmentSequenceList = alignmentSequenceVector;
+ }
+
+ /**
+ * Sets the value of field 'gapChar'.
+ *
+ * @param gapChar
+ * the value of field 'gapChar'.
+ */
+ public void setGapChar(final java.lang.String gapChar) {
+ this._gapChar = gapChar;
+ }
+
+ /**
+ * 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(final java.lang.String id) {
+ this._id = id;
+ }
+
+ /**
+ * Sets the value of field 'modifiable'.
+ *
+ * @param modifiable
+ * the value of field 'modifiable'.
+ */
+ public void setModifiable(final java.lang.String modifiable) {
+ this._modifiable = modifiable;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setProperty(final int index,
+ final uk.ac.vamsas.objects.core.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._propertyList.size()) {
+ throw new IndexOutOfBoundsException("setProperty: Index value '" + index
+ + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
+ }
+
+ this._propertyList.set(index, vProperty);
+ }
+
+ /**
+ *
+ *
+ * @param vPropertyArray
+ */
+ public void setProperty(
+ final uk.ac.vamsas.objects.core.Property[] vPropertyArray) {
+ // -- copy array
+ _propertyList.clear();
+
+ for (int i = 0; i < vPropertyArray.length; i++) {
+ this._propertyList.add(vPropertyArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_propertyList' by copying the given Vector. All elements
+ * will be checked for type safety.
+ *
+ * @param vPropertyList
+ * the Vector to copy.
+ */
+ public void setProperty(final java.util.Vector vPropertyList) {
+ // copy vector
+ this._propertyList.clear();
+
+ this._propertyList.addAll(vPropertyList);
+ }
+
+ /**
+ * Sets the value of '_propertyList' by setting it to the given Vector. No
+ * type checking is performed.
+ *
+ * @deprecated
+ *
+ * @param propertyVector
+ * the Vector to set.
+ */
+ public void setPropertyAsReference(final java.util.Vector propertyVector) {
+ this._propertyList = propertyVector;
+ }
+
+ /**
+ * Sets the value of field 'provenance'.
+ *
+ * @param provenance
+ * the value of field 'provenance'.
+ */
+ public void setProvenance(
+ final uk.ac.vamsas.objects.core.Provenance provenance) {
+ this._provenance = provenance;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setTree(final int index,
+ final uk.ac.vamsas.objects.core.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size()) {
+ throw new IndexOutOfBoundsException("setTree: Index value '" + index
+ + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ this._treeList.set(index, vTree);
+ }
+
+ /**
+ *
+ *
+ * @param vTreeArray
+ */
+ public void setTree(final uk.ac.vamsas.objects.core.Tree[] vTreeArray) {
+ // -- copy array
+ _treeList.clear();
+
+ for (int i = 0; i < vTreeArray.length; i++) {
+ this._treeList.add(vTreeArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_treeList' by copying the given Vector. All elements
+ * will be checked for type safety.
+ *
+ * @param vTreeList
+ * the Vector to copy.
+ */
+ public void setTree(final java.util.Vector vTreeList) {
+ // copy vector
+ this._treeList.clear();
+
+ this._treeList.addAll(vTreeList);
+ }
+
+ /**
+ * Sets the value of '_treeList' by setting it to the given Vector. No type
+ * checking is performed.
+ *
+ * @deprecated
+ *
+ * @param treeVector
+ * the Vector to set.
+ */
+ public void setTreeAsReference(final java.util.Vector treeVector) {
+ this._treeList = treeVector;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException
+ * if object is null or if any SAXException is thrown during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ * @return the unmarshaled uk.ac.vamsas.objects.core.Alignment
+ */
+ public static uk.ac.vamsas.objects.core.Alignment unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ return (uk.ac.vamsas.objects.core.Alignment) Unmarshaller.unmarshal(
+ uk.ac.vamsas.objects.core.Alignment.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException
+ * if this object is an invalid instance according to the schema
+ */
+ public void validate() throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
}
git://source.jalview.org / vamsas.git / blobdiff