X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FSequenceSet.java;h=c9e124e9425ab8fed899c35d7b27d3289e9fe8d5;hb=190a4893d444dde29d9bc2c825b483491fa0088d;hp=1be0f6564a92e53b2811807e74a2749e515a450f;hpb=65540422b57569f5bb9766742eccacc75f1368f0;p=jalview.git diff --git a/src/jalview/schemabinding/version2/SequenceSet.java b/src/jalview/schemabinding/version2/SequenceSet.java old mode 100755 new mode 100644 index 1be0f65..c9e124e --- a/src/jalview/schemabinding/version2/SequenceSet.java +++ b/src/jalview/schemabinding/version2/SequenceSet.java @@ -1,818 +1,824 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program 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 General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ -package jalview.schemabinding.version2; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class SequenceSet. - * - * @version $Revision$ $Date$ - */ -public class SequenceSet implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _gapChar. - */ - private java.lang.String _gapChar; - - /** - * reference to set where jalview will gather the dataset - * sequences for all sequences in the set. - * - */ - private java.lang.String _datasetId; - - /** - * Field _sequenceList. - */ - private java.util.Vector _sequenceList; - - /** - * Field _annotationList. - */ - private java.util.Vector _annotationList; - - /** - * Field _sequenceSetPropertiesList. - */ - private java.util.Vector _sequenceSetPropertiesList; - - /** - * Field _alcodonFrameList. - */ - private java.util.Vector _alcodonFrameList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public SequenceSet() { - super(); - this._sequenceList = new java.util.Vector(); - this._annotationList = new java.util.Vector(); - this._sequenceSetPropertiesList = new java.util.Vector(); - this._alcodonFrameList = new java.util.Vector(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * - * - * @param vAlcodonFrame - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addAlcodonFrame( - final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) - throws java.lang.IndexOutOfBoundsException { - this._alcodonFrameList.addElement(vAlcodonFrame); - } - - /** - * - * - * @param index - * @param vAlcodonFrame - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addAlcodonFrame( - final int index, - final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) - throws java.lang.IndexOutOfBoundsException { - this._alcodonFrameList.add(index, vAlcodonFrame); - } - - /** - * - * - * @param vAnnotation - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addAnnotation( - final jalview.schemabinding.version2.Annotation vAnnotation) - throws java.lang.IndexOutOfBoundsException { - this._annotationList.addElement(vAnnotation); - } - - /** - * - * - * @param index - * @param vAnnotation - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addAnnotation( - final int index, - final jalview.schemabinding.version2.Annotation vAnnotation) - throws java.lang.IndexOutOfBoundsException { - this._annotationList.add(index, vAnnotation); - } - - /** - * - * - * @param vSequence - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addSequence( - final jalview.schemabinding.version2.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException { - this._sequenceList.addElement(vSequence); - } - - /** - * - * - * @param index - * @param vSequence - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addSequence( - final int index, - final jalview.schemabinding.version2.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException { - this._sequenceList.add(index, vSequence); - } - - /** - * - * - * @param vSequenceSetProperties - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addSequenceSetProperties( - final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) - throws java.lang.IndexOutOfBoundsException { - this._sequenceSetPropertiesList.addElement(vSequenceSetProperties); - } - - /** - * - * - * @param index - * @param vSequenceSetProperties - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addSequenceSetProperties( - final int index, - final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) - throws java.lang.IndexOutOfBoundsException { - this._sequenceSetPropertiesList.add(index, vSequenceSetProperties); - } - - /** - * Method enumerateAlcodonFrame. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.AlcodonFrame elements - */ - public java.util.Enumeration enumerateAlcodonFrame( - ) { - return this._alcodonFrameList.elements(); - } - - /** - * Method enumerateAnnotation. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.Annotation elements - */ - public java.util.Enumeration enumerateAnnotation( - ) { - return this._annotationList.elements(); - } - - /** - * Method enumerateSequence. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.Sequence elements - */ - public java.util.Enumeration enumerateSequence( - ) { - return this._sequenceList.elements(); - } - - /** - * Method enumerateSequenceSetProperties. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.SequenceSetProperties elements - */ - public java.util.Enumeration enumerateSequenceSetProperties( - ) { - return this._sequenceSetPropertiesList.elements(); - } - - /** - * Method getAlcodonFrame. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.AlcodonFrame at the given inde - */ - public jalview.schemabinding.version2.AlcodonFrame getAlcodonFrame( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._alcodonFrameList.size()) { - throw new IndexOutOfBoundsException("getAlcodonFrame: Index value '" + index + "' not in range [0.." + (this._alcodonFrameList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.AlcodonFrame) _alcodonFrameList.get(index); - } - - /** - * Method getAlcodonFrame.Returns the contents of the - * collection in an Array.
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 know that the Array returned is of - * exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.AlcodonFrame[] getAlcodonFrame( - ) { - jalview.schemabinding.version2.AlcodonFrame[] array = new jalview.schemabinding.version2.AlcodonFrame[0]; - return (jalview.schemabinding.version2.AlcodonFrame[]) this._alcodonFrameList.toArray(array); - } - - /** - * Method getAlcodonFrameCount. - * - * @return the size of this collection - */ - public int getAlcodonFrameCount( - ) { - return this._alcodonFrameList.size(); - } - - /** - * Method getAnnotation. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.Annotation at the given index - */ - public jalview.schemabinding.version2.Annotation getAnnotation( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._annotationList.size()) { - throw new IndexOutOfBoundsException("getAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Annotation) _annotationList.get(index); - } - - /** - * Method getAnnotation.Returns the contents of the collection - * in an Array.
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 know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.Annotation[] getAnnotation( - ) { - jalview.schemabinding.version2.Annotation[] array = new jalview.schemabinding.version2.Annotation[0]; - return (jalview.schemabinding.version2.Annotation[]) this._annotationList.toArray(array); - } - - /** - * Method getAnnotationCount. - * - * @return the size of this collection - */ - public int getAnnotationCount( - ) { - return this._annotationList.size(); - } - - /** - * Returns the value of field 'datasetId'. The field - * 'datasetId' has the following description: reference to set - * where jalview will gather the dataset sequences for all - * sequences in the set. - * - * - * @return the value of field 'DatasetId'. - */ - public java.lang.String getDatasetId( - ) { - return this._datasetId; - } - - /** - * Returns the value of field 'gapChar'. - * - * @return the value of field 'GapChar'. - */ - public java.lang.String getGapChar( - ) { - return this._gapChar; - } - - /** - * Method getSequence. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.Sequence at the given index - */ - public jalview.schemabinding.version2.Sequence getSequence( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._sequenceList.size()) { - throw new IndexOutOfBoundsException("getSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Sequence) _sequenceList.get(index); - } - - /** - * Method getSequence.Returns the contents of the collection in - * an Array.
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 know - * that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.schemabinding.version2.Sequence[] getSequence( - ) { - jalview.schemabinding.version2.Sequence[] array = new jalview.schemabinding.version2.Sequence[0]; - return (jalview.schemabinding.version2.Sequence[]) this._sequenceList.toArray(array); - } - - /** - * Method getSequenceCount. - * - * @return the size of this collection - */ - public int getSequenceCount( - ) { - return this._sequenceList.size(); - } - - /** - * Method getSequenceSetProperties. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.SequenceSetProperties at the - * given index - */ - public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._sequenceSetPropertiesList.size()) { - throw new IndexOutOfBoundsException("getSequenceSetProperties: Index value '" + index + "' not in range [0.." + (this._sequenceSetPropertiesList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList.get(index); - } - - /** - * Method getSequenceSetProperties.Returns the contents of the - * collection in an Array.
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 know that the Array returned is of
- * exactly the correct length.
- *
- * @return this collection as an Array
- */
- public jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties(
- ) {
- jalview.schemabinding.version2.SequenceSetProperties[] array = new jalview.schemabinding.version2.SequenceSetProperties[0];
- return (jalview.schemabinding.version2.SequenceSetProperties[]) this._sequenceSetPropertiesList.toArray(array);
- }
-
- /**
- * Method getSequenceSetPropertiesCount.
- *
- * @return the size of this collection
- */
- public int getSequenceSetPropertiesCount(
- ) {
- return this._sequenceSetPropertiesList.size();
- }
-
- /**
- * 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 removeAlcodonFrame.
- *
- * @param vAlcodonFrame
- * @return true if the object was removed from the collection.
- */
- public boolean removeAlcodonFrame(
- final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) {
- boolean removed = _alcodonFrameList.remove(vAlcodonFrame);
- return removed;
- }
-
- /**
- * Method removeAlcodonFrameAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.AlcodonFrame removeAlcodonFrameAt(
- final int index) {
- java.lang.Object obj = this._alcodonFrameList.remove(index);
- return (jalview.schemabinding.version2.AlcodonFrame) obj;
- }
-
- /**
- */
- public void removeAllAlcodonFrame(
- ) {
- this._alcodonFrameList.clear();
- }
-
- /**
- */
- public void removeAllAnnotation(
- ) {
- this._annotationList.clear();
- }
-
- /**
- */
- public void removeAllSequence(
- ) {
- this._sequenceList.clear();
- }
-
- /**
- */
- public void removeAllSequenceSetProperties(
- ) {
- this._sequenceSetPropertiesList.clear();
- }
-
- /**
- * Method removeAnnotation.
- *
- * @param vAnnotation
- * @return true if the object was removed from the collection.
- */
- public boolean removeAnnotation(
- final jalview.schemabinding.version2.Annotation vAnnotation) {
- boolean removed = _annotationList.remove(vAnnotation);
- return removed;
- }
-
- /**
- * Method removeAnnotationAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.Annotation removeAnnotationAt(
- final int index) {
- java.lang.Object obj = this._annotationList.remove(index);
- return (jalview.schemabinding.version2.Annotation) obj;
- }
-
- /**
- * Method removeSequence.
- *
- * @param vSequence
- * @return true if the object was removed from the collection.
- */
- public boolean removeSequence(
- final jalview.schemabinding.version2.Sequence vSequence) {
- boolean removed = _sequenceList.remove(vSequence);
- return removed;
- }
-
- /**
- * Method removeSequenceAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.Sequence removeSequenceAt(
- final int index) {
- java.lang.Object obj = this._sequenceList.remove(index);
- return (jalview.schemabinding.version2.Sequence) obj;
- }
-
- /**
- * Method removeSequenceSetProperties.
- *
- * @param vSequenceSetProperties
- * @return true if the object was removed from the collection.
- */
- public boolean removeSequenceSetProperties(
- final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) {
- boolean removed = _sequenceSetPropertiesList.remove(vSequenceSetProperties);
- return removed;
- }
-
- /**
- * Method removeSequenceSetPropertiesAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetPropertiesAt(
- final int index) {
- java.lang.Object obj = this._sequenceSetPropertiesList.remove(index);
- return (jalview.schemabinding.version2.SequenceSetProperties) obj;
- }
-
- /**
- *
- *
- * @param index
- * @param vAlcodonFrame
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setAlcodonFrame(
- final int index,
- final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._alcodonFrameList.size()) {
- throw new IndexOutOfBoundsException("setAlcodonFrame: Index value '" + index + "' not in range [0.." + (this._alcodonFrameList.size() - 1) + "]");
- }
-
- this._alcodonFrameList.set(index, vAlcodonFrame);
- }
-
- /**
- *
- *
- * @param vAlcodonFrameArray
- */
- public void setAlcodonFrame(
- final jalview.schemabinding.version2.AlcodonFrame[] vAlcodonFrameArray) {
- //-- copy array
- _alcodonFrameList.clear();
-
- for (int i = 0; i < vAlcodonFrameArray.length; i++) {
- this._alcodonFrameList.add(vAlcodonFrameArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vAnnotation
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setAnnotation(
- final int index,
- final jalview.schemabinding.version2.Annotation vAnnotation)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._annotationList.size()) {
- throw new IndexOutOfBoundsException("setAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]");
- }
-
- this._annotationList.set(index, vAnnotation);
- }
-
- /**
- *
- *
- * @param vAnnotationArray
- */
- public void setAnnotation(
- final jalview.schemabinding.version2.Annotation[] vAnnotationArray) {
- //-- copy array
- _annotationList.clear();
-
- for (int i = 0; i < vAnnotationArray.length; i++) {
- this._annotationList.add(vAnnotationArray[i]);
- }
- }
-
- /**
- * Sets the value of field 'datasetId'. The field 'datasetId'
- * has the following description: reference to set where
- * jalview will gather the dataset sequences for all sequences
- * in the set.
- *
- *
- * @param datasetId the value of field 'datasetId'.
- */
- public void setDatasetId(
- final java.lang.String datasetId) {
- this._datasetId = datasetId;
- }
-
- /**
- * Sets the value of field 'gapChar'.
- *
- * @param gapChar the value of field 'gapChar'.
- */
- public void setGapChar(
- final java.lang.String gapChar) {
- this._gapChar = gapChar;
- }
-
- /**
- *
- *
- * @param index
- * @param vSequence
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setSequence(
- final int index,
- final jalview.schemabinding.version2.Sequence vSequence)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._sequenceList.size()) {
- throw new IndexOutOfBoundsException("setSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");
- }
-
- this._sequenceList.set(index, vSequence);
- }
-
- /**
- *
- *
- * @param vSequenceArray
- */
- public void setSequence(
- final jalview.schemabinding.version2.Sequence[] vSequenceArray) {
- //-- copy array
- _sequenceList.clear();
-
- for (int i = 0; i < vSequenceArray.length; i++) {
- this._sequenceList.add(vSequenceArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vSequenceSetProperties
- * @throws java.lang.IndexOutOfBoundsException if the index
- * given is outside the bounds of the collection
- */
- public void setSequenceSetProperties(
- final int index,
- final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)
- throws java.lang.IndexOutOfBoundsException {
- // check bounds for index
- if (index < 0 || index >= this._sequenceSetPropertiesList.size()) {
- throw new IndexOutOfBoundsException("setSequenceSetProperties: Index value '" + index + "' not in range [0.." + (this._sequenceSetPropertiesList.size() - 1) + "]");
- }
-
- this._sequenceSetPropertiesList.set(index, vSequenceSetProperties);
- }
-
- /**
- *
- *
- * @param vSequenceSetPropertiesArray
- */
- public void setSequenceSetProperties(
- final jalview.schemabinding.version2.SequenceSetProperties[] vSequenceSetPropertiesArray) {
- //-- copy array
- _sequenceSetPropertiesList.clear();
-
- for (int i = 0; i < vSequenceSetPropertiesArray.length; i++) {
- this._sequenceSetPropertiesList.add(vSequenceSetPropertiesArray[i]);
- }
- }
-
- /**
- * 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
- * jalview.schemabinding.version2.SequenceSet
- */
- public static jalview.schemabinding.version2.SequenceSet unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
- return (jalview.schemabinding.version2.SequenceSet) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceSet.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);
- }
-
-}
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see
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 know that the Array returned is of + * exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.AlcodonFrame[] getAlcodonFrame( + ) { + jalview.schemabinding.version2.AlcodonFrame[] array = new jalview.schemabinding.version2.AlcodonFrame[0]; + return (jalview.schemabinding.version2.AlcodonFrame[]) this._alcodonFrameList.toArray(array); + } + + /** + * Method getAlcodonFrameCount. + * + * @return the size of this collection + */ + public int getAlcodonFrameCount( + ) { + return this._alcodonFrameList.size(); + } + + /** + * Method getAnnotation. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.Annotation at the given index + */ + public jalview.schemabinding.version2.Annotation getAnnotation( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._annotationList.size()) { + throw new IndexOutOfBoundsException("getAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.Annotation) _annotationList.get(index); + } + + /** + * Method getAnnotation.Returns the contents of the collection + * in an Array.
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 know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.Annotation[] getAnnotation( + ) { + jalview.schemabinding.version2.Annotation[] array = new jalview.schemabinding.version2.Annotation[0]; + return (jalview.schemabinding.version2.Annotation[]) this._annotationList.toArray(array); + } + + /** + * Method getAnnotationCount. + * + * @return the size of this collection + */ + public int getAnnotationCount( + ) { + return this._annotationList.size(); + } + + /** + * Returns the value of field 'datasetId'. The field + * 'datasetId' has the following description: reference to set + * where jalview will gather the dataset sequences for all + * sequences in the set. + * + * + * @return the value of field 'DatasetId'. + */ + public java.lang.String getDatasetId( + ) { + return this._datasetId; + } + + /** + * Returns the value of field 'gapChar'. + * + * @return the value of field 'GapChar'. + */ + public java.lang.String getGapChar( + ) { + return this._gapChar; + } + + /** + * Method getSequence. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.Sequence at the given index + */ + public jalview.schemabinding.version2.Sequence getSequence( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._sequenceList.size()) { + throw new IndexOutOfBoundsException("getSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.Sequence) _sequenceList.get(index); + } + + /** + * Method getSequence.Returns the contents of the collection in + * an Array.
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 know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.Sequence[] getSequence( + ) { + jalview.schemabinding.version2.Sequence[] array = new jalview.schemabinding.version2.Sequence[0]; + return (jalview.schemabinding.version2.Sequence[]) this._sequenceList.toArray(array); + } + + /** + * Method getSequenceCount. + * + * @return the size of this collection + */ + public int getSequenceCount( + ) { + return this._sequenceList.size(); + } + + /** + * Method getSequenceSetProperties. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.SequenceSetProperties at the + * given index + */ + public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._sequenceSetPropertiesList.size()) { + throw new IndexOutOfBoundsException("getSequenceSetProperties: Index value '" + index + "' not in range [0.." + (this._sequenceSetPropertiesList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList.get(index); + } + + /** + * Method getSequenceSetProperties.Returns the contents of the + * collection in an Array.
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 know that the Array returned is of + * exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties( + ) { + jalview.schemabinding.version2.SequenceSetProperties[] array = new jalview.schemabinding.version2.SequenceSetProperties[0]; + return (jalview.schemabinding.version2.SequenceSetProperties[]) this._sequenceSetPropertiesList.toArray(array); + } + + /** + * Method getSequenceSetPropertiesCount. + * + * @return the size of this collection + */ + public int getSequenceSetPropertiesCount( + ) { + return this._sequenceSetPropertiesList.size(); + } + + /** + * 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 removeAlcodonFrame. + * + * @param vAlcodonFrame + * @return true if the object was removed from the collection. + */ + public boolean removeAlcodonFrame( + final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) { + boolean removed = _alcodonFrameList.remove(vAlcodonFrame); + return removed; + } + + /** + * Method removeAlcodonFrameAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.AlcodonFrame removeAlcodonFrameAt( + final int index) { + java.lang.Object obj = this._alcodonFrameList.remove(index); + return (jalview.schemabinding.version2.AlcodonFrame) obj; + } + + /** + */ + public void removeAllAlcodonFrame( + ) { + this._alcodonFrameList.clear(); + } + + /** + */ + public void removeAllAnnotation( + ) { + this._annotationList.clear(); + } + + /** + */ + public void removeAllSequence( + ) { + this._sequenceList.clear(); + } + + /** + */ + public void removeAllSequenceSetProperties( + ) { + this._sequenceSetPropertiesList.clear(); + } + + /** + * Method removeAnnotation. + * + * @param vAnnotation + * @return true if the object was removed from the collection. + */ + public boolean removeAnnotation( + final jalview.schemabinding.version2.Annotation vAnnotation) { + boolean removed = _annotationList.remove(vAnnotation); + return removed; + } + + /** + * Method removeAnnotationAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.Annotation removeAnnotationAt( + final int index) { + java.lang.Object obj = this._annotationList.remove(index); + return (jalview.schemabinding.version2.Annotation) obj; + } + + /** + * Method removeSequence. + * + * @param vSequence + * @return true if the object was removed from the collection. + */ + public boolean removeSequence( + final jalview.schemabinding.version2.Sequence vSequence) { + boolean removed = _sequenceList.remove(vSequence); + return removed; + } + + /** + * Method removeSequenceAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.Sequence removeSequenceAt( + final int index) { + java.lang.Object obj = this._sequenceList.remove(index); + return (jalview.schemabinding.version2.Sequence) obj; + } + + /** + * Method removeSequenceSetProperties. + * + * @param vSequenceSetProperties + * @return true if the object was removed from the collection. + */ + public boolean removeSequenceSetProperties( + final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) { + boolean removed = _sequenceSetPropertiesList.remove(vSequenceSetProperties); + return removed; + } + + /** + * Method removeSequenceSetPropertiesAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetPropertiesAt( + final int index) { + java.lang.Object obj = this._sequenceSetPropertiesList.remove(index); + return (jalview.schemabinding.version2.SequenceSetProperties) obj; + } + + /** + * + * + * @param index + * @param vAlcodonFrame + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setAlcodonFrame( + final int index, + final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._alcodonFrameList.size()) { + throw new IndexOutOfBoundsException("setAlcodonFrame: Index value '" + index + "' not in range [0.." + (this._alcodonFrameList.size() - 1) + "]"); + } + + this._alcodonFrameList.set(index, vAlcodonFrame); + } + + /** + * + * + * @param vAlcodonFrameArray + */ + public void setAlcodonFrame( + final jalview.schemabinding.version2.AlcodonFrame[] vAlcodonFrameArray) { + //-- copy array + _alcodonFrameList.clear(); + + for (int i = 0; i < vAlcodonFrameArray.length; i++) { + this._alcodonFrameList.add(vAlcodonFrameArray[i]); + } + } + + /** + * + * + * @param index + * @param vAnnotation + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setAnnotation( + final int index, + final jalview.schemabinding.version2.Annotation vAnnotation) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._annotationList.size()) { + throw new IndexOutOfBoundsException("setAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]"); + } + + this._annotationList.set(index, vAnnotation); + } + + /** + * + * + * @param vAnnotationArray + */ + public void setAnnotation( + final jalview.schemabinding.version2.Annotation[] vAnnotationArray) { + //-- copy array + _annotationList.clear(); + + for (int i = 0; i < vAnnotationArray.length; i++) { + this._annotationList.add(vAnnotationArray[i]); + } + } + + /** + * Sets the value of field 'datasetId'. The field 'datasetId' + * has the following description: reference to set where + * jalview will gather the dataset sequences for all sequences + * in the set. + * + * + * @param datasetId the value of field 'datasetId'. + */ + public void setDatasetId( + final java.lang.String datasetId) { + this._datasetId = datasetId; + } + + /** + * Sets the value of field 'gapChar'. + * + * @param gapChar the value of field 'gapChar'. + */ + public void setGapChar( + final java.lang.String gapChar) { + this._gapChar = gapChar; + } + + /** + * + * + * @param index + * @param vSequence + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setSequence( + final int index, + final jalview.schemabinding.version2.Sequence vSequence) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._sequenceList.size()) { + throw new IndexOutOfBoundsException("setSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]"); + } + + this._sequenceList.set(index, vSequence); + } + + /** + * + * + * @param vSequenceArray + */ + public void setSequence( + final jalview.schemabinding.version2.Sequence[] vSequenceArray) { + //-- copy array + _sequenceList.clear(); + + for (int i = 0; i < vSequenceArray.length; i++) { + this._sequenceList.add(vSequenceArray[i]); + } + } + + /** + * + * + * @param index + * @param vSequenceSetProperties + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setSequenceSetProperties( + final int index, + final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._sequenceSetPropertiesList.size()) { + throw new IndexOutOfBoundsException("setSequenceSetProperties: Index value '" + index + "' not in range [0.." + (this._sequenceSetPropertiesList.size() - 1) + "]"); + } + + this._sequenceSetPropertiesList.set(index, vSequenceSetProperties); + } + + /** + * + * + * @param vSequenceSetPropertiesArray + */ + public void setSequenceSetProperties( + final jalview.schemabinding.version2.SequenceSetProperties[] vSequenceSetPropertiesArray) { + //-- copy array + _sequenceSetPropertiesList.clear(); + + for (int i = 0; i < vSequenceSetPropertiesArray.length; i++) { + this._sequenceSetPropertiesList.add(vSequenceSetPropertiesArray[i]); + } + } + + /** + * 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 + * jalview.schemabinding.version2.SequenceSet + */ + public static jalview.schemabinding.version2.SequenceSet unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.SequenceSet) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceSet.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); + } + +}