/*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
- * Schema.
- * $Id:AlignmentSequence.java 264 2006-12-14 17:42:54Z JimP $
+ * 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 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 AlignmentSequence.
*
- * @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 AlignmentSequence extends uk.ac.vamsas.objects.core.SequenceType
-implements java.io.Serializable
-{
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Primary Key for vamsas object
- * referencing
- */
- private java.lang.String _id;
-
- /**
- * Dataset Sequence from which
- * this alignment sequence is taken from
- *
- */
- private java.lang.Object _refid;
-
- /**
- * Field _alignmentSequenceAnnotationList
- */
- private java.util.Vector _alignmentSequenceAnnotationList;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public AlignmentSequence()
- {
- super();
- _alignmentSequenceAnnotationList = new Vector();
- } //-- uk.ac.vamsas.objects.core.AlignmentSequence()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addAlignmentSequenceAnnotation
- *
- *
- *
- * @param vAlignmentSequenceAnnotation
- */
- public void addAlignmentSequenceAnnotation(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
- throws java.lang.IndexOutOfBoundsException
- {
- _alignmentSequenceAnnotationList.addElement(vAlignmentSequenceAnnotation);
- } //-- void addAlignmentSequenceAnnotation(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation)
-
- /**
- * Method addAlignmentSequenceAnnotation
- *
- *
- *
- * @param index
- * @param vAlignmentSequenceAnnotation
- */
- public void addAlignmentSequenceAnnotation(int index, uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
- throws java.lang.IndexOutOfBoundsException
- {
- _alignmentSequenceAnnotationList.insertElementAt(vAlignmentSequenceAnnotation, index);
- } //-- void addAlignmentSequenceAnnotation(int, uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation)
-
- /**
- * Method enumerateAlignmentSequenceAnnotation
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateAlignmentSequenceAnnotation()
- {
- return _alignmentSequenceAnnotationList.elements();
- } //-- java.util.Enumeration enumerateAlignmentSequenceAnnotation()
-
- /**
- * 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 AlignmentSequence) {
-
- AlignmentSequence temp = (AlignmentSequence)obj;
- if (this._id != null) {
- if (temp._id == null) return false;
- else if (!(this._id.equals(temp._id)))
- return false;
+public class AlignmentSequence extends uk.ac.vamsas.objects.core.SequenceType
+ implements java.io.Serializable {
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Primary Key for vamsas object referencing
+ */
+ private java.lang.String _id;
+
+ /**
+ * Dataset Sequence from which this alignment sequence is taken from
+ *
+ */
+ private java.lang.Object _refid;
+
+ /**
+ * Field _alignmentSequenceAnnotationList.
+ */
+ private java.util.Vector _alignmentSequenceAnnotationList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public AlignmentSequence() {
+ super();
+ this._alignmentSequenceAnnotationList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vAlignmentSequenceAnnotation
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAlignmentSequenceAnnotation(
+ final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
+ throws java.lang.IndexOutOfBoundsException {
+ this._alignmentSequenceAnnotationList
+ .addElement(vAlignmentSequenceAnnotation);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlignmentSequenceAnnotation
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addAlignmentSequenceAnnotation(
+ final int index,
+ final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
+ throws java.lang.IndexOutOfBoundsException {
+ this._alignmentSequenceAnnotationList.add(index,
+ vAlignmentSequenceAnnotation);
+ }
+
+ /**
+ * Method enumerateAlignmentSequenceAnnotation.
+ *
+ * @return an Enumeration over all
+ * uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation element
+ */
+ public java.util.Enumeration enumerateAlignmentSequenceAnnotation() {
+ return this._alignmentSequenceAnnotationList.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 AlignmentSequence) {
+
+ AlignmentSequence temp = (AlignmentSequence) obj;
+ boolean thcycle;
+ boolean tmcycle;
+ if (this._id != null) {
+ if (temp._id == null)
+ return false;
+ if (this._id != temp._id) {
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._id);
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._id);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
}
- else if (temp._id != null)
- return false;
- if (this._refid != null) {
- if (temp._refid == null) return false;
- else if (!(this._refid.equals(temp._refid)))
- return false;
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
}
- else if (temp._refid != null)
- return false;
- if (this._alignmentSequenceAnnotationList != null) {
- if (temp._alignmentSequenceAnnotationList == null) return false;
- else if (!(this._alignmentSequenceAnnotationList.equals(temp._alignmentSequenceAnnotationList)))
- return false;
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._id.equals(temp._id)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+ return false;
}
- else if (temp._alignmentSequenceAnnotationList != null)
- return false;
- return true;
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._id);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._id);
+ }
}
+ } else if (temp._id != null)
return false;
- } //-- boolean equals(java.lang.Object)
-
- /**
- * Method getAlignmentSequenceAnnotation
- *
- *
- *
- * @param index
- * @return AlignmentSequenceAnnotation
- */
- public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _alignmentSequenceAnnotationList.size())) {
- throw new IndexOutOfBoundsException("getAlignmentSequenceAnnotation: Index value '"+index+"' not in range [0.."+_alignmentSequenceAnnotationList.size()+ "]");
- }
-
- return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.elementAt(index);
- } //-- uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(int)
-
- /**
- * Method getAlignmentSequenceAnnotation
- *
- *
- *
- * @return AlignmentSequenceAnnotation
- */
- public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation()
- {
- int size = _alignmentSequenceAnnotationList.size();
- uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] mArray = new uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList.elementAt(index);
- }
- return mArray;
- } //-- uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation()
-
- /**
- * Method getAlignmentSequenceAnnotationCount
- *
- *
- *
- * @return int
- */
- public int getAlignmentSequenceAnnotationCount()
- {
- return _alignmentSequenceAnnotationList.size();
- } //-- int getAlignmentSequenceAnnotationCount()
-
- /**
- * Returns the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- * @return String
- * @return the value of field 'id'.
- */
- public java.lang.String getId()
- {
- return this._id;
- } //-- java.lang.String getId()
-
- /**
- * Returns the value of field 'refid'. The field 'refid' has
- * the following description: Dataset Sequence from which
- * this alignment sequence is taken from
- *
- *
- * @return Object
- * @return the value of field 'refid'.
- */
- public java.lang.Object getRefid()
- {
- return this._refid;
- } //-- java.lang.Object getRefid()
-
- /**
- * Method isValid
- *
- *
- *
- * @return boolean
- */
- public boolean isValid()
- {
- try {
- validate();
- }
- catch (org.exolab.castor.xml.ValidationException vex) {
+ if (this._refid != null) {
+ if (temp._refid == null)
+ return false;
+ if (this._refid != temp._refid) {
+ thcycle = org.castor.util.CycleBreaker.startingToCycle(this._refid);
+ tmcycle = org.castor.util.CycleBreaker.startingToCycle(temp._refid);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._refid);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._refid);
+ }
+ ;
return false;
+ }
+ if (!thcycle) {
+ if (!this._refid.equals(temp._refid)) {
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._refid);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._refid);
+ return false;
+ }
+ org.castor.util.CycleBreaker.releaseCycleHandle(this._refid);
+ org.castor.util.CycleBreaker.releaseCycleHandle(temp._refid);
+ }
}
- 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 removeAlignmentSequenceAnnotation
- *
- *
- *
- * @param index
- * @return AlignmentSequenceAnnotation
- */
- public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotation(int index)
- {
- java.lang.Object obj = _alignmentSequenceAnnotationList.elementAt(index);
- _alignmentSequenceAnnotationList.removeElementAt(index);
- return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) obj;
- } //-- uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotation(int)
-
- /**
- * Method removeAllAlignmentSequenceAnnotation
- *
- */
- public void removeAllAlignmentSequenceAnnotation()
- {
- _alignmentSequenceAnnotationList.removeAllElements();
- } //-- void removeAllAlignmentSequenceAnnotation()
-
- /**
- * Method setAlignmentSequenceAnnotation
- *
- *
- *
- * @param index
- * @param vAlignmentSequenceAnnotation
- */
- public void setAlignmentSequenceAnnotation(int index, uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _alignmentSequenceAnnotationList.size())) {
- throw new IndexOutOfBoundsException("setAlignmentSequenceAnnotation: Index value '"+index+"' not in range [0.."+_alignmentSequenceAnnotationList.size()+ "]");
- }
- _alignmentSequenceAnnotationList.setElementAt(vAlignmentSequenceAnnotation, index);
- } //-- void setAlignmentSequenceAnnotation(int, uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation)
-
- /**
- * Method setAlignmentSequenceAnnotation
- *
- *
- *
- * @param alignmentSequenceAnnotationArray
- */
- public void setAlignmentSequenceAnnotation(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] alignmentSequenceAnnotationArray)
- {
- //-- copy array
- _alignmentSequenceAnnotationList.removeAllElements();
- for (int i = 0; i < alignmentSequenceAnnotationArray.length; i++) {
- _alignmentSequenceAnnotationList.addElement(alignmentSequenceAnnotationArray[i]);
+ } else if (temp._refid != null)
+ return false;
+ if (this._alignmentSequenceAnnotationList != null) {
+ if (temp._alignmentSequenceAnnotationList == null)
+ return false;
+ if (this._alignmentSequenceAnnotationList != temp._alignmentSequenceAnnotationList) {
+ thcycle = org.castor.util.CycleBreaker
+ .startingToCycle(this._alignmentSequenceAnnotationList);
+ tmcycle = org.castor.util.CycleBreaker
+ .startingToCycle(temp._alignmentSequenceAnnotationList);
+ if (thcycle != tmcycle) {
+ if (!thcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._alignmentSequenceAnnotationList);
+ }
+ ;
+ if (!tmcycle) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._alignmentSequenceAnnotationList);
+ }
+ ;
+ return false;
+ }
+ if (!thcycle) {
+ if (!this._alignmentSequenceAnnotationList
+ .equals(temp._alignmentSequenceAnnotationList)) {
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._alignmentSequenceAnnotationList);
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._alignmentSequenceAnnotationList);
+ return false;
+ }
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(this._alignmentSequenceAnnotationList);
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(temp._alignmentSequenceAnnotationList);
+ }
}
- } //-- void setAlignmentSequenceAnnotation(uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation)
-
- /**
- * Sets the value of field 'id'. The field 'id' has the
- * following description: Primary Key for vamsas object
- * referencing
- *
- * @param id the value of field 'id'.
- */
- public void setId(java.lang.String id)
- {
- this._id = id;
- } //-- void setId(java.lang.String)
-
- /**
- * Sets the value of field 'refid'. The field 'refid' has the
- * following description: Dataset Sequence from which
- * this alignment sequence is taken from
- *
- *
- * @param refid the value of field 'refid'.
- */
- public void setRefid(java.lang.Object refid)
- {
- this._refid = refid;
- } //-- void setRefid(java.lang.Object)
-
- /**
- * 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.AlignmentSequence) Unmarshaller.unmarshal(uk.ac.vamsas.objects.core.AlignmentSequence.class, reader);
- } //-- uk.ac.vamsas.objects.core.SequenceType unmarshal(java.io.Reader)
-
- /**
- * Method validate
- *
+ } else if (temp._alignmentSequenceAnnotationList != null)
+ return false;
+ return true;
+ }
+ return false;
+ }
+
+ /**
+ * Method getAlignmentSequenceAnnotation.
+ *
+ * @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.AlignmentSequenceAnnotation at the given
+ * index
+ */
+ public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation getAlignmentSequenceAnnotation(
+ final int index) throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._alignmentSequenceAnnotationList.size()) {
+ throw new IndexOutOfBoundsException(
+ "getAlignmentSequenceAnnotation: Index value '" + index
+ + "' not in range [0.."
+ + (this._alignmentSequenceAnnotationList.size() - 1) + "]");
+ }
+
+ return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) _alignmentSequenceAnnotationList
+ .get(index);
+ }
+
+ /**
+ * Method getAlignmentSequenceAnnotation.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.AlignmentSequenceAnnotation[] getAlignmentSequenceAnnotation() {
+ uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] array = new uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[0];
+ return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[]) this._alignmentSequenceAnnotationList
+ .toArray(array);
+ }
+
+ /**
+ * Method getAlignmentSequenceAnnotationAsReference.Returns a reference to
+ * '_alignmentSequenceAnnotationList'. No type checking is performed on any
+ * modifications to the Vector.
+ *
+ * @return a reference to the Vector backing this class
+ */
+ public java.util.Vector getAlignmentSequenceAnnotationAsReference() {
+ return this._alignmentSequenceAnnotationList;
+ }
+
+ /**
+ * Method getAlignmentSequenceAnnotationCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAlignmentSequenceAnnotationCount() {
+ return this._alignmentSequenceAnnotationList.size();
+ }
+
+ /**
+ * Returns the value of field 'id'. The field 'id' has the following
+ * description: Primary Key for vamsas object referencing
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId() {
+ return this._id;
+ }
+
+ /**
+ * Returns the value of field 'refid'. The field 'refid' has the following
+ * description: Dataset Sequence from which this alignment sequence is taken
+ * from
+ *
+ *
+ * @return the value of field 'Refid'.
+ */
+ public java.lang.Object getRefid() {
+ return this._refid;
+ }
+
+ /**
+ * 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 (_id != null && !org.castor.util.CycleBreaker.startingToCycle(_id)) {
+ result = 37 * result + _id.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_id);
+ }
+ if (_refid != null && !org.castor.util.CycleBreaker.startingToCycle(_refid)) {
+ result = 37 * result + _refid.hashCode();
+ org.castor.util.CycleBreaker.releaseCycleHandle(_refid);
+ }
+ if (_alignmentSequenceAnnotationList != null
+ && !org.castor.util.CycleBreaker
+ .startingToCycle(_alignmentSequenceAnnotationList)) {
+ result = 37 * result + _alignmentSequenceAnnotationList.hashCode();
+ org.castor.util.CycleBreaker
+ .releaseCycleHandle(_alignmentSequenceAnnotationList);
+ }
+
+ 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);
+ }
+
+ /**
+ * Method removeAlignmentSequenceAnnotation.
+ *
+ * @param vAlignmentSequenceAnnotation
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAlignmentSequenceAnnotation(
+ final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation) {
+ boolean removed = _alignmentSequenceAnnotationList
+ .remove(vAlignmentSequenceAnnotation);
+ return removed;
+ }
+
+ /**
+ * Method removeAlignmentSequenceAnnotationAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation removeAlignmentSequenceAnnotationAt(
+ final int index) {
+ java.lang.Object obj = this._alignmentSequenceAnnotationList.remove(index);
+ return (uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation) obj;
+ }
+
+ /**
*/
- 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 removeAllAlignmentSequenceAnnotation() {
+ this._alignmentSequenceAnnotationList.clear();
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlignmentSequenceAnnotation
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setAlignmentSequenceAnnotation(
+ final int index,
+ final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation vAlignmentSequenceAnnotation)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._alignmentSequenceAnnotationList.size()) {
+ throw new IndexOutOfBoundsException(
+ "setAlignmentSequenceAnnotation: Index value '" + index
+ + "' not in range [0.."
+ + (this._alignmentSequenceAnnotationList.size() - 1) + "]");
+ }
+
+ this._alignmentSequenceAnnotationList.set(index,
+ vAlignmentSequenceAnnotation);
+ }
+
+ /**
+ *
+ *
+ * @param vAlignmentSequenceAnnotationArray
+ */
+ public void setAlignmentSequenceAnnotation(
+ final uk.ac.vamsas.objects.core.AlignmentSequenceAnnotation[] vAlignmentSequenceAnnotationArray) {
+ // -- copy array
+ _alignmentSequenceAnnotationList.clear();
+
+ for (int i = 0; i < vAlignmentSequenceAnnotationArray.length; i++) {
+ this._alignmentSequenceAnnotationList
+ .add(vAlignmentSequenceAnnotationArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of '_alignmentSequenceAnnotationList' by copying the given
+ * Vector. All elements will be checked for type safety.
+ *
+ * @param vAlignmentSequenceAnnotationList
+ * the Vector to copy.
+ */
+ public void setAlignmentSequenceAnnotation(
+ final java.util.Vector vAlignmentSequenceAnnotationList) {
+ // copy vector
+ this._alignmentSequenceAnnotationList.clear();
+
+ this._alignmentSequenceAnnotationList
+ .addAll(vAlignmentSequenceAnnotationList);
+ }
+
+ /**
+ * Sets the value of '_alignmentSequenceAnnotationList' by setting it to the
+ * given Vector. No type checking is performed.
+ *
+ * @deprecated
+ *
+ * @param alignmentSequenceAnnotationVector
+ * the Vector to set.
+ */
+ public void setAlignmentSequenceAnnotationAsReference(
+ final java.util.Vector alignmentSequenceAnnotationVector) {
+ this._alignmentSequenceAnnotationList = alignmentSequenceAnnotationVector;
+ }
+
+ /**
+ * Sets the value of field 'id'. The field 'id' has the following description:
+ * Primary Key for vamsas object referencing
+ *
+ * @param id
+ * the value of field 'id'.
+ */
+ public void setId(final java.lang.String id) {
+ this._id = id;
+ }
+
+ /**
+ * Sets the value of field 'refid'. The field 'refid' has the following
+ * description: Dataset Sequence from which this alignment sequence is taken
+ * from
+ *
+ *
+ * @param refid
+ * the value of field 'refid'.
+ */
+ public void setRefid(final java.lang.Object refid) {
+ this._refid = refid;
+ }
+
+ /**
+ * 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.AlignmentSequence.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