/*
- * 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 SequenceType.
*
- * @version $Revision$ $Date$
+ * @version $Revision$ $Date: 2007-06-28 14:51:44 +0100 (Thu, 28 Jun 2007)
+ * $
*/
-public class SequenceType extends uk.ac.vamsas.client.Vobject
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _start.
- */
- private long _start;
-
- /**
- * keeps track of state for field: _start
- */
- private boolean _has_start;
-
- /**
- * Field _end.
- */
- private long _end;
-
- /**
- * keeps track of state for field: _end
- */
- private boolean _has_end;
-
- /**
- * Field _sequence.
- */
- private java.lang.String _sequence;
-
- /**
- * Field _name.
- */
- private java.lang.String _name;
-
- /**
- * Field _description.
- */
- private java.lang.String _description;
-
- /**
- * additional typed properties
- */
- private java.util.Vector _propertyList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public SequenceType() {
- super();
- this._propertyList = new java.util.Vector();
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- *
- *
- * @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);
- }
-
- /**
- */
- public void deleteEnd(
- ) {
- this._has_end= false;
- }
-
- /**
- */
- public void deleteStart(
- ) {
- this._has_start= false;
- }
-
- /**
- * Method enumerateProperty.
- *
- * @return an Enumeration over all
- * uk.ac.vamsas.objects.core.Property elements
- */
- public java.util.Enumeration enumerateProperty(
- ) {
- return this._propertyList.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 SequenceType extends uk.ac.vamsas.client.Vobject implements
+ java.io.Serializable {
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _start.
+ */
+ private long _start;
+
+ /**
+ * keeps track of state for field: _start
+ */
+ private boolean _has_start;
+
+ /**
+ * Field _end.
+ */
+ private long _end;
+
+ /**
+ * keeps track of state for field: _end
+ */
+ private boolean _has_end;
+
+ /**
+ * Field _sequence.
+ */
+ private java.lang.String _sequence;
+
+ /**
+ * Field _name.
+ */
+ private java.lang.String _name;
+
+ /**
+ * Field _description.
+ */
+ private java.lang.String _description;
+
+ /**
+ * additional typed properties
+ */
+ private java.util.Vector _propertyList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public SequenceType() {
+ super();
+ this._propertyList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @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);
+ }
+
+ /**
+ */
+ public void deleteEnd() {
+ this._has_end = false;
+ }
+
+ /**
+ */
+ public void deleteStart() {
+ this._has_start = false;
+ }
+
+ /**
+ * Method enumerateProperty.
+ *
+ * @return an Enumeration over all uk.ac.vamsas.objects.core.Property elements
+ */
+ public java.util.Enumeration enumerateProperty() {
+ return this._propertyList.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 SequenceType) {
+
+ SequenceType temp = (SequenceType) obj;
+ boolean thcycle;
+ boolean tmcycle;
+ if (this._start != temp._start)
+ return false;
+ if (this._has_start != temp._has_start)
+ return false;
+ if (this._end != temp._end)
+ return false;
+ if (this._has_end != temp._has_end)
+ return false;
+ if (this._sequence != null) {
+ if (temp._sequence == null)
+ return false;
+ if (this._sequence != temp._sequence) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._sequence);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._sequence);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._sequence);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequence);
+ }
+ ;
return false;
-
- if (obj instanceof SequenceType) {
-
- SequenceType temp = (SequenceType)obj;
- boolean thcycle;
- boolean tmcycle;
- if (this._start != temp._start)
- return false;
- if (this._has_start != temp._has_start)
- return false;
- if (this._end != temp._end)
- return false;
- if (this._has_end != temp._has_end)
- return false;
- if (this._sequence != null) {
- if (temp._sequence == null) return false;
- if (this._sequence != temp._sequence) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._sequence);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._sequence);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._sequence); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequence); };
- return false;
- }
- if (!thcycle) {
- if (!this._sequence.equals(temp._sequence)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._sequence);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequence);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._sequence);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequence);
- }
- }
- } else if (temp._sequence != null)
- return false;
- if (this._name != null) {
- if (temp._name == null) return false;
- if (this._name != temp._name) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._name);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._name);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._name); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._name); };
- return false;
- }
- if (!thcycle) {
- if (!this._name.equals(temp._name)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._name);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._name);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._name);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._name);
- }
- }
- } else if (temp._name != null)
- return false;
- if (this._description != null) {
- if (temp._description == null) return false;
- if (this._description != temp._description) {
- thcycle=org.castor.util.CycleBreaker.startingToCycle(this._description);
- tmcycle=org.castor.util.CycleBreaker.startingToCycle(temp._description);
- if (thcycle!=tmcycle) {
- if (!thcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(this._description); };
- if (!tmcycle) { org.castor.util.CycleBreaker.releaseCycleHandle(temp._description); };
- return false;
- }
- if (!thcycle) {
- if (!this._description.equals(temp._description)) {
- org.castor.util.CycleBreaker.releaseCycleHandle(this._description);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._description);
- return false;
- }
- org.castor.util.CycleBreaker.releaseCycleHandle(this._description);
- org.castor.util.CycleBreaker.releaseCycleHandle(temp._description);
- }
- }
- } else if (temp._description != 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;
- return true;
+ }
+ if (!thcycle) {
+ if (!this._sequence.equals(temp._sequence)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._sequence);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequence);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._sequence);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequence);
+ }
}
+ } else if (temp._sequence != null)
return false;
- }
-
- /**
- * Returns the value of field 'description'.
- *
- * @return the value of field 'Description'.
- */
- public java.lang.String getDescription(
- ) {
- return this._description;
- }
-
- /**
- * Returns the value of field 'end'.
- *
- * @return the value of field 'End'.
- */
- public long getEnd(
- ) {
- return this._end;
- }
-
- /**
- * Returns the value of field 'name'.
- *
- * @return the value of field 'Name'.
- */
- public java.lang.String getName(
- ) {
- return this._name;
- }
-
- /**
- * 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 'sequence'.
- *
- * @return the value of field 'Sequence'.
- */
- public java.lang.String getSequence(
- ) {
- return this._sequence;
- }
-
- /**
- * Returns the value of field 'start'.
- *
- * @return the value of field 'Start'.
- */
- public long getStart(
- ) {
- return this._start;
- }
-
- /**
- * Method hasEnd.
- *
- * @return true if at least one End has been added
- */
- public boolean hasEnd(
- ) {
- return this._has_end;
- }
-
- /**
- * Method hasStart.
- *
- * @return true if at least one Start has been added
- */
- public boolean hasStart(
- ) {
- return this._has_start;
- }
-
- /**
- * 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;
- result = 37 * result + (int)(_start^(_start>>>32));
- result = 37 * result + (int)(_end^(_end>>>32));
- if (_sequence != null
- && !org.castor.util.CycleBreaker.startingToCycle(_sequence)) {
- result = 37 * result + _sequence.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_sequence);
- }
- if (_name != null
- && !org.castor.util.CycleBreaker.startingToCycle(_name)) {
- result = 37 * result + _name.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_name);
- }
- if (_description != null
- && !org.castor.util.CycleBreaker.startingToCycle(_description)) {
- result = 37 * result + _description.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_description);
- }
- if (_propertyList != null
- && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) {
- result = 37 * result + _propertyList.hashCode();
- org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList);
- }
-
- 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) {
+ if (this._name != null) {
+ if (temp._name == null)
+ return false;
+ if (this._name != temp._name) {
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._name);
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._name);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._name);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._name);
+ }
+ ;
return false;
+ }
+ if (!thcycle) {
+ if (!this._name.equals(temp._name)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._name);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._name);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._name);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._name);
+ }
}
- 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 removeAllProperty(
- ) {
- this._propertyList.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;
- }
-
- /**
- * Sets the value of field 'description'.
- *
- * @param description the value of field 'description'.
- */
- public void setDescription(
- final java.lang.String description) {
- this._description = description;
- }
-
- /**
- * Sets the value of field 'end'.
- *
- * @param end the value of field 'end'.
- */
- public void setEnd(
- final long end) {
- this._end = end;
- this._has_end = true;
- }
-
- /**
- * Sets the value of field 'name'.
- *
- * @param name the value of field 'name'.
- */
- public void setName(
- final java.lang.String name) {
- this._name = name;
- }
-
- /**
- *
- *
- * @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._name != null)
+ return false;
+ if (this._description != null) {
+ if (temp._description == null)
+ return false;
+ if (this._description != temp._description) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._description);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._description);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._description);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._description);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._description.equals(temp._description)) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._description);
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._description);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._description);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._description);
+ }
}
-
- 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._description != 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);
+ }
}
- }
-
- /**
- * 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 'sequence'.
- *
- * @param sequence the value of field 'sequence'.
- */
- public void setSequence(
- final java.lang.String sequence) {
- this._sequence = sequence;
- }
-
- /**
- * Sets the value of field 'start'.
- *
- * @param start the value of field 'start'.
- */
- public void setStart(
- final long start) {
- this._start = start;
- this._has_start = true;
- }
-
- /**
- * 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.SequenceTyp
- */
- public static uk.ac.vamsas.objects.core.SequenceType unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (uk.ac.vamsas.objects.core.SequenceType) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.SequenceType.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._propertyList != null)
+ return false;
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Returns the value of field 'description'.
+ *
+ * @return the value of field 'Description'.
+ */
+ public java.lang.String getDescription() {
+ return this._description;
+ }
+
+ /**
+ * Returns the value of field 'end'.
+ *
+ * @return the value of field 'End'.
+ */
+ public long getEnd() {
+ return this._end;
+ }
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName() {
+ return this._name;
+ }
+
+ /**
+ * 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 'sequence'.
+ *
+ * @return the value of field 'Sequence'.
+ */
+ public java.lang.String getSequence() {
+ return this._sequence;
+ }
+
+ /**
+ * Returns the value of field 'start'.
+ *
+ * @return the value of field 'Start'.
+ */
+ public long getStart() {
+ return this._start;
+ }
+
+ /**
+ * Method hasEnd.
+ *
+ * @return true if at least one End has been added
+ */
+ public boolean hasEnd() {
+ return this._has_end;
+ }
+
+ /**
+ * Method hasStart.
+ *
+ * @return true if at least one Start has been added
+ */
+ public boolean hasStart() {
+ return this._has_start;
+ }
+
+ /**
+ * 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;
+ result = 37 * result + (int) (_start ^ (_start >>> 32));
+ result = 37 * result + (int) (_end ^ (_end >>> 32));
+ if (_sequence != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_sequence)) {
+ result = 37 * result + _sequence.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_sequence);
+ }
+ if (_name != null && !org.castor.util.CycleBreaker.startingToCycle(_name)) {
+ result = 37 * result + _name.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_name);
+ }
+ if (_description != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_description)) {
+ result = 37 * result + _description.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_description);
+ }
+ if (_propertyList != null
+ && !org.castor.util.CycleBreaker.startingToCycle(_propertyList)) {
+ result = 37 * result + _propertyList.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_propertyList);
+ }
+
+ 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 removeAllProperty() {
+ this._propertyList.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;
+ }
+
+ /**
+ * Sets the value of field 'description'.
+ *
+ * @param description
+ * the value of field 'description'.
+ */
+ public void setDescription(final java.lang.String description) {
+ this._description = description;
+ }
+
+ /**
+ * Sets the value of field 'end'.
+ *
+ * @param end
+ * the value of field 'end'.
+ */
+ public void setEnd(final long end) {
+ this._end = end;
+ this._has_end = true;
+ }
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name
+ * the value of field 'name'.
+ */
+ public void setName(final java.lang.String name) {
+ this._name = name;
+ }
+
+ /**
+ *
+ *
+ * @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 'sequence'.
+ *
+ * @param sequence
+ * the value of field 'sequence'.
+ */
+ public void setSequence(final java.lang.String sequence) {
+ this._sequence = sequence;
+ }
+
+ /**
+ * Sets the value of field 'start'.
+ *
+ * @param start
+ * the value of field 'start'.
+ */
+ public void setStart(final long start) {
+ this._start = start;
+ this._has_start = true;
+ }
+
+ /**
+ * 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.SequenceTyp
+ */
+ public static uk.ac.vamsas.objects.core.SequenceType unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException {
+ return (uk.ac.vamsas.objects.core.SequenceType) Unmarshaller.unmarshal(
+ uk.ac.vamsas.objects.core.SequenceType.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