-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- * \r
- * This program 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 2\r
- * of the License, or (at your option) any later version.\r
- * \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\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 AlcodonFrame.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class AlcodonFrame implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _alcodonList.\r
- */\r
- private java.util.Vector _alcodonList;\r
-\r
- /**\r
- * Field _alcodMapList.\r
- */\r
- private java.util.Vector _alcodMapList;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public AlcodonFrame()\r
- {\r
- super();\r
- this._alcodonList = new java.util.Vector();\r
- this._alcodMapList = new java.util.Vector();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vAlcodMap\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addAlcodMap(\r
- final jalview.schemabinding.version2.AlcodMap vAlcodMap)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._alcodMapList.addElement(vAlcodMap);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vAlcodMap\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addAlcodMap(final int index,\r
- final jalview.schemabinding.version2.AlcodMap vAlcodMap)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._alcodMapList.add(index, vAlcodMap);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vAlcodon\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addAlcodon(\r
- final jalview.schemabinding.version2.Alcodon vAlcodon)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._alcodonList.addElement(vAlcodon);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vAlcodon\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addAlcodon(final int index,\r
- final jalview.schemabinding.version2.Alcodon vAlcodon)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._alcodonList.add(index, vAlcodon);\r
- }\r
-\r
- /**\r
- * Method enumerateAlcodMap.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.AlcodMap\r
- * elements\r
- */\r
- public java.util.Enumeration enumerateAlcodMap()\r
- {\r
- return this._alcodMapList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateAlcodon.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.Alcodon\r
- * elements\r
- */\r
- public java.util.Enumeration enumerateAlcodon()\r
- {\r
- return this._alcodonList.elements();\r
- }\r
-\r
- /**\r
- * Method getAlcodMap.\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.AlcodMap at the\r
- * given index\r
- */\r
- public jalview.schemabinding.version2.AlcodMap getAlcodMap(final int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._alcodMapList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getAlcodMap: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._alcodMapList.size() - 1) + "]");\r
- }\r
-\r
- return (jalview.schemabinding.version2.AlcodMap) _alcodMapList\r
- .get(index);\r
- }\r
-\r
- /**\r
- * Method getAlcodMap.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.AlcodMap[] getAlcodMap()\r
- {\r
- jalview.schemabinding.version2.AlcodMap[] array = new jalview.schemabinding.version2.AlcodMap[0];\r
- return (jalview.schemabinding.version2.AlcodMap[]) this._alcodMapList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getAlcodMapCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getAlcodMapCount()\r
- {\r
- return this._alcodMapList.size();\r
- }\r
-\r
- /**\r
- * Method getAlcodon.\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.Alcodon at the\r
- * given index\r
- */\r
- public jalview.schemabinding.version2.Alcodon getAlcodon(final int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._alcodonList.size())\r
- {\r
- throw new IndexOutOfBoundsException("getAlcodon: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._alcodonList.size() - 1) + "]");\r
- }\r
-\r
- return (jalview.schemabinding.version2.Alcodon) _alcodonList.get(index);\r
- }\r
-\r
- /**\r
- * Method getAlcodon.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.Alcodon[] getAlcodon()\r
- {\r
- jalview.schemabinding.version2.Alcodon[] array = new jalview.schemabinding.version2.Alcodon[0];\r
- return (jalview.schemabinding.version2.Alcodon[]) this._alcodonList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getAlcodonCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getAlcodonCount()\r
- {\r
- return this._alcodonList.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\r
- * 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\r
- * 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 removeAlcodMap.\r
- * \r
- * @param vAlcodMap\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeAlcodMap(\r
- final jalview.schemabinding.version2.AlcodMap vAlcodMap)\r
- {\r
- boolean removed = _alcodMapList.remove(vAlcodMap);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeAlcodMapAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.AlcodMap removeAlcodMapAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._alcodMapList.remove(index);\r
- return (jalview.schemabinding.version2.AlcodMap) obj;\r
- }\r
-\r
- /**\r
- * Method removeAlcodon.\r
- * \r
- * @param vAlcodon\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeAlcodon(\r
- final jalview.schemabinding.version2.Alcodon vAlcodon)\r
- {\r
- boolean removed = _alcodonList.remove(vAlcodon);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeAlcodonAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.Alcodon removeAlcodonAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._alcodonList.remove(index);\r
- return (jalview.schemabinding.version2.Alcodon) obj;\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllAlcodMap()\r
- {\r
- this._alcodMapList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllAlcodon()\r
- {\r
- this._alcodonList.clear();\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vAlcodMap\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setAlcodMap(final int index,\r
- final jalview.schemabinding.version2.AlcodMap vAlcodMap)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._alcodMapList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setAlcodMap: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._alcodMapList.size() - 1) + "]");\r
- }\r
-\r
- this._alcodMapList.set(index, vAlcodMap);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vAlcodMapArray\r
- */\r
- public void setAlcodMap(\r
- final jalview.schemabinding.version2.AlcodMap[] vAlcodMapArray)\r
- {\r
- // -- copy array\r
- _alcodMapList.clear();\r
-\r
- for (int i = 0; i < vAlcodMapArray.length; i++)\r
- {\r
- this._alcodMapList.add(vAlcodMapArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vAlcodon\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setAlcodon(final int index,\r
- final jalview.schemabinding.version2.Alcodon vAlcodon)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._alcodonList.size())\r
- {\r
- throw new IndexOutOfBoundsException("setAlcodon: Index value '"\r
- + index + "' not in range [0.."\r
- + (this._alcodonList.size() - 1) + "]");\r
- }\r
-\r
- this._alcodonList.set(index, vAlcodon);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vAlcodonArray\r
- */\r
- public void setAlcodon(\r
- final jalview.schemabinding.version2.Alcodon[] vAlcodonArray)\r
- {\r
- // -- copy array\r
- _alcodonList.clear();\r
-\r
- for (int i = 0; i < vAlcodonArray.length; i++)\r
- {\r
- this._alcodonList.add(vAlcodonArray[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\r
- * schema\r
- * @return the unmarshaled jalview.schemabinding.version2.AlcodonFrame\r
- */\r
- public static jalview.schemabinding.version2.AlcodonFrame 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.AlcodonFrame) Unmarshaller\r
- .unmarshal(jalview.schemabinding.version2.AlcodonFrame.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\r
- * 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, J Engelhardt, LM Lui, 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 AlcodonFrame.
+ *
+ * @version $Revision$ $Date$
+ */
+public class AlcodonFrame implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _alcodonList.
+ */
+ private java.util.Vector _alcodonList;
+
+ /**
+ * Field _alcodMapList.
+ */
+ private java.util.Vector _alcodMapList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public AlcodonFrame() {
+ super();
+ this._alcodonList = new java.util.Vector();
+ this._alcodMapList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vAlcodMap
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addAlcodMap(
+ final jalview.schemabinding.version2.AlcodMap vAlcodMap)
+ throws java.lang.IndexOutOfBoundsException {
+ this._alcodMapList.addElement(vAlcodMap);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlcodMap
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addAlcodMap(
+ final int index,
+ final jalview.schemabinding.version2.AlcodMap vAlcodMap)
+ throws java.lang.IndexOutOfBoundsException {
+ this._alcodMapList.add(index, vAlcodMap);
+ }
+
+ /**
+ *
+ *
+ * @param vAlcodon
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addAlcodon(
+ final jalview.schemabinding.version2.Alcodon vAlcodon)
+ throws java.lang.IndexOutOfBoundsException {
+ this._alcodonList.addElement(vAlcodon);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlcodon
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addAlcodon(
+ final int index,
+ final jalview.schemabinding.version2.Alcodon vAlcodon)
+ throws java.lang.IndexOutOfBoundsException {
+ this._alcodonList.add(index, vAlcodon);
+ }
+
+ /**
+ * Method enumerateAlcodMap.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.AlcodMap elements
+ */
+ public java.util.Enumeration enumerateAlcodMap(
+ ) {
+ return this._alcodMapList.elements();
+ }
+
+ /**
+ * Method enumerateAlcodon.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.Alcodon elements
+ */
+ public java.util.Enumeration enumerateAlcodon(
+ ) {
+ return this._alcodonList.elements();
+ }
+
+ /**
+ * Method getAlcodMap.
+ *
+ * @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.AlcodMap at the given index
+ */
+ public jalview.schemabinding.version2.AlcodMap getAlcodMap(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._alcodMapList.size()) {
+ throw new IndexOutOfBoundsException("getAlcodMap: Index value '" + index + "' not in range [0.." + (this._alcodMapList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.AlcodMap) _alcodMapList.get(index);
+ }
+
+ /**
+ * Method getAlcodMap.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.AlcodMap[] getAlcodMap(
+ ) {
+ jalview.schemabinding.version2.AlcodMap[] array = new jalview.schemabinding.version2.AlcodMap[0];
+ return (jalview.schemabinding.version2.AlcodMap[]) this._alcodMapList.toArray(array);
+ }
+
+ /**
+ * Method getAlcodMapCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAlcodMapCount(
+ ) {
+ return this._alcodMapList.size();
+ }
+
+ /**
+ * Method getAlcodon.
+ *
+ * @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.Alcodon at the given index
+ */
+ public jalview.schemabinding.version2.Alcodon getAlcodon(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._alcodonList.size()) {
+ throw new IndexOutOfBoundsException("getAlcodon: Index value '" + index + "' not in range [0.." + (this._alcodonList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.Alcodon) _alcodonList.get(index);
+ }
+
+ /**
+ * Method getAlcodon.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.Alcodon[] getAlcodon(
+ ) {
+ jalview.schemabinding.version2.Alcodon[] array = new jalview.schemabinding.version2.Alcodon[0];
+ return (jalview.schemabinding.version2.Alcodon[]) this._alcodonList.toArray(array);
+ }
+
+ /**
+ * Method getAlcodonCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAlcodonCount(
+ ) {
+ return this._alcodonList.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 removeAlcodMap.
+ *
+ * @param vAlcodMap
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAlcodMap(
+ final jalview.schemabinding.version2.AlcodMap vAlcodMap) {
+ boolean removed = _alcodMapList.remove(vAlcodMap);
+ return removed;
+ }
+
+ /**
+ * Method removeAlcodMapAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.AlcodMap removeAlcodMapAt(
+ final int index) {
+ java.lang.Object obj = this._alcodMapList.remove(index);
+ return (jalview.schemabinding.version2.AlcodMap) obj;
+ }
+
+ /**
+ * Method removeAlcodon.
+ *
+ * @param vAlcodon
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAlcodon(
+ final jalview.schemabinding.version2.Alcodon vAlcodon) {
+ boolean removed = _alcodonList.remove(vAlcodon);
+ return removed;
+ }
+
+ /**
+ * Method removeAlcodonAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.Alcodon removeAlcodonAt(
+ final int index) {
+ java.lang.Object obj = this._alcodonList.remove(index);
+ return (jalview.schemabinding.version2.Alcodon) obj;
+ }
+
+ /**
+ */
+ public void removeAllAlcodMap(
+ ) {
+ this._alcodMapList.clear();
+ }
+
+ /**
+ */
+ public void removeAllAlcodon(
+ ) {
+ this._alcodonList.clear();
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlcodMap
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setAlcodMap(
+ final int index,
+ final jalview.schemabinding.version2.AlcodMap vAlcodMap)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._alcodMapList.size()) {
+ throw new IndexOutOfBoundsException("setAlcodMap: Index value '" + index + "' not in range [0.." + (this._alcodMapList.size() - 1) + "]");
+ }
+
+ this._alcodMapList.set(index, vAlcodMap);
+ }
+
+ /**
+ *
+ *
+ * @param vAlcodMapArray
+ */
+ public void setAlcodMap(
+ final jalview.schemabinding.version2.AlcodMap[] vAlcodMapArray) {
+ //-- copy array
+ _alcodMapList.clear();
+
+ for (int i = 0; i < vAlcodMapArray.length; i++) {
+ this._alcodMapList.add(vAlcodMapArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlcodon
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setAlcodon(
+ final int index,
+ final jalview.schemabinding.version2.Alcodon vAlcodon)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._alcodonList.size()) {
+ throw new IndexOutOfBoundsException("setAlcodon: Index value '" + index + "' not in range [0.." + (this._alcodonList.size() - 1) + "]");
+ }
+
+ this._alcodonList.set(index, vAlcodon);
+ }
+
+ /**
+ *
+ *
+ * @param vAlcodonArray
+ */
+ public void setAlcodon(
+ final jalview.schemabinding.version2.Alcodon[] vAlcodonArray) {
+ //-- copy array
+ _alcodonList.clear();
+
+ for (int i = 0; i < vAlcodonArray.length; i++) {
+ this._alcodonList.add(vAlcodonArray[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.AlcodonFrame
+ */
+ public static jalview.schemabinding.version2.AlcodonFrame unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.schemabinding.version2.AlcodonFrame) Unmarshaller.unmarshal(jalview.schemabinding.version2.AlcodonFrame.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