-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)\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 Feature.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Feature implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _begin.\r
- */\r
- private int _begin;\r
-\r
- /**\r
- * keeps track of state for field: _begin\r
- */\r
- private boolean _has_begin;\r
-\r
- /**\r
- * Field _end.\r
- */\r
- private int _end;\r
-\r
- /**\r
- * keeps track of state for field: _end\r
- */\r
- private boolean _has_end;\r
-\r
- /**\r
- * Field _type.\r
- */\r
- private java.lang.String _type;\r
-\r
- /**\r
- * Field _description.\r
- */\r
- private java.lang.String _description;\r
-\r
- /**\r
- * Field _status.\r
- */\r
- private java.lang.String _status;\r
-\r
- /**\r
- * Field _featureGroup.\r
- */\r
- private java.lang.String _featureGroup;\r
-\r
- /**\r
- * Field _score.\r
- */\r
- private float _score;\r
-\r
- /**\r
- * keeps track of state for field: _score\r
- */\r
- private boolean _has_score;\r
-\r
- /**\r
- * Field _otherDataList.\r
- */\r
- private java.util.Vector _otherDataList;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public Feature()\r
- {\r
- super();\r
- this._otherDataList = new java.util.Vector();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vOtherData\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addOtherData(\r
- final jalview.schemabinding.version2.OtherData vOtherData)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._otherDataList.addElement(vOtherData);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vOtherData\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addOtherData(final int index,\r
- final jalview.schemabinding.version2.OtherData vOtherData)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._otherDataList.add(index, vOtherData);\r
- }\r
-\r
- /**\r
- */\r
- public void deleteBegin()\r
- {\r
- this._has_begin = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteEnd()\r
- {\r
- this._has_end = false;\r
- }\r
-\r
- /**\r
- */\r
- public void deleteScore()\r
- {\r
- this._has_score = false;\r
- }\r
-\r
- /**\r
- * Method enumerateOtherData.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.OtherData\r
- * elements\r
- */\r
- public java.util.Enumeration enumerateOtherData()\r
- {\r
- return this._otherDataList.elements();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'begin'.\r
- * \r
- * @return the value of field 'Begin'.\r
- */\r
- public int getBegin()\r
- {\r
- return this._begin;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'description'.\r
- * \r
- * @return the value of field 'Description'.\r
- */\r
- public java.lang.String getDescription()\r
- {\r
- return this._description;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'end'.\r
- * \r
- * @return the value of field 'End'.\r
- */\r
- public int getEnd()\r
- {\r
- return this._end;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'featureGroup'.\r
- * \r
- * @return the value of field 'FeatureGroup'.\r
- */\r
- public java.lang.String getFeatureGroup()\r
- {\r
- return this._featureGroup;\r
- }\r
-\r
- /**\r
- * Method getOtherData.\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.OtherData at the\r
- * given index\r
- */\r
- public jalview.schemabinding.version2.OtherData getOtherData(\r
- final int index) throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._otherDataList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getOtherData: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._otherDataList.size() - 1) + "]");\r
- }\r
-\r
- return (jalview.schemabinding.version2.OtherData) _otherDataList\r
- .get(index);\r
- }\r
-\r
- /**\r
- * Method getOtherData.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.OtherData[] getOtherData()\r
- {\r
- jalview.schemabinding.version2.OtherData[] array = new jalview.schemabinding.version2.OtherData[0];\r
- return (jalview.schemabinding.version2.OtherData[]) this._otherDataList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getOtherDataCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getOtherDataCount()\r
- {\r
- return this._otherDataList.size();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'score'.\r
- * \r
- * @return the value of field 'Score'.\r
- */\r
- public float getScore()\r
- {\r
- return this._score;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'status'.\r
- * \r
- * @return the value of field 'Status'.\r
- */\r
- public java.lang.String getStatus()\r
- {\r
- return this._status;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'type'.\r
- * \r
- * @return the value of field 'Type'.\r
- */\r
- public java.lang.String getType()\r
- {\r
- return this._type;\r
- }\r
-\r
- /**\r
- * Method hasBegin.\r
- * \r
- * @return true if at least one Begin has been added\r
- */\r
- public boolean hasBegin()\r
- {\r
- return this._has_begin;\r
- }\r
-\r
- /**\r
- * Method hasEnd.\r
- * \r
- * @return true if at least one End has been added\r
- */\r
- public boolean hasEnd()\r
- {\r
- return this._has_end;\r
- }\r
-\r
- /**\r
- * Method hasScore.\r
- * \r
- * @return true if at least one Score has been added\r
- */\r
- public boolean hasScore()\r
- {\r
- return this._has_score;\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
- */\r
- public void removeAllOtherData()\r
- {\r
- this._otherDataList.clear();\r
- }\r
-\r
- /**\r
- * Method removeOtherData.\r
- * \r
- * @param vOtherData\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeOtherData(\r
- final jalview.schemabinding.version2.OtherData vOtherData)\r
- {\r
- boolean removed = _otherDataList.remove(vOtherData);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeOtherDataAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.OtherData removeOtherDataAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._otherDataList.remove(index);\r
- return (jalview.schemabinding.version2.OtherData) obj;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'begin'.\r
- * \r
- * @param begin\r
- * the value of field 'begin'.\r
- */\r
- public void setBegin(final int begin)\r
- {\r
- this._begin = begin;\r
- this._has_begin = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'description'.\r
- * \r
- * @param description\r
- * the value of field 'description'.\r
- */\r
- public void setDescription(final java.lang.String description)\r
- {\r
- this._description = description;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'end'.\r
- * \r
- * @param end\r
- * the value of field 'end'.\r
- */\r
- public void setEnd(final int end)\r
- {\r
- this._end = end;\r
- this._has_end = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'featureGroup'.\r
- * \r
- * @param featureGroup\r
- * the value of field 'featureGroup'.\r
- */\r
- public void setFeatureGroup(final java.lang.String featureGroup)\r
- {\r
- this._featureGroup = featureGroup;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vOtherData\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setOtherData(final int index,\r
- final jalview.schemabinding.version2.OtherData vOtherData)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._otherDataList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setOtherData: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._otherDataList.size() - 1) + "]");\r
- }\r
-\r
- this._otherDataList.set(index, vOtherData);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vOtherDataArray\r
- */\r
- public void setOtherData(\r
- final jalview.schemabinding.version2.OtherData[] vOtherDataArray)\r
- {\r
- // -- copy array\r
- _otherDataList.clear();\r
-\r
- for (int i = 0; i < vOtherDataArray.length; i++)\r
- {\r
- this._otherDataList.add(vOtherDataArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * Sets the value of field 'score'.\r
- * \r
- * @param score\r
- * the value of field 'score'.\r
- */\r
- public void setScore(final float score)\r
- {\r
- this._score = score;\r
- this._has_score = true;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'status'.\r
- * \r
- * @param status\r
- * the value of field 'status'.\r
- */\r
- public void setStatus(final java.lang.String status)\r
- {\r
- this._status = status;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'type'.\r
- * \r
- * @param type\r
- * the value of field 'type'.\r
- */\r
- public void setType(final java.lang.String type)\r
- {\r
- this._type = type;\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.Featur\r
- */\r
- public static jalview.schemabinding.version2.Feature 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.Feature) Unmarshaller.unmarshal(\r
- jalview.schemabinding.version2.Feature.class, 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 2.7)
+ * 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 <http://www.gnu.org/licenses/>.
+ *******************************************************************************/
+/*
+ * 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 Feature.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Feature implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _begin.
+ */
+ private int _begin;
+
+ /**
+ * keeps track of state for field: _begin
+ */
+ private boolean _has_begin;
+
+ /**
+ * Field _end.
+ */
+ private int _end;
+
+ /**
+ * keeps track of state for field: _end
+ */
+ private boolean _has_end;
+
+ /**
+ * Field _type.
+ */
+ private java.lang.String _type;
+
+ /**
+ * Field _description.
+ */
+ private java.lang.String _description;
+
+ /**
+ * Field _status.
+ */
+ private java.lang.String _status;
+
+ /**
+ * Field _featureGroup.
+ */
+ private java.lang.String _featureGroup;
+
+ /**
+ * Field _score.
+ */
+ private float _score;
+
+ /**
+ * keeps track of state for field: _score
+ */
+ private boolean _has_score;
+
+ /**
+ * Field _otherDataList.
+ */
+ private java.util.Vector _otherDataList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Feature() {
+ super();
+ this._otherDataList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vOtherData
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addOtherData(
+ final jalview.schemabinding.version2.OtherData vOtherData)
+ throws java.lang.IndexOutOfBoundsException {
+ this._otherDataList.addElement(vOtherData);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vOtherData
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addOtherData(
+ final int index,
+ final jalview.schemabinding.version2.OtherData vOtherData)
+ throws java.lang.IndexOutOfBoundsException {
+ this._otherDataList.add(index, vOtherData);
+ }
+
+ /**
+ */
+ public void deleteBegin(
+ ) {
+ this._has_begin= false;
+ }
+
+ /**
+ */
+ public void deleteEnd(
+ ) {
+ this._has_end= false;
+ }
+
+ /**
+ */
+ public void deleteScore(
+ ) {
+ this._has_score= false;
+ }
+
+ /**
+ * Method enumerateOtherData.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.OtherData elements
+ */
+ public java.util.Enumeration enumerateOtherData(
+ ) {
+ return this._otherDataList.elements();
+ }
+
+ /**
+ * Returns the value of field 'begin'.
+ *
+ * @return the value of field 'Begin'.
+ */
+ public int getBegin(
+ ) {
+ return this._begin;
+ }
+
+ /**
+ * Returns the value of field 'description'.
+ *
+ * @return the value of field 'Description'.
+ */
+ public java.lang.String getDescription(
+ ) {
+ return this._description;
+ }
+
+ /**
+ * Returns the value of field 'end'.
+ *
+ * @return the value of field 'End'.
+ */
+ public int getEnd(
+ ) {
+ return this._end;
+ }
+
+ /**
+ * Returns the value of field 'featureGroup'.
+ *
+ * @return the value of field 'FeatureGroup'.
+ */
+ public java.lang.String getFeatureGroup(
+ ) {
+ return this._featureGroup;
+ }
+
+ /**
+ * Method getOtherData.
+ *
+ * @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.OtherData at the given index
+ */
+ public jalview.schemabinding.version2.OtherData getOtherData(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._otherDataList.size()) {
+ throw new IndexOutOfBoundsException("getOtherData: Index value '" + index + "' not in range [0.." + (this._otherDataList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.OtherData) _otherDataList.get(index);
+ }
+
+ /**
+ * Method getOtherData.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.OtherData[] getOtherData(
+ ) {
+ jalview.schemabinding.version2.OtherData[] array = new jalview.schemabinding.version2.OtherData[0];
+ return (jalview.schemabinding.version2.OtherData[]) this._otherDataList.toArray(array);
+ }
+
+ /**
+ * Method getOtherDataCount.
+ *
+ * @return the size of this collection
+ */
+ public int getOtherDataCount(
+ ) {
+ return this._otherDataList.size();
+ }
+
+ /**
+ * Returns the value of field 'score'.
+ *
+ * @return the value of field 'Score'.
+ */
+ public float getScore(
+ ) {
+ return this._score;
+ }
+
+ /**
+ * Returns the value of field 'status'.
+ *
+ * @return the value of field 'Status'.
+ */
+ public java.lang.String getStatus(
+ ) {
+ return this._status;
+ }
+
+ /**
+ * Returns the value of field 'type'.
+ *
+ * @return the value of field 'Type'.
+ */
+ public java.lang.String getType(
+ ) {
+ return this._type;
+ }
+
+ /**
+ * Method hasBegin.
+ *
+ * @return true if at least one Begin has been added
+ */
+ public boolean hasBegin(
+ ) {
+ return this._has_begin;
+ }
+
+ /**
+ * Method hasEnd.
+ *
+ * @return true if at least one End has been added
+ */
+ public boolean hasEnd(
+ ) {
+ return this._has_end;
+ }
+
+ /**
+ * Method hasScore.
+ *
+ * @return true if at least one Score has been added
+ */
+ public boolean hasScore(
+ ) {
+ return this._has_score;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllOtherData(
+ ) {
+ this._otherDataList.clear();
+ }
+
+ /**
+ * Method removeOtherData.
+ *
+ * @param vOtherData
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeOtherData(
+ final jalview.schemabinding.version2.OtherData vOtherData) {
+ boolean removed = _otherDataList.remove(vOtherData);
+ return removed;
+ }
+
+ /**
+ * Method removeOtherDataAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.OtherData removeOtherDataAt(
+ final int index) {
+ java.lang.Object obj = this._otherDataList.remove(index);
+ return (jalview.schemabinding.version2.OtherData) obj;
+ }
+
+ /**
+ * Sets the value of field 'begin'.
+ *
+ * @param begin the value of field 'begin'.
+ */
+ public void setBegin(
+ final int begin) {
+ this._begin = begin;
+ this._has_begin = true;
+ }
+
+ /**
+ * Sets the value of field 'description'.
+ *
+ * @param description the value of field 'description'.
+ */
+ public void setDescription(
+ final java.lang.String description) {
+ this._description = description;
+ }
+
+ /**
+ * Sets the value of field 'end'.
+ *
+ * @param end the value of field 'end'.
+ */
+ public void setEnd(
+ final int end) {
+ this._end = end;
+ this._has_end = true;
+ }
+
+ /**
+ * Sets the value of field 'featureGroup'.
+ *
+ * @param featureGroup the value of field 'featureGroup'.
+ */
+ public void setFeatureGroup(
+ final java.lang.String featureGroup) {
+ this._featureGroup = featureGroup;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vOtherData
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setOtherData(
+ final int index,
+ final jalview.schemabinding.version2.OtherData vOtherData)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._otherDataList.size()) {
+ throw new IndexOutOfBoundsException("setOtherData: Index value '" + index + "' not in range [0.." + (this._otherDataList.size() - 1) + "]");
+ }
+
+ this._otherDataList.set(index, vOtherData);
+ }
+
+ /**
+ *
+ *
+ * @param vOtherDataArray
+ */
+ public void setOtherData(
+ final jalview.schemabinding.version2.OtherData[] vOtherDataArray) {
+ //-- copy array
+ _otherDataList.clear();
+
+ for (int i = 0; i < vOtherDataArray.length; i++) {
+ this._otherDataList.add(vOtherDataArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'score'.
+ *
+ * @param score the value of field 'score'.
+ */
+ public void setScore(
+ final float score) {
+ this._score = score;
+ this._has_score = true;
+ }
+
+ /**
+ * Sets the value of field 'status'.
+ *
+ * @param status the value of field 'status'.
+ */
+ public void setStatus(
+ final java.lang.String status) {
+ this._status = status;
+ }
+
+ /**
+ * Sets the value of field 'type'.
+ *
+ * @param type the value of field 'type'.
+ */
+ public void setType(
+ final java.lang.String type) {
+ this._type = type;
+ }
+
+ /**
+ * 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.Featur
+ */
+ public static jalview.schemabinding.version2.Feature unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(jalview.schemabinding.version2.Feature.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