/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id:Provenance.java 264 2006-12-14 17:42:54Z JimP $
+ * This file is part of the Vamsas Client version 0.2.
+ * Copyright 2010 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 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 Provenance.
*
- * @version $Revision:264 $ $Date:2006-12-14 17:42:54 +0000 (Thu, 14 Dec 2006) $
+ * @version $Revision$ $Date: 2007-06-28 14:51:44 +0100 (Thu, 28 Jun 2007)
+ * $
*/
-public class Provenance extends uk.ac.vamsas.client.Vobject
-implements java.io.Serializable
-{
+public class Provenance extends uk.ac.vamsas.client.Vobject implements
+ java.io.Serializable {
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
+ /**
+ * Field _entryList.
+ */
+ private java.util.Vector _entryList;
- /**
- * Field _entryList
- */
- private java.util.Vector _entryList;
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+ public Provenance() {
+ super();
+ this._entryList = new java.util.Vector();
+ }
- //----------------/
- //- Constructors -/
- //----------------/
+ // -----------/
+ // - Methods -/
+ // -----------/
- public Provenance()
- {
- super();
- _entryList = new Vector();
- } //-- uk.ac.vamsas.objects.core.Provenance()
+ /**
+ *
+ *
+ * @param vEntry
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addEntry(final uk.ac.vamsas.objects.core.Entry vEntry)
+ throws java.lang.IndexOutOfBoundsException {
+ this._entryList.addElement(vEntry);
+ }
+ /**
+ *
+ *
+ * @param index
+ * @param vEntry
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addEntry(final int index,
+ final uk.ac.vamsas.objects.core.Entry vEntry)
+ throws java.lang.IndexOutOfBoundsException {
+ this._entryList.add(index, vEntry);
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ /**
+ * Method enumerateEntry.
+ *
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.Entry elements
+ */
+ public java.util.Enumeration enumerateEntry() {
+ return this._entryList.elements();
+ }
- /**
- * Method addEntry
- *
- *
- *
- * @param vEntry
- */
- public void addEntry(uk.ac.vamsas.objects.core.Entry vEntry)
- throws java.lang.IndexOutOfBoundsException
- {
- _entryList.addElement(vEntry);
- } //-- void addEntry(uk.ac.vamsas.objects.core.Entry)
-
- /**
- * Method addEntry
- *
- *
- *
- * @param index
- * @param vEntry
- */
- public void addEntry(int index, uk.ac.vamsas.objects.core.Entry vEntry)
- throws java.lang.IndexOutOfBoundsException
- {
- _entryList.insertElementAt(vEntry, index);
- } //-- void addEntry(int, uk.ac.vamsas.objects.core.Entry)
-
- /**
- * Method enumerateEntry
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateEntry()
- {
- return _entryList.elements();
- } //-- java.util.Enumeration enumerateEntry()
-
- /**
- * 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)
+ /**
+ * 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 Provenance) {
+
+ Provenance temp = (Provenance) obj;
+ boolean thcycle;
+ boolean tmcycle;
+ if (this._entryList != null) {
+ if (temp._entryList == null)
+ return false;
+ if (this._entryList != temp._entryList) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._entryList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._entryList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._entryList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._entryList);
+ }
+ ;
return false;
-
- if (obj instanceof Provenance) {
-
- Provenance temp = (Provenance)obj;
- if (this._entryList != null) {
- if (temp._entryList == null) return false;
- else if (!(this._entryList.equals(temp._entryList)))
- return false;
+ }
+ if (!thcycle) {
+ if (!this._entryList.equals(temp._entryList)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._entryList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._entryList);
+ return false;
}
- else if (temp._entryList != null)
- return false;
- return true;
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._entryList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._entryList);
+ }
}
+ } else if (temp._entryList != null)
return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Method getEntry
- *
- *
- *
- * @param index
- * @return Entry
- */
- public uk.ac.vamsas.objects.core.Entry getEntry(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _entryList.size())) {
- throw new IndexOutOfBoundsException("getEntry: Index value '"+index+"' not in range [0.."+_entryList.size()+ "]");
- }
-
- return (uk.ac.vamsas.objects.core.Entry) _entryList.elementAt(index);
- } //-- uk.ac.vamsas.objects.core.Entry getEntry(int)
-
- /**
- * Method getEntry
- *
- *
- *
- * @return Entry
- */
- public uk.ac.vamsas.objects.core.Entry[] getEntry()
- {
- int size = _entryList.size();
- uk.ac.vamsas.objects.core.Entry[] mArray = new uk.ac.vamsas.objects.core.Entry[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (uk.ac.vamsas.objects.core.Entry) _entryList.elementAt(index);
- }
- return mArray;
- } //-- uk.ac.vamsas.objects.core.Entry[] getEntry()
-
- /**
- * Method getEntryCount
- *
- *
- *
- * @return int
- */
- public int getEntryCount()
- {
- return _entryList.size();
- } //-- int getEntryCount()
-
- /**
- * Method isValid
- *
- *
- *
- * @return boolean
- */
- public boolean isValid()
- {
- try {
- validate();
- }
- catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- } //-- boolean isValid()
-
- /**
- * Method marshal
- *
- *
- *
- * @param out
- */
- public void marshal(java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
- Marshaller.marshal(this, out);
- } //-- void marshal(java.io.Writer)
-
- /**
- * Method marshal
- *
- *
- *
- * @param handler
- */
- public void marshal(org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
- Marshaller.marshal(this, handler);
- } //-- void marshal(org.xml.sax.ContentHandler)
-
- /**
- * Method removeAllEntry
- *
- */
- public void removeAllEntry()
- {
- _entryList.removeAllElements();
- } //-- void removeAllEntry()
-
- /**
- * Method removeEntry
- *
- *
- *
- * @param index
- * @return Entry
- */
- public uk.ac.vamsas.objects.core.Entry removeEntry(int index)
- {
- java.lang.Object obj = _entryList.elementAt(index);
- _entryList.removeElementAt(index);
- return (uk.ac.vamsas.objects.core.Entry) obj;
- } //-- uk.ac.vamsas.objects.core.Entry removeEntry(int)
-
- /**
- * Method setEntry
- *
- *
- *
- * @param index
- * @param vEntry
- */
- public void setEntry(int index, uk.ac.vamsas.objects.core.Entry vEntry)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _entryList.size())) {
- throw new IndexOutOfBoundsException("setEntry: Index value '"+index+"' not in range [0.."+_entryList.size()+ "]");
- }
- _entryList.setElementAt(vEntry, index);
- } //-- void setEntry(int, uk.ac.vamsas.objects.core.Entry)
-
- /**
- * Method setEntry
- *
- *
- *
- * @param entryArray
- */
- public void setEntry(uk.ac.vamsas.objects.core.Entry[] entryArray)
- {
- //-- copy array
- _entryList.removeAllElements();
- for (int i = 0; i < entryArray.length; i++) {
- _entryList.addElement(entryArray[i]);
- }
- } //-- void setEntry(uk.ac.vamsas.objects.core.Entry)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return Provenance
- */
- public static uk.ac.vamsas.objects.core.Provenance unmarshal(java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
- return (uk.ac.vamsas.objects.core.Provenance) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.Provenance.class, reader);
- } //-- uk.ac.vamsas.objects.core.Provenance unmarshal(java.io.Reader)
-
- /**
- * Method validate
- *
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Method getEntry.
+ *
+ * @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.Entry at the given index
+ */
+ public uk.ac.vamsas.objects.core.Entry getEntry(final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._entryList.size()) {
+ throw new IndexOutOfBoundsException("getEntry: Index value '" + index
+ + "' not in range [0.." + (this._entryList.size() - 1) + "]");
+ }
+
+ return (uk.ac.vamsas.objects.core.Entry) _entryList.get(index);
+ }
+
+ /**
+ * Method getEntry.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.Entry[] getEntry() {
+ uk.ac.vamsas.objects.core.Entry[] array = new uk.ac.vamsas.objects.core.Entry[0];
+ return (uk.ac.vamsas.objects.core.Entry[]) this._entryList.toArray(array);
+ }
+
+ /**
+ * Method getEntryAsReference.Returns a reference to '_entryList'. No type
+ * checking is performed on any modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getEntryAsReference() {
+ return this._entryList;
+ }
+
+ /**
+ * Method getEntryCount.
+ *
+ * @return the size of this collection
+ */
+ public int getEntryCount() {
+ return this._entryList.size();
+ }
+
+ /**
+ * 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 (_entryList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_entryList)) {
+ result = 37 * result + _entryList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_entryList);
+ }
+
+ return result;
+ }
+
+ /**
+ * 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 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 removeAllEntry() {
+ this._entryList.clear();
+ }
+
+ /**
+ * Method removeEntry.
+ *
+ * @param vEntry
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeEntry(final uk.ac.vamsas.objects.core.Entry vEntry) {
+ boolean removed = _entryList.remove(vEntry);
+ return removed;
+ }
+
+ /**
+ * Method removeEntryAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.Entry removeEntryAt(final int index) {
+ java.lang.Object obj = this._entryList.remove(index);
+ return (uk.ac.vamsas.objects.core.Entry) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vEntry
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setEntry(final int index,
+ final uk.ac.vamsas.objects.core.Entry vEntry)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._entryList.size()) {
+ throw new IndexOutOfBoundsException("setEntry: Index value '" + index
+ + "' not in range [0.." + (this._entryList.size() - 1) + "]");
+ }
+
+ this._entryList.set(index, vEntry);
+ }
+
+ /**
+ *
+ *
+ * @param vEntryArray
+ */
+ public void setEntry(final uk.ac.vamsas.objects.core.Entry[] vEntryArray) {
+ // -- copy array
+ _entryList.clear();
+
+ for (int i = 0; i < vEntryArray.length; i++) {
+ this._entryList.add(vEntryArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_entryList' by copying the given Vector. All elements
+ * will be checked for type safety.
+ *
+ * @param vEntryList
+ * the Vector to copy.
+ */
+ public void setEntry(final java.util.Vector vEntryList) {
+ // copy vector
+ this._entryList.clear();
+
+ this._entryList.addAll(vEntryList);
+ }
+
+ /**
+ * Sets the value of '_entryList' by setting it to the given Vector. No type
+ * checking is performed.
+ *
+ * @deprecated
+ *
+ * @param entryVector
+ * the Vector to set.
+ */
+ public void setEntryAsReference(final java.util.Vector entryVector) {
+ this._entryList = entryVector;
+ }
+
+ /**
+ * 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.Provenance
+ */
+ public static uk.ac.vamsas.objects.core.Provenance unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ return (uk.ac.vamsas.objects.core.Provenance) Unmarshaller.unmarshal(
+ uk.ac.vamsas.objects.core.Provenance.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