X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Fcore%2FVamsasDocument.java;h=c964ec6b7ff8478fc10395fd32fcbbf88ec6402d;hb=844ccad5a3fcbedec17b2af66d460f31abc7cff1;hp=8da041cff3d43e5535748aaeef886f463b2a62e1;hpb=667c5f732b74c1a0e0ac50cd26d93634811663ee;p=vamsas.git
diff --git a/src/uk/ac/vamsas/objects/core/VamsasDocument.java b/src/uk/ac/vamsas/objects/core/VamsasDocument.java
index 8da041c..c964ec6 100644
--- a/src/uk/ac/vamsas/objects/core/VamsasDocument.java
+++ b/src/uk/ac/vamsas/objects/core/VamsasDocument.java
@@ -1,725 +1,1043 @@
/*
- * This class was automatically generated with
- * Castor 0.9.9M2, 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 .
*/
-
package uk.ac.vamsas.objects.core;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- 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 VamsasDocument.
*
- * @version $Revision$ $Date$
+ * @version $Revision$ $Date: 2007-06-28 14:51:44 +0100 (Thu, 28 Jun 2007)
+ * $
*/
-public class VamsasDocument extends uk.ac.vamsas.client.Vobject
-implements java.io.Serializable
-{
+public class VamsasDocument extends uk.ac.vamsas.client.Vobject implements
+ java.io.Serializable {
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
+ /**
+ * Vamsas Document Version Number
+ */
+ private java.lang.String _version;
- /**
- * Vamsas Document Version Number
- */
- private java.lang.String _version;
+ /**
+ * Field _lockFile.
+ */
+ private uk.ac.vamsas.objects.core.LockFile _lockFile;
- /**
- * Field _lockFile
- */
- private uk.ac.vamsas.objects.core.LockFile _lockFile;
+ /**
+ * Field _provenance.
+ */
+ private uk.ac.vamsas.objects.core.Provenance _provenance;
- /**
- * Field _provenance
- */
- private Provenance _provenance;
+ /**
+ * contains unassociated trees and a number of analysis sets
+ *
+ */
+ private java.util.Vector _VAMSASList;
- /**
- * contains unassociated trees and a number of analysis sets
- *
- */
- private java.util.Vector _VAMSASList;
+ /**
+ * Field _applicationDataList.
+ */
+ private java.util.Vector _applicationDataList;
- /**
- * Field _applicationDataList
- */
- private java.util.Vector _applicationDataList;
+ /**
+ * Field _attachmentList.
+ */
+ private java.util.Vector _attachmentList;
- /**
- * Field _attachmentList
- */
- private java.util.Vector _attachmentList;
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+ public VamsasDocument() {
+ super();
+ this._VAMSASList = new java.util.Vector();
+ this._applicationDataList = new java.util.Vector();
+ this._attachmentList = new java.util.Vector();
+ }
- //----------------/
- //- Constructors -/
- //----------------/
+ // -----------/
+ // - Methods -/
+ // -----------/
- public VamsasDocument()
- {
- super();
- _VAMSASList = new Vector();
- _applicationDataList = new Vector();
- _attachmentList = new Vector();
- } //-- uk.ac.vamsas.objects.core.VamsasDocument()
+ /**
+ *
+ *
+ * @param vApplicationData
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addApplicationData(
+ final uk.ac.vamsas.objects.core.ApplicationData vApplicationData)
+ throws java.lang.IndexOutOfBoundsException {
+ this._applicationDataList.addElement(vApplicationData);
+ }
+ /**
+ *
+ *
+ * @param index
+ * @param vApplicationData
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addApplicationData(final int index,
+ final uk.ac.vamsas.objects.core.ApplicationData vApplicationData)
+ throws java.lang.IndexOutOfBoundsException {
+ this._applicationDataList.add(index, vApplicationData);
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ /**
+ *
+ *
+ * @param vAttachment
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAttachment(
+ final uk.ac.vamsas.objects.core.Attachment vAttachment)
+ throws java.lang.IndexOutOfBoundsException {
+ this._attachmentList.addElement(vAttachment);
+ }
- /**
- * Method addApplicationData
- *
- *
- *
- * @param vApplicationData
- */
- public void addApplicationData(ApplicationData vApplicationData)
- throws java.lang.IndexOutOfBoundsException
- {
- _applicationDataList.addElement(vApplicationData);
- } //-- void addApplicationData(ApplicationData)
-
- /**
- * Method addApplicationData
- *
- *
- *
- * @param index
- * @param vApplicationData
- */
- public void addApplicationData(int index, ApplicationData vApplicationData)
- throws java.lang.IndexOutOfBoundsException
- {
- _applicationDataList.insertElementAt(vApplicationData, index);
- } //-- void addApplicationData(int, ApplicationData)
-
- /**
- * Method addAttachment
- *
- *
- *
- * @param vAttachment
- */
- public void addAttachment(Attachment vAttachment)
- throws java.lang.IndexOutOfBoundsException
- {
- _attachmentList.addElement(vAttachment);
- } //-- void addAttachment(Attachment)
-
- /**
- * Method addAttachment
- *
- *
- *
- * @param index
- * @param vAttachment
- */
- public void addAttachment(int index, Attachment vAttachment)
- throws java.lang.IndexOutOfBoundsException
- {
- _attachmentList.insertElementAt(vAttachment, index);
- } //-- void addAttachment(int, Attachment)
-
- /**
- * Method addVAMSAS
- *
- *
- *
- * @param vVAMSAS
- */
- public void addVAMSAS(VAMSAS vVAMSAS)
- throws java.lang.IndexOutOfBoundsException
- {
- _VAMSASList.addElement(vVAMSAS);
- } //-- void addVAMSAS(VAMSAS)
-
- /**
- * Method addVAMSAS
- *
- *
- *
- * @param index
- * @param vVAMSAS
- */
- public void addVAMSAS(int index, VAMSAS vVAMSAS)
- throws java.lang.IndexOutOfBoundsException
- {
- _VAMSASList.insertElementAt(vVAMSAS, index);
- } //-- void addVAMSAS(int, VAMSAS)
-
- /**
- * Method enumerateApplicationData
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateApplicationData()
- {
- return _applicationDataList.elements();
- } //-- java.util.Enumeration enumerateApplicationData()
-
- /**
- * Method enumerateAttachment
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateAttachment()
- {
- return _attachmentList.elements();
- } //-- java.util.Enumeration enumerateAttachment()
-
- /**
- * Method enumerateVAMSAS
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateVAMSAS()
- {
- return _VAMSASList.elements();
- } //-- java.util.Enumeration enumerateVAMSAS()
-
- /**
- * 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 VamsasDocument) {
-
- VamsasDocument temp = (VamsasDocument)obj;
- if (this._version != null) {
- if (temp._version == null) return false;
- else if (!(this._version.equals(temp._version)))
- return false;
+ /**
+ *
+ *
+ * @param index
+ * @param vAttachment
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAttachment(final int index,
+ final uk.ac.vamsas.objects.core.Attachment vAttachment)
+ throws java.lang.IndexOutOfBoundsException {
+ this._attachmentList.add(index, vAttachment);
+ }
+
+ /**
+ *
+ *
+ * @param vVAMSAS
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addVAMSAS(final uk.ac.vamsas.objects.core.VAMSAS vVAMSAS)
+ throws java.lang.IndexOutOfBoundsException {
+ this._VAMSASList.addElement(vVAMSAS);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vVAMSAS
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addVAMSAS(final int index,
+ final uk.ac.vamsas.objects.core.VAMSAS vVAMSAS)
+ throws java.lang.IndexOutOfBoundsException {
+ this._VAMSASList.add(index, vVAMSAS);
+ }
+
+ /**
+ * Method enumerateApplicationData.
+ *
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.ApplicationData
+ * elements
+ */
+ public java.util.Enumeration enumerateApplicationData() {
+ return this._applicationDataList.elements();
+ }
+
+ /**
+ * Method enumerateAttachment.
+ *
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.Attachment
+ * elements
+ */
+ public java.util.Enumeration enumerateAttachment() {
+ return this._attachmentList.elements();
+ }
+
+ /**
+ * Method enumerateVAMSAS.
+ *
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.VAMSAS elements
+ */
+ public java.util.Enumeration enumerateVAMSAS() {
+ return this._VAMSASList.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 VamsasDocument) {
+
+ VamsasDocument temp = (VamsasDocument) obj;
+ boolean thcycle;
+ boolean tmcycle;
+ if (this._version != null) {
+ if (temp._version == null)
+ return false;
+ if (this._version != temp._version) {
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._version);
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._version);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
}
- else if (temp._version != null)
- return false;
- if (this._lockFile != null) {
- if (temp._lockFile == null) return false;
- else if (!(this._lockFile.equals(temp._lockFile)))
- return false;
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
}
- else if (temp._lockFile != null)
- return false;
- if (this._provenance != null) {
- if (temp._provenance == null) return false;
- else if (!(this._provenance.equals(temp._provenance)))
- return false;
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._version.equals(temp._version)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
+ return false;
}
- else if (temp._provenance != null)
- return false;
- if (this._VAMSASList != null) {
- if (temp._VAMSASList == null) return false;
- else if (!(this._VAMSASList.equals(temp._VAMSASList)))
- return false;
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._version);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._version);
+ }
+ }
+ } else if (temp._version != null)
+ return false;
+ if (this._lockFile != null) {
+ if (temp._lockFile == null)
+ return false;
+ if (this._lockFile != temp._lockFile) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._lockFile);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._lockFile);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._lockFile);
}
- else if (temp._VAMSASList != null)
- return false;
- if (this._applicationDataList != null) {
- if (temp._applicationDataList == null) return false;
- else if (!(this._applicationDataList.equals(temp._applicationDataList)))
- return false;
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._lockFile);
}
- else if (temp._applicationDataList != null)
- return false;
- if (this._attachmentList != null) {
- if (temp._attachmentList == null) return false;
- else if (!(this._attachmentList.equals(temp._attachmentList)))
- return false;
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._lockFile.equals(temp._lockFile)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._lockFile);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._lockFile);
+ return false;
}
- else if (temp._attachmentList != null)
- return false;
- return true;
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._lockFile);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._lockFile);
+ }
}
+ } else if (temp._lockFile != null)
return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Method getApplicationData
- *
- *
- *
- * @param index
- * @return ApplicationData
- */
- public ApplicationData getApplicationData(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _applicationDataList.size())) {
- throw new IndexOutOfBoundsException("getApplicationData: Index value '"+index+"' not in range [0.."+_applicationDataList.size()+ "]");
- }
-
- return (ApplicationData) _applicationDataList.elementAt(index);
- } //-- ApplicationData getApplicationData(int)
-
- /**
- * Method getApplicationData
- *
- *
- *
- * @return ApplicationData
- */
- public ApplicationData[] getApplicationData()
- {
- int size = _applicationDataList.size();
- ApplicationData[] mArray = new ApplicationData[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (ApplicationData) _applicationDataList.elementAt(index);
- }
- return mArray;
- } //-- ApplicationData[] getApplicationData()
-
- /**
- * Method getApplicationDataCount
- *
- *
- *
- * @return int
- */
- public int getApplicationDataCount()
- {
- return _applicationDataList.size();
- } //-- int getApplicationDataCount()
-
- /**
- * Method getAttachment
- *
- *
- *
- * @param index
- * @return Attachment
- */
- public Attachment getAttachment(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _attachmentList.size())) {
- throw new IndexOutOfBoundsException("getAttachment: Index value '"+index+"' not in range [0.."+_attachmentList.size()+ "]");
- }
-
- return (Attachment) _attachmentList.elementAt(index);
- } //-- Attachment getAttachment(int)
-
- /**
- * Method getAttachment
- *
- *
- *
- * @return Attachment
- */
- public Attachment[] getAttachment()
- {
- int size = _attachmentList.size();
- Attachment[] mArray = new Attachment[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (Attachment) _attachmentList.elementAt(index);
- }
- return mArray;
- } //-- Attachment[] getAttachment()
-
- /**
- * Method getAttachmentCount
- *
- *
- *
- * @return int
- */
- public int getAttachmentCount()
- {
- return _attachmentList.size();
- } //-- int getAttachmentCount()
-
- /**
- * Returns the value of field 'lockFile'.
- *
- * @return LockFile
- * @return the value of field 'lockFile'.
- */
- public uk.ac.vamsas.objects.core.LockFile getLockFile()
- {
- return this._lockFile;
- } //-- uk.ac.vamsas.objects.core.LockFile getLockFile()
-
- /**
- * Returns the value of field 'provenance'.
- *
- * @return Provenance
- * @return the value of field 'provenance'.
- */
- public Provenance getProvenance()
- {
- return this._provenance;
- } //-- Provenance getProvenance()
-
- /**
- * Method getVAMSAS
- *
- *
- *
- * @param index
- * @return VAMSAS
- */
- public VAMSAS getVAMSAS(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _VAMSASList.size())) {
- throw new IndexOutOfBoundsException("getVAMSAS: Index value '"+index+"' not in range [0.."+_VAMSASList.size()+ "]");
- }
-
- return (VAMSAS) _VAMSASList.elementAt(index);
- } //-- VAMSAS getVAMSAS(int)
-
- /**
- * Method getVAMSAS
- *
- *
- *
- * @return VAMSAS
- */
- public VAMSAS[] getVAMSAS()
- {
- int size = _VAMSASList.size();
- VAMSAS[] mArray = new VAMSAS[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (VAMSAS) _VAMSASList.elementAt(index);
- }
- return mArray;
- } //-- VAMSAS[] getVAMSAS()
-
- /**
- * Method getVAMSASCount
- *
- *
- *
- * @return int
- */
- public int getVAMSASCount()
- {
- return _VAMSASList.size();
- } //-- int getVAMSASCount()
-
- /**
- * Returns the value of field 'version'. The field 'version'
- * has the following description: Vamsas Document Version
- * Number
- *
- * @return String
- * @return the value of field 'version'.
- */
- public java.lang.String getVersion()
- {
- return this._version;
- } //-- java.lang.String getVersion()
-
- /**
- * Method isValid
- *
- *
- *
- * @return boolean
- */
- public boolean isValid()
- {
- try {
- validate();
- }
- catch (org.exolab.castor.xml.ValidationException vex) {
+ 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);
+ }
}
- 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 removeAllApplicationData
- *
- */
- public void removeAllApplicationData()
- {
- _applicationDataList.removeAllElements();
- } //-- void removeAllApplicationData()
-
- /**
- * Method removeAllAttachment
- *
- */
- public void removeAllAttachment()
- {
- _attachmentList.removeAllElements();
- } //-- void removeAllAttachment()
-
- /**
- * Method removeAllVAMSAS
- *
- */
- public void removeAllVAMSAS()
- {
- _VAMSASList.removeAllElements();
- } //-- void removeAllVAMSAS()
-
- /**
- * Method removeApplicationData
- *
- *
- *
- * @param index
- * @return ApplicationData
- */
- public ApplicationData removeApplicationData(int index)
- {
- java.lang.Object obj = _applicationDataList.elementAt(index);
- _applicationDataList.removeElementAt(index);
- return (ApplicationData) obj;
- } //-- ApplicationData removeApplicationData(int)
-
- /**
- * Method removeAttachment
- *
- *
- *
- * @param index
- * @return Attachment
- */
- public Attachment removeAttachment(int index)
- {
- java.lang.Object obj = _attachmentList.elementAt(index);
- _attachmentList.removeElementAt(index);
- return (Attachment) obj;
- } //-- Attachment removeAttachment(int)
-
- /**
- * Method removeVAMSAS
- *
- *
- *
- * @param index
- * @return VAMSAS
- */
- public VAMSAS removeVAMSAS(int index)
- {
- java.lang.Object obj = _VAMSASList.elementAt(index);
- _VAMSASList.removeElementAt(index);
- return (VAMSAS) obj;
- } //-- VAMSAS removeVAMSAS(int)
-
- /**
- * Method setApplicationData
- *
- *
- *
- * @param index
- * @param vApplicationData
- */
- public void setApplicationData(int index, ApplicationData vApplicationData)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _applicationDataList.size())) {
- throw new IndexOutOfBoundsException("setApplicationData: Index value '"+index+"' not in range [0.."+_applicationDataList.size()+ "]");
- }
- _applicationDataList.setElementAt(vApplicationData, index);
- } //-- void setApplicationData(int, ApplicationData)
-
- /**
- * Method setApplicationData
- *
- *
- *
- * @param applicationDataArray
- */
- public void setApplicationData(ApplicationData[] applicationDataArray)
- {
- //-- copy array
- _applicationDataList.removeAllElements();
- for (int i = 0; i < applicationDataArray.length; i++) {
- _applicationDataList.addElement(applicationDataArray[i]);
+ } else if (temp._provenance != null)
+ return false;
+ if (this._VAMSASList != null) {
+ if (temp._VAMSASList == null)
+ return false;
+ if (this._VAMSASList != temp._VAMSASList) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._VAMSASList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._VAMSASList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._VAMSASList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._VAMSASList.equals(temp._VAMSASList)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._VAMSASList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._VAMSASList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._VAMSASList);
+ }
}
- } //-- void setApplicationData(ApplicationData)
-
- /**
- * Method setAttachment
- *
- *
- *
- * @param index
- * @param vAttachment
- */
- public void setAttachment(int index, Attachment vAttachment)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _attachmentList.size())) {
- throw new IndexOutOfBoundsException("setAttachment: Index value '"+index+"' not in range [0.."+_attachmentList.size()+ "]");
+ } else if (temp._VAMSASList != null)
+ return false;
+ if (this._applicationDataList != null) {
+ if (temp._applicationDataList == null)
+ return false;
+ if (this._applicationDataList != temp._applicationDataList) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._applicationDataList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._applicationDataList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._applicationDataList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._applicationDataList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._applicationDataList.equals(temp._applicationDataList)) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._applicationDataList);
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._applicationDataList);
+ return false;
+ }
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._applicationDataList);
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._applicationDataList);
+ }
}
- _attachmentList.setElementAt(vAttachment, index);
- } //-- void setAttachment(int, Attachment)
-
- /**
- * Method setAttachment
- *
- *
- *
- * @param attachmentArray
- */
- public void setAttachment(Attachment[] attachmentArray)
- {
- //-- copy array
- _attachmentList.removeAllElements();
- for (int i = 0; i < attachmentArray.length; i++) {
- _attachmentList.addElement(attachmentArray[i]);
+ } else if (temp._applicationDataList != null)
+ return false;
+ if (this._attachmentList != null) {
+ if (temp._attachmentList == null)
+ return false;
+ if (this._attachmentList != temp._attachmentList) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._attachmentList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._attachmentList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._attachmentList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._attachmentList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._attachmentList.equals(temp._attachmentList)) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._attachmentList);
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._attachmentList);
+ return false;
+ }
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._attachmentList);
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._attachmentList);
+ }
}
- } //-- void setAttachment(Attachment)
+ } else if (temp._attachmentList != null)
+ return false;
+ return true;
+ }
+ return false;
+ }
- /**
- * Sets the value of field 'lockFile'.
- *
- * @param lockFile the value of field 'lockFile'.
- */
- public void setLockFile(uk.ac.vamsas.objects.core.LockFile lockFile)
- {
- this._lockFile = lockFile;
- } //-- void setLockFile(uk.ac.vamsas.objects.core.LockFile)
-
- /**
- * Sets the value of field 'provenance'.
- *
- * @param provenance the value of field 'provenance'.
- */
- public void setProvenance(Provenance provenance)
- {
- this._provenance = provenance;
- } //-- void setProvenance(Provenance)
-
- /**
- * Method setVAMSAS
- *
- *
- *
- * @param index
- * @param vVAMSAS
- */
- public void setVAMSAS(int index, VAMSAS vVAMSAS)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _VAMSASList.size())) {
- throw new IndexOutOfBoundsException("setVAMSAS: Index value '"+index+"' not in range [0.."+_VAMSASList.size()+ "]");
- }
- _VAMSASList.setElementAt(vVAMSAS, index);
- } //-- void setVAMSAS(int, VAMSAS)
-
- /**
- * Method setVAMSAS
- *
- *
- *
- * @param VAMSASArray
- */
- public void setVAMSAS(VAMSAS[] VAMSASArray)
- {
- //-- copy array
- _VAMSASList.removeAllElements();
- for (int i = 0; i < VAMSASArray.length; i++) {
- _VAMSASList.addElement(VAMSASArray[i]);
- }
- } //-- void setVAMSAS(VAMSAS)
+ /**
+ * Method getApplicationData.
+ *
+ * @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.ApplicationData at the
+ * given index
+ */
+ public uk.ac.vamsas.objects.core.ApplicationData getApplicationData(
+ final int index) throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._applicationDataList.size()) {
+ throw new IndexOutOfBoundsException("getApplicationData: Index value '"
+ + index + "' not in range [0.."
+ + (this._applicationDataList.size() - 1) + "]");
+ }
+
+ return (uk.ac.vamsas.objects.core.ApplicationData) _applicationDataList
+ .get(index);
+ }
+
+ /**
+ * Method getApplicationData.Returns the contents of the collection in an
+ * Array.
+ *
+ * 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
+ * know that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public uk.ac.vamsas.objects.core.ApplicationData[] getApplicationData() {
+ uk.ac.vamsas.objects.core.ApplicationData[] array = new uk.ac.vamsas.objects.core.ApplicationData[0];
+ return (uk.ac.vamsas.objects.core.ApplicationData[]) this._applicationDataList
+ .toArray(array);
+ }
+
+ /**
+ * Method getApplicationDataAsReference.Returns a reference to
+ * '_applicationDataList'. No type checking is performed on any modifications
+ * to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getApplicationDataAsReference() {
+ return this._applicationDataList;
+ }
+
+ /**
+ * Method getApplicationDataCount.
+ *
+ * @return the size of this collection
+ */
+ public int getApplicationDataCount() {
+ return this._applicationDataList.size();
+ }
+
+ /**
+ * Method getAttachment.
+ *
+ * @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.Attachment at the given
+ * index
+ */
+ public uk.ac.vamsas.objects.core.Attachment getAttachment(final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._attachmentList.size()) {
+ throw new IndexOutOfBoundsException("getAttachment: Index value '"
+ + index + "' not in range [0.." + (this._attachmentList.size() - 1)
+ + "]");
+ }
+
+ return (uk.ac.vamsas.objects.core.Attachment) _attachmentList.get(index);
+ }
+
+ /**
+ * Method getAttachment.Returns the contents of the collection in an Array.
+ *
+ * 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
+ * know that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public uk.ac.vamsas.objects.core.Attachment[] getAttachment() {
+ uk.ac.vamsas.objects.core.Attachment[] array = new uk.ac.vamsas.objects.core.Attachment[0];
+ return (uk.ac.vamsas.objects.core.Attachment[]) this._attachmentList
+ .toArray(array);
+ }
+
+ /**
+ * Method getAttachmentAsReference.Returns a reference to '_attachmentList'.
+ * No type checking is performed on any modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getAttachmentAsReference() {
+ return this._attachmentList;
+ }
+
+ /**
+ * Method getAttachmentCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAttachmentCount() {
+ return this._attachmentList.size();
+ }
+
+ /**
+ * Returns the value of field 'lockFile'.
+ *
+ * @return the value of field 'LockFile'.
+ */
+ public uk.ac.vamsas.objects.core.LockFile getLockFile() {
+ return this._lockFile;
+ }
+
+ /**
+ * Returns the value of field 'provenance'.
+ *
+ * @return the value of field 'Provenance'.
+ */
+ public uk.ac.vamsas.objects.core.Provenance getProvenance() {
+ return this._provenance;
+ }
+
+ /**
+ * Method getVAMSAS.
+ *
+ * @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.VAMSAS at the given
+ * index
+ */
+ public uk.ac.vamsas.objects.core.VAMSAS getVAMSAS(final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._VAMSASList.size()) {
+ throw new IndexOutOfBoundsException("getVAMSAS: Index value '" + index
+ + "' not in range [0.." + (this._VAMSASList.size() - 1) + "]");
+ }
+
+ return (uk.ac.vamsas.objects.core.VAMSAS) _VAMSASList.get(index);
+ }
+
+ /**
+ * Method getVAMSAS.Returns the contents of the collection in an Array.
+ *
+ * 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
+ * know that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public uk.ac.vamsas.objects.core.VAMSAS[] getVAMSAS() {
+ uk.ac.vamsas.objects.core.VAMSAS[] array = new uk.ac.vamsas.objects.core.VAMSAS[0];
+ return (uk.ac.vamsas.objects.core.VAMSAS[]) this._VAMSASList.toArray(array);
+ }
+
+ /**
+ * Method getVAMSASAsReference.Returns a reference to '_VAMSASList'. No type
+ * checking is performed on any modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getVAMSASAsReference() {
+ return this._VAMSASList;
+ }
+
+ /**
+ * Method getVAMSASCount.
+ *
+ * @return the size of this collection
+ */
+ public int getVAMSASCount() {
+ return this._VAMSASList.size();
+ }
+
+ /**
+ * Returns the value of field 'version'. The field 'version' has the following
+ * description: Vamsas Document Version Number
+ *
+ * @return the value of field 'Version'.
+ */
+ public java.lang.String getVersion() {
+ return this._version;
+ }
+
+ /**
+ * Overrides the java.lang.Object.hashCode method.
+ *
+ * The following steps came from Effective Java Programming Language
+ * Guide by Joshua Bloch, Chapter 3
+ *
+ * @return a hash code value for the object.
+ */
+ public int hashCode() {
+ int result = super.hashCode();
+
+ long tmp;
+ if (_version != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_version)) {
+ result = 37 * result + _version.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_version);
+ }
+ if (_lockFile != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_lockFile)) {
+ result = 37 * result + _lockFile.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_lockFile);
+ }
+ if (_provenance != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_provenance)) {
+ result = 37 * result + _provenance.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_provenance);
+ }
+ if (_VAMSASList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_VAMSASList)) {
+ result = 37 * result + _VAMSASList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_VAMSASList);
+ }
+ if (_applicationDataList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_applicationDataList)) {
+ result = 37 * result + _applicationDataList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_applicationDataList);
+ }
+ if (_attachmentList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_attachmentList)) {
+ result = 37 * result + _attachmentList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_attachmentList);
+ }
+
+ return result;
+ }
- /**
- * Sets the value of field 'version'. The field 'version' has
- * the following description: Vamsas Document Version Number
- *
- * @param version the value of field 'version'.
+ /**
+ * 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);
+ }
+
+ /**
*/
- public void setVersion(java.lang.String version)
- {
- this._version = version;
- } //-- void setVersion(java.lang.String)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return VamsasDocument
+ public void removeAllApplicationData() {
+ this._applicationDataList.clear();
+ }
+
+ /**
*/
- public static uk.ac.vamsas.objects.core.VamsasDocument unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (uk.ac.vamsas.objects.core.VamsasDocument) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.VamsasDocument.class, reader);
- } //-- uk.ac.vamsas.objects.core.VamsasDocument unmarshal(java.io.Reader)
-
- /**
- * Method validate
- *
+ public void removeAllAttachment() {
+ this._attachmentList.clear();
+ }
+
+ /**
*/
- 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()
+ public void removeAllVAMSAS() {
+ this._VAMSASList.clear();
+ }
+
+ /**
+ * Method removeApplicationData.
+ *
+ * @param vApplicationData
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeApplicationData(
+ final uk.ac.vamsas.objects.core.ApplicationData vApplicationData) {
+ boolean removed = _applicationDataList.remove(vApplicationData);
+ return removed;
+ }
+
+ /**
+ * Method removeApplicationDataAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.ApplicationData removeApplicationDataAt(
+ final int index) {
+ java.lang.Object obj = this._applicationDataList.remove(index);
+ return (uk.ac.vamsas.objects.core.ApplicationData) obj;
+ }
+
+ /**
+ * Method removeAttachment.
+ *
+ * @param vAttachment
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAttachment(
+ final uk.ac.vamsas.objects.core.Attachment vAttachment) {
+ boolean removed = _attachmentList.remove(vAttachment);
+ return removed;
+ }
+
+ /**
+ * Method removeAttachmentAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.Attachment removeAttachmentAt(final int index) {
+ java.lang.Object obj = this._attachmentList.remove(index);
+ return (uk.ac.vamsas.objects.core.Attachment) obj;
+ }
+
+ /**
+ * Method removeVAMSAS.
+ *
+ * @param vVAMSAS
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeVAMSAS(final uk.ac.vamsas.objects.core.VAMSAS vVAMSAS) {
+ boolean removed = _VAMSASList.remove(vVAMSAS);
+ return removed;
+ }
+
+ /**
+ * Method removeVAMSASAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.VAMSAS removeVAMSASAt(final int index) {
+ java.lang.Object obj = this._VAMSASList.remove(index);
+ return (uk.ac.vamsas.objects.core.VAMSAS) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vApplicationData
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setApplicationData(final int index,
+ final uk.ac.vamsas.objects.core.ApplicationData vApplicationData)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._applicationDataList.size()) {
+ throw new IndexOutOfBoundsException("setApplicationData: Index value '"
+ + index + "' not in range [0.."
+ + (this._applicationDataList.size() - 1) + "]");
+ }
+
+ this._applicationDataList.set(index, vApplicationData);
+ }
+
+ /**
+ *
+ *
+ * @param vApplicationDataArray
+ */
+ public void setApplicationData(
+ final uk.ac.vamsas.objects.core.ApplicationData[] vApplicationDataArray) {
+ // -- copy array
+ _applicationDataList.clear();
+
+ for (int i = 0; i < vApplicationDataArray.length; i++) {
+ this._applicationDataList.add(vApplicationDataArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_applicationDataList' by copying the given Vector. All
+ * elements will be checked for type safety.
+ *
+ * @param vApplicationDataList
+ * the Vector to copy.
+ */
+ public void setApplicationData(final java.util.Vector vApplicationDataList) {
+ // copy vector
+ this._applicationDataList.clear();
+
+ this._applicationDataList.addAll(vApplicationDataList);
+ }
+
+ /**
+ * Sets the value of '_applicationDataList' by setting it to the given Vector.
+ * No type checking is performed.
+ *
+ * @deprecated
+ *
+ * @param applicationDataVector
+ * the Vector to set.
+ */
+ public void setApplicationDataAsReference(
+ final java.util.Vector applicationDataVector) {
+ this._applicationDataList = applicationDataVector;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAttachment
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setAttachment(final int index,
+ final uk.ac.vamsas.objects.core.Attachment vAttachment)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._attachmentList.size()) {
+ throw new IndexOutOfBoundsException("setAttachment: Index value '"
+ + index + "' not in range [0.." + (this._attachmentList.size() - 1)
+ + "]");
+ }
+
+ this._attachmentList.set(index, vAttachment);
+ }
+
+ /**
+ *
+ *
+ * @param vAttachmentArray
+ */
+ public void setAttachment(
+ final uk.ac.vamsas.objects.core.Attachment[] vAttachmentArray) {
+ // -- copy array
+ _attachmentList.clear();
+
+ for (int i = 0; i < vAttachmentArray.length; i++) {
+ this._attachmentList.add(vAttachmentArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_attachmentList' by copying the given Vector. All
+ * elements will be checked for type safety.
+ *
+ * @param vAttachmentList
+ * the Vector to copy.
+ */
+ public void setAttachment(final java.util.Vector vAttachmentList) {
+ // copy vector
+ this._attachmentList.clear();
+
+ this._attachmentList.addAll(vAttachmentList);
+ }
+
+ /**
+ * Sets the value of '_attachmentList' by setting it to the given Vector. No
+ * type checking is performed.
+ *
+ * @deprecated
+ *
+ * @param attachmentVector
+ * the Vector to set.
+ */
+ public void setAttachmentAsReference(final java.util.Vector attachmentVector) {
+ this._attachmentList = attachmentVector;
+ }
+
+ /**
+ * Sets the value of field 'lockFile'.
+ *
+ * @param lockFile
+ * the value of field 'lockFile'.
+ */
+ public void setLockFile(final uk.ac.vamsas.objects.core.LockFile lockFile) {
+ this._lockFile = lockFile;
+ }
+
+ /**
+ * 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 vVAMSAS
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setVAMSAS(final int index,
+ final uk.ac.vamsas.objects.core.VAMSAS vVAMSAS)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._VAMSASList.size()) {
+ throw new IndexOutOfBoundsException("setVAMSAS: Index value '" + index
+ + "' not in range [0.." + (this._VAMSASList.size() - 1) + "]");
+ }
+
+ this._VAMSASList.set(index, vVAMSAS);
+ }
+
+ /**
+ *
+ *
+ * @param vVAMSASArray
+ */
+ public void setVAMSAS(final uk.ac.vamsas.objects.core.VAMSAS[] vVAMSASArray) {
+ // -- copy array
+ _VAMSASList.clear();
+
+ for (int i = 0; i < vVAMSASArray.length; i++) {
+ this._VAMSASList.add(vVAMSASArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_VAMSASList' by copying the given Vector. All elements
+ * will be checked for type safety.
+ *
+ * @param vVAMSASList
+ * the Vector to copy.
+ */
+ public void setVAMSAS(final java.util.Vector vVAMSASList) {
+ // copy vector
+ this._VAMSASList.clear();
+
+ this._VAMSASList.addAll(vVAMSASList);
+ }
+
+ /**
+ * Sets the value of '_VAMSASList' by setting it to the given Vector. No type
+ * checking is performed.
+ *
+ * @deprecated
+ *
+ * @param VAMSASVector
+ * the Vector to set.
+ */
+ public void setVAMSASAsReference(final java.util.Vector VAMSASVector) {
+ this._VAMSASList = VAMSASVector;
+ }
+
+ /**
+ * Sets the value of field 'version'. The field 'version' has the following
+ * description: Vamsas Document Version Number
+ *
+ * @param version
+ * the value of field 'version'.
+ */
+ public void setVersion(final java.lang.String version) {
+ this._version = version;
+ }
+
+ /**
+ * 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.VamsasDocument
+ */
+ public static uk.ac.vamsas.objects.core.VamsasDocument unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ return (uk.ac.vamsas.objects.core.VamsasDocument) Unmarshaller.unmarshal(
+ uk.ac.vamsas.objects.core.VamsasDocument.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);
+ }
}