/*
- * 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 Provenance.
*
- * @version $Revision$ $Date$
+ * @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
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _entryList.
- */
- private java.util.Vector _entryList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Provenance() {
- super();
- this._entryList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @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);
- }
-
- /**
- * Method enumerateEntry.
- *
- * @return an Enumeration over all
- * uk.ac.vamsas.objects.core.Entry elements
- */
- public java.util.Enumeration enumerateEntry(
- ) {
- return this._entryList.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 Provenance extends uk.ac.vamsas.client.Vobject implements
+ java.io.Serializable {
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _entryList.
+ */
+ private java.util.Vector _entryList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Provenance() {
+ super();
+ this._entryList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @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);
+ }
+
+ /**
+ * Method enumerateEntry.
+ *
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.Entry elements
+ */
+ public java.util.Enumeration enumerateEntry() {
+ return this._entryList.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 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;
- 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 (!thcycle) {
- if (!this._entryList.equals(temp._entryList)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._entryList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._entryList);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._entryList);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._entryList);
- }
- }
- } else if (temp._entryList != null)
- return false;
- return true;
+ }
+ if (!thcycle) {
+ if (!this._entryList.equals(temp._entryList)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._entryList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._entryList);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._entryList);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._entryList);
+ }
}
+ } else if (temp._entryList != null)
return false;
+ return true;
}
-
- /**
- * 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 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;
+ 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) + "]");
}
- /**
- * 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);
+ 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);
}
- /**
- *
- *
- * @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]);
- }
+ 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;
}
-
- /**
- * Sets the value of '_entryList' by copying the given Vector.
- * All elements will be checked for type safety.
- *
- * @param vEntryList the Vector to copy.
+ 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 setEntry(
- final java.util.Vector vEntryList) {
- // copy vector
- this._entryList.clear();
-
- this._entryList.addAll(vEntryList);
+ 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) + "]");
}
- /**
- * 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;
- }
+ this._entryList.set(index, vEntry);
+ }
- /**
- * 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);
- }
+ /**
+ *
+ *
+ * @param vEntryArray
+ */
+ public void setEntry(final uk.ac.vamsas.objects.core.Entry[] vEntryArray) {
+ // -- copy array
+ _entryList.clear();
- /**
- *
- *
- * @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);
+ 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