/*\r
- * This class was automatically generated with\r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
- * Schema.\r
- * $Id$\r
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)\r
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview is free software: you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License \r
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
*/\r
-\r
package jalview.schemabinding.version2;\r
\r
//---------------------------------/\r
//- Imported classes and packages -/\r
//---------------------------------/\r
\r
-import java.util.*;\r
-\r
-import org.exolab.castor.xml.*;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
\r
/**\r
* Class SequenceSet.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
-public class SequenceSet\r
- implements java.io.Serializable\r
+public class SequenceSet implements java.io.Serializable\r
{\r
\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
+ // --------------------------/\r
+ // - Class/Member Variables -/\r
+ // --------------------------/\r
\r
/**\r
- * Field _gapChar\r
+ * Field _gapChar.\r
*/\r
private java.lang.String _gapChar;\r
\r
/**\r
- * Field _sequenceList\r
+ * reference to set where jalview will gather the dataset sequences for all\r
+ * sequences in the set.\r
+ * \r
+ */\r
+ private java.lang.String _datasetId;\r
+\r
+ /**\r
+ * Field _sequenceList.\r
*/\r
private java.util.Vector _sequenceList;\r
\r
/**\r
- * Field _annotationList\r
+ * Field _annotationList.\r
*/\r
private java.util.Vector _annotationList;\r
\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
+ /**\r
+ * Field _sequenceSetPropertiesList.\r
+ */\r
+ private java.util.Vector _sequenceSetPropertiesList;\r
+\r
+ /**\r
+ * Field _alcodonFrameList.\r
+ */\r
+ private java.util.Vector _alcodonFrameList;\r
+\r
+ // ----------------/\r
+ // - Constructors -/\r
+ // ----------------/\r
\r
public SequenceSet()\r
{\r
super();\r
- _sequenceList = new Vector();\r
- _annotationList = new Vector();\r
- } //-- jalview.schemabinding.version2.SequenceSet()\r
+ this._sequenceList = new java.util.Vector();\r
+ this._annotationList = new java.util.Vector();\r
+ this._sequenceSetPropertiesList = new java.util.Vector();\r
+ this._alcodonFrameList = new java.util.Vector();\r
+ }\r
+\r
+ // -----------/\r
+ // - Methods -/\r
+ // -----------/\r
\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
+ /**\r
+ * \r
+ * \r
+ * @param vAlcodonFrame\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addAlcodonFrame(\r
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._alcodonFrameList.addElement(vAlcodonFrame);\r
+ }\r
\r
/**\r
- * Method addAnnotation\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAlcodonFrame\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addAlcodonFrame(final int index,\r
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._alcodonFrameList.add(index, vAlcodonFrame);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
* @param vAnnotation\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
*/\r
- public void addAnnotation(jalview.schemabinding.version2.Annotation\r
- vAnnotation)\r
- throws java.lang.IndexOutOfBoundsException\r
+ public void addAnnotation(\r
+ final jalview.schemabinding.version2.Annotation vAnnotation)\r
+ throws java.lang.IndexOutOfBoundsException\r
{\r
- _annotationList.addElement(vAnnotation);\r
- } //-- void addAnnotation(jalview.schemabinding.version2.Annotation)\r
+ this._annotationList.addElement(vAnnotation);\r
+ }\r
\r
/**\r
- * Method addAnnotation\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
* @param index\r
* @param vAnnotation\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
*/\r
- public void addAnnotation(int index,\r
- jalview.schemabinding.version2.Annotation\r
- vAnnotation)\r
- throws java.lang.IndexOutOfBoundsException\r
+ public void addAnnotation(final int index,\r
+ final jalview.schemabinding.version2.Annotation vAnnotation)\r
+ throws java.lang.IndexOutOfBoundsException\r
{\r
- _annotationList.insertElementAt(vAnnotation, index);\r
- } //-- void addAnnotation(int, jalview.schemabinding.version2.Annotation)\r
+ this._annotationList.add(index, vAnnotation);\r
+ }\r
\r
/**\r
- * Method addSequence\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
* @param vSequence\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
*/\r
- public void addSequence(jalview.schemabinding.version2.Sequence vSequence)\r
- throws java.lang.IndexOutOfBoundsException\r
+ public void addSequence(\r
+ final jalview.schemabinding.version2.Sequence vSequence)\r
+ throws java.lang.IndexOutOfBoundsException\r
{\r
- _sequenceList.addElement(vSequence);\r
- } //-- void addSequence(jalview.schemabinding.version2.Sequence)\r
+ this._sequenceList.addElement(vSequence);\r
+ }\r
\r
/**\r
- * Method addSequence\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
* @param index\r
* @param vSequence\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addSequence(final int index,\r
+ final jalview.schemabinding.version2.Sequence vSequence)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._sequenceList.add(index, vSequence);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vSequenceSetProperties\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addSequenceSetProperties(\r
+ final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._sequenceSetPropertiesList.addElement(vSequenceSetProperties);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vSequenceSetProperties\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addSequenceSetProperties(\r
+ final int index,\r
+ final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._sequenceSetPropertiesList.add(index, vSequenceSetProperties);\r
+ }\r
+\r
+ /**\r
+ * Method enumerateAlcodonFrame.\r
+ * \r
+ * @return an Enumeration over all jalview.schemabinding.version2.AlcodonFrame\r
+ * elements\r
*/\r
- public void addSequence(int index,\r
- jalview.schemabinding.version2.Sequence vSequence)\r
- throws java.lang.IndexOutOfBoundsException\r
+ public java.util.Enumeration enumerateAlcodonFrame()\r
{\r
- _sequenceList.insertElementAt(vSequence, index);\r
- } //-- void addSequence(int, jalview.schemabinding.version2.Sequence)\r
+ return this._alcodonFrameList.elements();\r
+ }\r
\r
/**\r
- * Method enumerateAnnotation\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
+ * Method enumerateAnnotation.\r
+ * \r
+ * @return an Enumeration over all jalview.schemabinding.version2.Annotation\r
+ * elements\r
*/\r
public java.util.Enumeration enumerateAnnotation()\r
{\r
- return _annotationList.elements();\r
- } //-- java.util.Enumeration enumerateAnnotation()\r
+ return this._annotationList.elements();\r
+ }\r
\r
/**\r
- * Method enumerateSequence\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
+ * Method enumerateSequence.\r
+ * \r
+ * @return an Enumeration over all jalview.schemabinding.version2.Sequence\r
+ * elements\r
*/\r
public java.util.Enumeration enumerateSequence()\r
{\r
- return _sequenceList.elements();\r
- } //-- java.util.Enumeration enumerateSequence()\r
+ return this._sequenceList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumerateSequenceSetProperties.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.SequenceSetProperties elements\r
+ */\r
+ public java.util.Enumeration enumerateSequenceSetProperties()\r
+ {\r
+ return this._sequenceSetPropertiesList.elements();\r
+ }\r
\r
/**\r
- * Method getAnnotation\r
- *\r
- *\r
- *\r
+ * Method getAlcodonFrame.\r
+ * \r
* @param index\r
- * @return Annotation\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ * @return the value of the jalview.schemabinding.version2.AlcodonFrame at the\r
+ * given inde\r
*/\r
- public jalview.schemabinding.version2.Annotation getAnnotation(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
+ public jalview.schemabinding.version2.AlcodonFrame getAlcodonFrame(\r
+ final int index) throws java.lang.IndexOutOfBoundsException\r
{\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _annotationList.size()))\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._alcodonFrameList.size())\r
{\r
- throw new IndexOutOfBoundsException();\r
+ throw new IndexOutOfBoundsException("getAlcodonFrame: Index value '"\r
+ + index + "' not in range [0.."\r
+ + (this._alcodonFrameList.size() - 1) + "]");\r
}\r
\r
- return (jalview.schemabinding.version2.Annotation) _annotationList.\r
- elementAt(index);\r
- } //-- jalview.schemabinding.version2.Annotation getAnnotation(int)\r
+ return (jalview.schemabinding.version2.AlcodonFrame) _alcodonFrameList\r
+ .get(index);\r
+ }\r
\r
/**\r
- * Method getAnnotation\r
- *\r
- *\r
- *\r
- * @return Annotation\r
+ * Method getAlcodonFrame.Returns the contents of the collection in an Array.\r
+ * <p>\r
+ * Note: Just in case the collection contents are changing in another thread,\r
+ * we pass a 0-length Array of the correct type into the API call. This way we\r
+ * <i>know</i> that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
*/\r
- public jalview.schemabinding.version2.Annotation[] getAnnotation()\r
+ public jalview.schemabinding.version2.AlcodonFrame[] getAlcodonFrame()\r
+ {\r
+ jalview.schemabinding.version2.AlcodonFrame[] array = new jalview.schemabinding.version2.AlcodonFrame[0];\r
+ return (jalview.schemabinding.version2.AlcodonFrame[]) this._alcodonFrameList\r
+ .toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getAlcodonFrameCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getAlcodonFrameCount()\r
+ {\r
+ return this._alcodonFrameList.size();\r
+ }\r
+\r
+ /**\r
+ * Method getAnnotation.\r
+ * \r
+ * @param index\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ * @return the value of the jalview.schemabinding.version2.Annotation at the\r
+ * given index\r
+ */\r
+ public jalview.schemabinding.version2.Annotation getAnnotation(\r
+ final int index) throws java.lang.IndexOutOfBoundsException\r
{\r
- int size = _annotationList.size();\r
- jalview.schemabinding.version2.Annotation[] mArray = new jalview.\r
- schemabinding.version2.Annotation[size];\r
- for (int index = 0; index < size; index++)\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._annotationList.size())\r
{\r
- mArray[index] = (jalview.schemabinding.version2.Annotation)\r
- _annotationList.elementAt(index);\r
+ throw new IndexOutOfBoundsException("getAnnotation: Index value '"\r
+ + index + "' not in range [0.."\r
+ + (this._annotationList.size() - 1) + "]");\r
}\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.Annotation[] getAnnotation()\r
+\r
+ return (jalview.schemabinding.version2.Annotation) _annotationList\r
+ .get(index);\r
+ }\r
\r
/**\r
- * Method getAnnotationCount\r
- *\r
- *\r
- *\r
- * @return int\r
+ * Method getAnnotation.Returns the contents of the collection in an Array.\r
+ * <p>\r
+ * Note: Just in case the collection contents are changing in another thread,\r
+ * we pass a 0-length Array of the correct type into the API call. This way we\r
+ * <i>know</i> that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.Annotation[] getAnnotation()\r
+ {\r
+ jalview.schemabinding.version2.Annotation[] array = new jalview.schemabinding.version2.Annotation[0];\r
+ return (jalview.schemabinding.version2.Annotation[]) this._annotationList\r
+ .toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getAnnotationCount.\r
+ * \r
+ * @return the size of this collection\r
*/\r
public int getAnnotationCount()\r
{\r
- return _annotationList.size();\r
- } //-- int getAnnotationCount()\r
+ return this._annotationList.size();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'datasetId'. The field 'datasetId' has the\r
+ * following description: reference to set where jalview will gather the\r
+ * dataset sequences for all sequences in the set.\r
+ * \r
+ * \r
+ * @return the value of field 'DatasetId'.\r
+ */\r
+ public java.lang.String getDatasetId()\r
+ {\r
+ return this._datasetId;\r
+ }\r
\r
/**\r
* Returns the value of field 'gapChar'.\r
- *\r
- * @return String\r
- * @return the value of field 'gapChar'.\r
+ * \r
+ * @return the value of field 'GapChar'.\r
*/\r
public java.lang.String getGapChar()\r
{\r
return this._gapChar;\r
- } //-- java.lang.String getGapChar()\r
+ }\r
\r
/**\r
- * Method getSequence\r
- *\r
- *\r
- *\r
+ * Method getSequence.\r
+ * \r
* @param index\r
- * @return Sequence\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ * @return the value of the jalview.schemabinding.version2.Sequence at the\r
+ * given index\r
*/\r
- public jalview.schemabinding.version2.Sequence getSequence(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
+ public jalview.schemabinding.version2.Sequence getSequence(final int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
{\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _sequenceList.size()))\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._sequenceList.size())\r
{\r
- throw new IndexOutOfBoundsException();\r
+ throw new IndexOutOfBoundsException("getSequence: Index value '"\r
+ + index + "' not in range [0.."\r
+ + (this._sequenceList.size() - 1) + "]");\r
}\r
\r
- return (jalview.schemabinding.version2.Sequence) _sequenceList.elementAt(\r
- index);\r
- } //-- jalview.schemabinding.version2.Sequence getSequence(int)\r
+ return (jalview.schemabinding.version2.Sequence) _sequenceList\r
+ .get(index);\r
+ }\r
\r
/**\r
- * Method getSequence\r
- *\r
- *\r
- *\r
- * @return Sequence\r
+ * Method getSequence.Returns the contents of the collection in an Array.\r
+ * <p>\r
+ * Note: Just in case the collection contents are changing in another thread,\r
+ * we pass a 0-length Array of the correct type into the API call. This way we\r
+ * <i>know</i> that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
*/\r
public jalview.schemabinding.version2.Sequence[] getSequence()\r
{\r
- int size = _sequenceList.size();\r
- jalview.schemabinding.version2.Sequence[] mArray = new jalview.\r
- schemabinding.version2.Sequence[size];\r
- for (int index = 0; index < size; index++)\r
+ jalview.schemabinding.version2.Sequence[] array = new jalview.schemabinding.version2.Sequence[0];\r
+ return (jalview.schemabinding.version2.Sequence[]) this._sequenceList\r
+ .toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getSequenceCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getSequenceCount()\r
+ {\r
+ return this._sequenceList.size();\r
+ }\r
+\r
+ /**\r
+ * Method getSequenceSetProperties.\r
+ * \r
+ * @param index\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.SequenceSetProperties at the given\r
+ * index\r
+ */\r
+ public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties(\r
+ final int index) throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._sequenceSetPropertiesList.size())\r
{\r
- mArray[index] = (jalview.schemabinding.version2.Sequence) _sequenceList.\r
- elementAt(index);\r
+ throw new IndexOutOfBoundsException(\r
+ "getSequenceSetProperties: Index value '" + index\r
+ + "' not in range [0.."\r
+ + (this._sequenceSetPropertiesList.size() - 1) + "]");\r
}\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.Sequence[] getSequence()\r
+\r
+ return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList\r
+ .get(index);\r
+ }\r
\r
/**\r
- * Method getSequenceCount\r
- *\r
- *\r
- *\r
- * @return int\r
+ * Method getSequenceSetProperties.Returns the contents of the collection in\r
+ * an Array.\r
+ * <p>\r
+ * Note: Just in case the collection contents are changing in another thread,\r
+ * we pass a 0-length Array of the correct type into the API call. This way we\r
+ * <i>know</i> that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
*/\r
- public int getSequenceCount()\r
+ public jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties()\r
{\r
- return _sequenceList.size();\r
- } //-- int getSequenceCount()\r
+ jalview.schemabinding.version2.SequenceSetProperties[] array = new jalview.schemabinding.version2.SequenceSetProperties[0];\r
+ return (jalview.schemabinding.version2.SequenceSetProperties[]) this._sequenceSetPropertiesList\r
+ .toArray(array);\r
+ }\r
\r
/**\r
- * Method isValid\r
- *\r
- *\r
- *\r
- * @return boolean\r
+ * Method getSequenceSetPropertiesCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getSequenceSetPropertiesCount()\r
+ {\r
+ return this._sequenceSetPropertiesList.size();\r
+ }\r
+\r
+ /**\r
+ * Method isValid.\r
+ * \r
+ * @return true if this object is valid according to the schema\r
*/\r
public boolean isValid()\r
{\r
try\r
{\r
validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
+ } catch (org.exolab.castor.xml.ValidationException vex)\r
{\r
return false;\r
}\r
return true;\r
- } //-- boolean isValid()\r
+ }\r
\r
/**\r
- * Method marshal\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
* @param out\r
+ * @throws org.exolab.castor.xml.MarshalException\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
*/\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
+ public void marshal(final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException\r
{\r
-\r
Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
+ }\r
\r
/**\r
- * Method marshal\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
* @param handler\r
+ * @throws java.io.IOException\r
+ * if an IOException occurs during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
*/\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
+ public void marshal(final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException,\r
+ org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException\r
{\r
-\r
Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
+ }\r
\r
/**\r
- * Method removeAllAnnotation\r
- *\r
+ * Method removeAlcodonFrame.\r
+ * \r
+ * @param vAlcodonFrame\r
+ * @return true if the object was removed from the collection.\r
*/\r
- public void removeAllAnnotation()\r
+ public boolean removeAlcodonFrame(\r
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)\r
{\r
- _annotationList.removeAllElements();\r
- } //-- void removeAllAnnotation()\r
+ boolean removed = _alcodonFrameList.remove(vAlcodonFrame);\r
+ return removed;\r
+ }\r
\r
/**\r
- * Method removeAllSequence\r
- *\r
+ * Method removeAlcodonFrameAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
*/\r
+ public jalview.schemabinding.version2.AlcodonFrame removeAlcodonFrameAt(\r
+ final int index)\r
+ {\r
+ java.lang.Object obj = this._alcodonFrameList.remove(index);\r
+ return (jalview.schemabinding.version2.AlcodonFrame) obj;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllAlcodonFrame()\r
+ {\r
+ this._alcodonFrameList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllAnnotation()\r
+ {\r
+ this._annotationList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
public void removeAllSequence()\r
{\r
- _sequenceList.removeAllElements();\r
- } //-- void removeAllSequence()\r
+ this._sequenceList.clear();\r
+ }\r
\r
/**\r
- * Method removeAnnotation\r
- *\r
- *\r
- *\r
+ */\r
+ public void removeAllSequenceSetProperties()\r
+ {\r
+ this._sequenceSetPropertiesList.clear();\r
+ }\r
+\r
+ /**\r
+ * Method removeAnnotation.\r
+ * \r
+ * @param vAnnotation\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeAnnotation(\r
+ final jalview.schemabinding.version2.Annotation vAnnotation)\r
+ {\r
+ boolean removed = _annotationList.remove(vAnnotation);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeAnnotationAt.\r
+ * \r
* @param index\r
- * @return Annotation\r
+ * @return the element removed from the collection\r
*/\r
- public jalview.schemabinding.version2.Annotation removeAnnotation(int index)\r
+ public jalview.schemabinding.version2.Annotation removeAnnotationAt(\r
+ final int index)\r
{\r
- java.lang.Object obj = _annotationList.elementAt(index);\r
- _annotationList.removeElementAt(index);\r
+ java.lang.Object obj = this._annotationList.remove(index);\r
return (jalview.schemabinding.version2.Annotation) obj;\r
- } //-- jalview.schemabinding.version2.Annotation removeAnnotation(int)\r
+ }\r
\r
/**\r
- * Method removeSequence\r
- *\r
- *\r
- *\r
+ * Method removeSequence.\r
+ * \r
+ * @param vSequence\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeSequence(\r
+ final jalview.schemabinding.version2.Sequence vSequence)\r
+ {\r
+ boolean removed = _sequenceList.remove(vSequence);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeSequenceAt.\r
+ * \r
* @param index\r
- * @return Sequence\r
+ * @return the element removed from the collection\r
*/\r
- public jalview.schemabinding.version2.Sequence removeSequence(int index)\r
+ public jalview.schemabinding.version2.Sequence removeSequenceAt(\r
+ final int index)\r
{\r
- java.lang.Object obj = _sequenceList.elementAt(index);\r
- _sequenceList.removeElementAt(index);\r
+ java.lang.Object obj = this._sequenceList.remove(index);\r
return (jalview.schemabinding.version2.Sequence) obj;\r
- } //-- jalview.schemabinding.version2.Sequence removeSequence(int)\r
+ }\r
+\r
+ /**\r
+ * Method removeSequenceSetProperties.\r
+ * \r
+ * @param vSequenceSetProperties\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeSequenceSetProperties(\r
+ final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)\r
+ {\r
+ boolean removed = _sequenceSetPropertiesList\r
+ .remove(vSequenceSetProperties);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeSequenceSetPropertiesAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetPropertiesAt(\r
+ final int index)\r
+ {\r
+ java.lang.Object obj = this._sequenceSetPropertiesList.remove(index);\r
+ return (jalview.schemabinding.version2.SequenceSetProperties) obj;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAlcodonFrame\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void setAlcodonFrame(final int index,\r
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._alcodonFrameList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException("setAlcodonFrame: Index value '"\r
+ + index + "' not in range [0.."\r
+ + (this._alcodonFrameList.size() - 1) + "]");\r
+ }\r
+\r
+ this._alcodonFrameList.set(index, vAlcodonFrame);\r
+ }\r
\r
/**\r
- * Method setAnnotation\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
+ * @param vAlcodonFrameArray\r
+ */\r
+ public void setAlcodonFrame(\r
+ final jalview.schemabinding.version2.AlcodonFrame[] vAlcodonFrameArray)\r
+ {\r
+ // -- copy array\r
+ _alcodonFrameList.clear();\r
+\r
+ for (int i = 0; i < vAlcodonFrameArray.length; i++)\r
+ {\r
+ this._alcodonFrameList.add(vAlcodonFrameArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
* @param index\r
* @param vAnnotation\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
*/\r
- public void setAnnotation(int index,\r
- jalview.schemabinding.version2.Annotation\r
- vAnnotation)\r
- throws java.lang.IndexOutOfBoundsException\r
+ public void setAnnotation(final int index,\r
+ final jalview.schemabinding.version2.Annotation vAnnotation)\r
+ throws java.lang.IndexOutOfBoundsException\r
{\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _annotationList.size()))\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._annotationList.size())\r
{\r
- throw new IndexOutOfBoundsException();\r
+ throw new IndexOutOfBoundsException("setAnnotation: Index value '"\r
+ + index + "' not in range [0.."\r
+ + (this._annotationList.size() - 1) + "]");\r
}\r
- _annotationList.setElementAt(vAnnotation, index);\r
- } //-- void setAnnotation(int, jalview.schemabinding.version2.Annotation)\r
+\r
+ this._annotationList.set(index, vAnnotation);\r
+ }\r
\r
/**\r
- * Method setAnnotation\r
- *\r
- *\r
- *\r
- * @param annotationArray\r
+ * \r
+ * \r
+ * @param vAnnotationArray\r
*/\r
- public void setAnnotation(jalview.schemabinding.version2.Annotation[]\r
- annotationArray)\r
+ public void setAnnotation(\r
+ final jalview.schemabinding.version2.Annotation[] vAnnotationArray)\r
{\r
- //-- copy array\r
- _annotationList.removeAllElements();\r
- for (int i = 0; i < annotationArray.length; i++)\r
+ // -- copy array\r
+ _annotationList.clear();\r
+\r
+ for (int i = 0; i < vAnnotationArray.length; i++)\r
{\r
- _annotationList.addElement(annotationArray[i]);\r
+ this._annotationList.add(vAnnotationArray[i]);\r
}\r
- } //-- void setAnnotation(jalview.schemabinding.version2.Annotation)\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'datasetId'. The field 'datasetId' has the\r
+ * following description: reference to set where jalview will gather the\r
+ * dataset sequences for all sequences in the set.\r
+ * \r
+ * \r
+ * @param datasetId\r
+ * the value of field 'datasetId'.\r
+ */\r
+ public void setDatasetId(final java.lang.String datasetId)\r
+ {\r
+ this._datasetId = datasetId;\r
+ }\r
\r
/**\r
* Sets the value of field 'gapChar'.\r
- *\r
- * @param gapChar the value of field 'gapChar'.\r
+ * \r
+ * @param gapChar\r
+ * the value of field 'gapChar'.\r
*/\r
- public void setGapChar(java.lang.String gapChar)\r
+ public void setGapChar(final java.lang.String gapChar)\r
{\r
this._gapChar = gapChar;\r
- } //-- void setGapChar(java.lang.String)\r
+ }\r
\r
/**\r
- * Method setSequence\r
- *\r
- *\r
- *\r
+ * \r
+ * \r
* @param index\r
* @param vSequence\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void setSequence(final int index,\r
+ final jalview.schemabinding.version2.Sequence vSequence)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._sequenceList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException("setSequence: Index value '"\r
+ + index + "' not in range [0.."\r
+ + (this._sequenceList.size() - 1) + "]");\r
+ }\r
+\r
+ this._sequenceList.set(index, vSequence);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vSequenceArray\r
+ */\r
+ public void setSequence(\r
+ final jalview.schemabinding.version2.Sequence[] vSequenceArray)\r
+ {\r
+ // -- copy array\r
+ _sequenceList.clear();\r
+\r
+ for (int i = 0; i < vSequenceArray.length; i++)\r
+ {\r
+ this._sequenceList.add(vSequenceArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vSequenceSetProperties\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
*/\r
- public void setSequence(int index,\r
- jalview.schemabinding.version2.Sequence vSequence)\r
- throws java.lang.IndexOutOfBoundsException\r
+ public void setSequenceSetProperties(\r
+ final int index,\r
+ final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties)\r
+ throws java.lang.IndexOutOfBoundsException\r
{\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _sequenceList.size()))\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._sequenceSetPropertiesList.size())\r
{\r
- throw new IndexOutOfBoundsException();\r
+ throw new IndexOutOfBoundsException(\r
+ "setSequenceSetProperties: Index value '" + index\r
+ + "' not in range [0.."\r
+ + (this._sequenceSetPropertiesList.size() - 1) + "]");\r
}\r
- _sequenceList.setElementAt(vSequence, index);\r
- } //-- void setSequence(int, jalview.schemabinding.version2.Sequence)\r
+\r
+ this._sequenceSetPropertiesList.set(index, vSequenceSetProperties);\r
+ }\r
\r
/**\r
- * Method setSequence\r
- *\r
- *\r
- *\r
- * @param sequenceArray\r
+ * \r
+ * \r
+ * @param vSequenceSetPropertiesArray\r
*/\r
- public void setSequence(jalview.schemabinding.version2.Sequence[]\r
- sequenceArray)\r
+ public void setSequenceSetProperties(\r
+ final jalview.schemabinding.version2.SequenceSetProperties[] vSequenceSetPropertiesArray)\r
{\r
- //-- copy array\r
- _sequenceList.removeAllElements();\r
- for (int i = 0; i < sequenceArray.length; i++)\r
+ // -- copy array\r
+ _sequenceSetPropertiesList.clear();\r
+\r
+ for (int i = 0; i < vSequenceSetPropertiesArray.length; i++)\r
{\r
- _sequenceList.addElement(sequenceArray[i]);\r
+ this._sequenceSetPropertiesList.add(vSequenceSetPropertiesArray[i]);\r
}\r
- } //-- void setSequence(jalview.schemabinding.version2.Sequence)\r
+ }\r
\r
/**\r
- * Method unmarshal\r
- *\r
- *\r
- *\r
+ * Method unmarshal.\r
+ * \r
* @param reader\r
- * @return Object\r
+ * @throws org.exolab.castor.xml.MarshalException\r
+ * if object is null or if any SAXException is thrown during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
+ * @return the unmarshaled jalview.schemabinding.version2.SequenceSet\r
*/\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
+ public static jalview.schemabinding.version2.SequenceSet unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException,\r
+ org.exolab.castor.xml.ValidationException\r
{\r
- return (jalview.schemabinding.version2.SequenceSet) Unmarshaller.unmarshal(\r
- jalview.schemabinding.version2.SequenceSet.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
+ return (jalview.schemabinding.version2.SequenceSet) Unmarshaller\r
+ .unmarshal(jalview.schemabinding.version2.SequenceSet.class,\r
+ reader);\r
+ }\r
\r
/**\r
- * Method validate\r
- *\r
+ * \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException\r
+ * if this object is an invalid instance according to the schema\r
*/\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
+ public void validate() throws org.exolab.castor.xml.ValidationException\r
{\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
- Validator();\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
validator.validate(this);\r
- } //-- void validate()\r
+ }\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff