-/*\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
-package jalview.schemabinding.version2;\r
-\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-\r
-/**\r
- * Class SequenceSet.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class SequenceSet implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _gapChar.\r
- */\r
- private java.lang.String _gapChar;\r
-\r
- /**\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
- */\r
- private java.util.Vector _annotationList;\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
- 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
- * \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
- * \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(\r
- final jalview.schemabinding.version2.Annotation vAnnotation)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._annotationList.addElement(vAnnotation);\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(final int index,\r
- final jalview.schemabinding.version2.Annotation vAnnotation)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._annotationList.add(index, vAnnotation);\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(\r
- final jalview.schemabinding.version2.Sequence vSequence)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._sequenceList.addElement(vSequence);\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 java.util.Enumeration enumerateAlcodonFrame()\r
- {\r
- return this._alcodonFrameList.elements();\r
- }\r
-\r
- /**\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 this._annotationList.elements();\r
- }\r
-\r
- /**\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 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 getAlcodonFrame.\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.AlcodonFrame at the\r
- * given inde\r
- */\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 >= this._alcodonFrameList.size())\r
- {\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.AlcodonFrame) _alcodonFrameList\r
- .get(index);\r
- }\r
-\r
- /**\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.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
- // check bounds for index\r
- if (index < 0 || index >= this._annotationList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getAnnotation: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._annotationList.size() - 1) + "]");\r
- }\r
-\r
- return (jalview.schemabinding.version2.Annotation) _annotationList\r
- .get(index);\r
- }\r
-\r
- /**\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 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 the value of field 'GapChar'.\r
- */\r
- public java.lang.String getGapChar()\r
- {\r
- return this._gapChar;\r
- }\r
-\r
- /**\r
- * Method getSequence.\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.Sequence at the\r
- * given index\r
- */\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 >= this._sequenceList.size())\r
- {\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\r
- .get(index);\r
- }\r
-\r
- /**\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
- 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
- throw new IndexOutOfBoundsException(\r
- "getSequenceSetProperties: Index value '" + index\r
- + "' not in range [0.."\r
- + (this._sequenceSetPropertiesList.size() - 1) + "]");\r
- }\r
-\r
- return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList\r
- .get(index);\r
- }\r
-\r
- /**\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 jalview.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties()\r
- {\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 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
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
- }\r
- return true;\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(final java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
- {\r
- Marshaller.marshal(this, out);\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(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
- Marshaller.marshal(this, handler);\r
- }\r
-\r
- /**\r
- * Method removeAlcodonFrame.\r
- * \r
- * @param vAlcodonFrame\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeAlcodonFrame(\r
- final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)\r
- {\r
- boolean removed = _alcodonFrameList.remove(vAlcodonFrame);\r
- return removed;\r
- }\r
-\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
- this._sequenceList.clear();\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 the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.Annotation removeAnnotationAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._annotationList.remove(index);\r
- return (jalview.schemabinding.version2.Annotation) obj;\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 the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.Sequence removeSequenceAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._sequenceList.remove(index);\r
- return (jalview.schemabinding.version2.Sequence) obj;\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
- * \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(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 >= this._annotationList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setAnnotation: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._annotationList.size() - 1) + "]");\r
- }\r
-\r
- this._annotationList.set(index, vAnnotation);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vAnnotationArray\r
- */\r
- public void setAnnotation(\r
- final jalview.schemabinding.version2.Annotation[] vAnnotationArray)\r
- {\r
- // -- copy array\r
- _annotationList.clear();\r
-\r
- for (int i = 0; i < vAnnotationArray.length; i++)\r
- {\r
- this._annotationList.add(vAnnotationArray[i]);\r
- }\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\r
- * the value of field 'gapChar'.\r
- */\r
- public void setGapChar(final java.lang.String gapChar)\r
- {\r
- this._gapChar = gapChar;\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 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 >= this._sequenceSetPropertiesList.size())\r
- {\r
- throw new IndexOutOfBoundsException(\r
- "setSequenceSetProperties: Index value '" + index\r
- + "' not in range [0.."\r
- + (this._sequenceSetPropertiesList.size() - 1) + "]");\r
- }\r
-\r
- this._sequenceSetPropertiesList.set(index, vSequenceSetProperties);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vSequenceSetPropertiesArray\r
- */\r
- public void setSequenceSetProperties(\r
- final jalview.schemabinding.version2.SequenceSetProperties[] vSequenceSetPropertiesArray)\r
- {\r
- // -- copy array\r
- _sequenceSetPropertiesList.clear();\r
-\r
- for (int i = 0; i < vSequenceSetPropertiesArray.length; i++)\r
- {\r
- this._sequenceSetPropertiesList.add(vSequenceSetPropertiesArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * Method unmarshal.\r
- * \r
- * @param reader\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 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\r
- .unmarshal(jalview.schemabinding.version2.SequenceSet.class,\r
- reader);\r
- }\r
-\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() throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- }\r
-\r
-}\r
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ ******************************************************************************/
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+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.
+ * <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 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.
+ * <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 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.
+ * <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 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.
+ * <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 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);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff