/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id$
+ * 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 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 int _start;
-
- /**
- * keeps track of state for field: _start
- */
- private boolean _has_start;
-
- /**
- * Field _end
- */
- private int _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;
-
- /**
- * Field _mappingList
- */
- private java.util.Vector _mappingList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public SequenceType()
- {
- super();
- _propertyList = new Vector();
- _mappingList = new Vector();
- } //-- uk.ac.vamsas.objects.core.SequenceType()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addMapping
- *
- *
- *
- * @param vMapping
- */
- public void addMapping(uk.ac.vamsas.objects.core.Mapping vMapping)
- throws java.lang.IndexOutOfBoundsException
- {
- _mappingList.addElement(vMapping);
- } //-- void addMapping(uk.ac.vamsas.objects.core.Mapping)
-
- /**
- * Method addMapping
- *
- *
- *
- * @param index
- * @param vMapping
- */
- public void addMapping(int index, uk.ac.vamsas.objects.core.Mapping vMapping)
- throws java.lang.IndexOutOfBoundsException
- {
- _mappingList.insertElementAt(vMapping, index);
- } //-- void addMapping(int, uk.ac.vamsas.objects.core.Mapping)
-
- /**
- * Method addProperty
- *
- *
- *
- * @param vProperty
- */
- public void addProperty(uk.ac.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- _propertyList.addElement(vProperty);
- } //-- void addProperty(uk.ac.vamsas.objects.core.Property)
-
- /**
- * Method addProperty
- *
- *
- *
- * @param index
- * @param vProperty
- */
- public void addProperty(int index, uk.ac.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- _propertyList.insertElementAt(vProperty, index);
- } //-- void addProperty(int, uk.ac.vamsas.objects.core.Property)
-
- /**
- * Method deleteEnd
- *
- */
- public void deleteEnd()
- {
- this._has_end= false;
- } //-- void deleteEnd()
-
- /**
- * Method deleteStart
- *
- */
- public void deleteStart()
- {
- this._has_start= false;
- } //-- void deleteStart()
-
- /**
- * Method enumerateMapping
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateMapping()
- {
- return _mappingList.elements();
- } //-- java.util.Enumeration enumerateMapping()
-
- /**
- * Method enumerateProperty
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateProperty()
- {
- return _propertyList.elements();
- } //-- java.util.Enumeration enumerateProperty()
-
- /**
- * 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 SequenceType) {
-
- SequenceType temp = (SequenceType)obj;
- 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;
- else if (!(this._sequence.equals(temp._sequence)))
- return 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);
}
- else if (temp._sequence != null)
- return false;
- if (this._name != null) {
- if (temp._name == null) return false;
- else if (!(this._name.equals(temp._name)))
- return false;
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._sequence);
}
- else if (temp._name != null)
- return false;
- if (this._description != null) {
- if (temp._description == null) return false;
- else if (!(this._description.equals(temp._description)))
- return false;
+ ;
+ 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);
}
- else if (temp._description != null)
- return false;
- if (this._propertyList != null) {
- if (temp._propertyList == null) return false;
- else if (!(this._propertyList.equals(temp._propertyList)))
- return false;
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._name);
}
- else if (temp._propertyList != null)
- return false;
- if (this._mappingList != null) {
- if (temp._mappingList == null) return false;
- else if (!(this._mappingList.equals(temp._mappingList)))
- return false;
+ ;
+ 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;
}
- else if (temp._mappingList != null)
- return false;
- return true;
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._name);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._name);
+ }
}
+ } else if (temp._name != null)
return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Returns the value of field 'description'.
- *
- * @return String
- * @return the value of field 'description'.
- */
- public java.lang.String getDescription()
- {
- return this._description;
- } //-- java.lang.String getDescription()
-
- /**
- * Returns the value of field 'end'.
- *
- * @return int
- * @return the value of field 'end'.
- */
- public int getEnd()
- {
- return this._end;
- } //-- int getEnd()
-
- /**
- * Method getMapping
- *
- *
- *
- * @param index
- * @return Mapping
- */
- public uk.ac.vamsas.objects.core.Mapping getMapping(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _mappingList.size())) {
- throw new IndexOutOfBoundsException("getMapping: Index value '"+index+"' not in range [0.."+_mappingList.size()+ "]");
- }
-
- return (uk.ac.vamsas.objects.core.Mapping) _mappingList.elementAt(index);
- } //-- uk.ac.vamsas.objects.core.Mapping getMapping(int)
-
- /**
- * Method getMapping
- *
- *
- *
- * @return Mapping
- */
- public uk.ac.vamsas.objects.core.Mapping[] getMapping()
- {
- int size = _mappingList.size();
- uk.ac.vamsas.objects.core.Mapping[] mArray = new uk.ac.vamsas.objects.core.Mapping[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (uk.ac.vamsas.objects.core.Mapping) _mappingList.elementAt(index);
- }
- return mArray;
- } //-- uk.ac.vamsas.objects.core.Mapping[] getMapping()
-
- /**
- * Method getMappingCount
- *
- *
- *
- * @return int
- */
- public int getMappingCount()
- {
- return _mappingList.size();
- } //-- int getMappingCount()
-
- /**
- * Returns the value of field 'name'.
- *
- * @return String
- * @return the value of field 'name'.
- */
- public java.lang.String getName()
- {
- return this._name;
- } //-- java.lang.String getName()
-
- /**
- * Method getProperty
- *
- *
- *
- * @param index
- * @return Property
- */
- public uk.ac.vamsas.objects.core.Property getProperty(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _propertyList.size())) {
- throw new IndexOutOfBoundsException("getProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
- }
-
- return (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);
- } //-- uk.ac.vamsas.objects.core.Property getProperty(int)
-
- /**
- * Method getProperty
- *
- *
- *
- * @return Property
- */
- public uk.ac.vamsas.objects.core.Property[] getProperty()
- {
- int size = _propertyList.size();
- uk.ac.vamsas.objects.core.Property[] mArray = new uk.ac.vamsas.objects.core.Property[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (uk.ac.vamsas.objects.core.Property) _propertyList.elementAt(index);
- }
- return mArray;
- } //-- uk.ac.vamsas.objects.core.Property[] getProperty()
-
- /**
- * Method getPropertyCount
- *
- *
- *
- * @return int
- */
- public int getPropertyCount()
- {
- return _propertyList.size();
- } //-- int getPropertyCount()
-
- /**
- * Returns the value of field 'sequence'.
- *
- * @return String
- * @return the value of field 'sequence'.
- */
- public java.lang.String getSequence()
- {
- return this._sequence;
- } //-- java.lang.String getSequence()
-
- /**
- * Returns the value of field 'start'.
- *
- * @return int
- * @return the value of field 'start'.
- */
- public int getStart()
- {
- return this._start;
- } //-- int getStart()
-
- /**
- * Method hasEnd
- *
- *
- *
- * @return boolean
- */
- public boolean hasEnd()
- {
- return this._has_end;
- } //-- boolean hasEnd()
-
- /**
- * Method hasStart
- *
- *
- *
- * @return boolean
- */
- public boolean hasStart()
- {
- return this._has_start;
- } //-- boolean hasStart()
-
- /**
- * Method isValid
- *
- *
- *
- * @return boolean
- */
- public boolean isValid()
- {
- try {
- validate();
- }
- catch (org.exolab.castor.xml.ValidationException vex) {
+ 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);
+ }
}
- 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 removeAllMapping
- *
- */
- public void removeAllMapping()
- {
- _mappingList.removeAllElements();
- } //-- void removeAllMapping()
-
- /**
- * Method removeAllProperty
- *
- */
- public void removeAllProperty()
- {
- _propertyList.removeAllElements();
- } //-- void removeAllProperty()
-
- /**
- * Method removeMapping
- *
- *
- *
- * @param index
- * @return Mapping
- */
- public uk.ac.vamsas.objects.core.Mapping removeMapping(int index)
- {
- java.lang.Object obj = _mappingList.elementAt(index);
- _mappingList.removeElementAt(index);
- return (uk.ac.vamsas.objects.core.Mapping) obj;
- } //-- uk.ac.vamsas.objects.core.Mapping removeMapping(int)
-
- /**
- * Method removeProperty
- *
- *
- *
- * @param index
- * @return Property
- */
- public uk.ac.vamsas.objects.core.Property removeProperty(int index)
- {
- java.lang.Object obj = _propertyList.elementAt(index);
- _propertyList.removeElementAt(index);
- return (uk.ac.vamsas.objects.core.Property) obj;
- } //-- uk.ac.vamsas.objects.core.Property removeProperty(int)
-
- /**
- * Sets the value of field 'description'.
- *
- * @param description the value of field 'description'.
- */
- public void setDescription(java.lang.String description)
- {
- this._description = description;
- } //-- void setDescription(java.lang.String)
-
- /**
- * Sets the value of field 'end'.
- *
- * @param end the value of field 'end'.
- */
- public void setEnd(int end)
- {
- this._end = end;
- this._has_end = true;
- } //-- void setEnd(int)
-
- /**
- * Method setMapping
- *
- *
- *
- * @param index
- * @param vMapping
- */
- public void setMapping(int index, uk.ac.vamsas.objects.core.Mapping vMapping)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _mappingList.size())) {
- throw new IndexOutOfBoundsException("setMapping: Index value '"+index+"' not in range [0.."+_mappingList.size()+ "]");
- }
- _mappingList.setElementAt(vMapping, index);
- } //-- void setMapping(int, uk.ac.vamsas.objects.core.Mapping)
-
- /**
- * Method setMapping
- *
- *
- *
- * @param mappingArray
- */
- public void setMapping(uk.ac.vamsas.objects.core.Mapping[] mappingArray)
- {
- //-- copy array
- _mappingList.removeAllElements();
- for (int i = 0; i < mappingArray.length; i++) {
- _mappingList.addElement(mappingArray[i]);
- }
- } //-- void setMapping(uk.ac.vamsas.objects.core.Mapping)
-
- /**
- * Sets the value of field 'name'.
- *
- * @param name the value of field 'name'.
- */
- public void setName(java.lang.String name)
- {
- this._name = name;
- } //-- void setName(java.lang.String)
-
- /**
- * Method setProperty
- *
- *
- *
- * @param index
- * @param vProperty
- */
- public void setProperty(int index, uk.ac.vamsas.objects.core.Property vProperty)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _propertyList.size())) {
- throw new IndexOutOfBoundsException("setProperty: Index value '"+index+"' not in range [0.."+_propertyList.size()+ "]");
- }
- _propertyList.setElementAt(vProperty, index);
- } //-- void setProperty(int, uk.ac.vamsas.objects.core.Property)
-
- /**
- * Method setProperty
- *
- *
- *
- * @param propertyArray
- */
- public void setProperty(uk.ac.vamsas.objects.core.Property[] propertyArray)
- {
- //-- copy array
- _propertyList.removeAllElements();
- for (int i = 0; i < propertyArray.length; i++) {
- _propertyList.addElement(propertyArray[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);
+ }
}
- } //-- void setProperty(uk.ac.vamsas.objects.core.Property)
-
- /**
- * Sets the value of field 'sequence'.
- *
- * @param sequence the value of field 'sequence'.
- */
- public void setSequence(java.lang.String sequence)
- {
- this._sequence = sequence;
- } //-- void setSequence(java.lang.String)
-
- /**
- * Sets the value of field 'start'.
- *
- * @param start the value of field 'start'.
- */
- public void setStart(int start)
- {
- this._start = start;
- this._has_start = true;
- } //-- void setStart(int)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return SequenceType
- */
- public static uk.ac.vamsas.objects.core.SequenceType unmarshal(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);
- } //-- uk.ac.vamsas.objects.core.SequenceType unmarshal(java.io.Reader)
-
- /**
- * Method validate
- *
- */
- 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()
+ } 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