/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1)\r
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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 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
+ * This file is part of Jalview.\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
+ * 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
- * 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
+ * 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
+//- Imported classes and packages -/\r
//---------------------------------/\r
\r
import org.exolab.castor.xml.Marshaller;\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
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public AlcodonFrame() {\r
- super();\r
- this._alcodonList = new java.util.Vector();\r
- this._alcodMapList = new java.util.Vector();\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
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vAlcodMap\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * 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
- this._alcodMapList.addElement(vAlcodMap);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vAlcodMap\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addAlcodMap(\r
- final int index,\r
- final jalview.schemabinding.version2.AlcodMap vAlcodMap)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._alcodMapList.add(index, vAlcodMap);\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
- /**\r
- * \r
- * \r
- * @param vAlcodon\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * 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
- this._alcodonList.addElement(vAlcodon);\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
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vAlcodon\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\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 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 addAlcodon(\r
- final int index,\r
- final jalview.schemabinding.version2.Alcodon vAlcodon)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._alcodonList.add(index, vAlcodon);\r
- }\r
+ public void removeAllAlcodMap()\r
+ {\r
+ this._alcodMapList.clear();\r
+ }\r
\r
- /**\r
- * Method enumerateAlcodMap.\r
- * \r
- * @return an Enumeration over all\r
- * jalview.schemabinding.version2.AlcodMap elements\r
+ /**\r
*/\r
- public java.util.Enumeration enumerateAlcodMap(\r
- ) {\r
- return this._alcodMapList.elements();\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
- /**\r
- * Method enumerateAlcodon.\r
- * \r
- * @return an Enumeration over all\r
- * jalview.schemabinding.version2.Alcodon elements\r
- */\r
- public java.util.Enumeration enumerateAlcodon(\r
- ) {\r
- return this._alcodonList.elements();\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
- * Method getAlcodMap.\r
- * \r
- * @param index\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- * @return the value of the\r
- * jalview.schemabinding.version2.AlcodMap at the given index\r
- */\r
- public jalview.schemabinding.version2.AlcodMap getAlcodMap(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._alcodMapList.size()) {\r
- throw new IndexOutOfBoundsException("getAlcodMap: Index value '" + index + "' not in range [0.." + (this._alcodMapList.size() - 1) + "]");\r
- }\r
- \r
- return (jalview.schemabinding.version2.AlcodMap) _alcodMapList.get(index);\r
- }\r
-\r
- /**\r
- * Method getAlcodMap.Returns the contents of the collection in\r
- * an Array. <p>Note: Just in case the collection contents\r
- * are changing in another thread, we pass a 0-length Array of\r
- * the correct type into the API call. This way we <i>know</i>\r
- * 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.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 if the index\r
- * given is outside the bounds of the collection\r
- * @return the value of the\r
- * jalview.schemabinding.version2.Alcodon at the given index\r
- */\r
- public jalview.schemabinding.version2.Alcodon getAlcodon(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._alcodonList.size()) {\r
- throw new IndexOutOfBoundsException("getAlcodon: Index value '" + index + "' not in range [0.." + (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\r
- * an Array. <p>Note: Just in case the collection contents\r
- * are changing in another thread, we pass a 0-length Array of\r
- * the correct type into the API call. This way we <i>know</i>\r
- * 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.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
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\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
- /**\r
- * \r
- * \r
- * @param out\r
- * @throws org.exolab.castor.xml.MarshalException if object is\r
- * null or if any SAXException is thrown during marshaling\r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- */\r
- public void marshal(\r
- final java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
- Marshaller.marshal(this, out);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param handler\r
- * @throws java.io.IOException if an IOException occurs during\r
- * marshaling\r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- * @throws org.exolab.castor.xml.MarshalException if object is\r
- * null or if any SAXException is thrown during marshaling\r
- */\r
- public void marshal(\r
- final org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\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
- 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
- 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
- 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
- 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 if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void setAlcodMap(\r
- final int index,\r
- final jalview.schemabinding.version2.AlcodMap vAlcodMap)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._alcodMapList.size()) {\r
- throw new IndexOutOfBoundsException("setAlcodMap: Index value '" + index + "' not in range [0.." + (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
- //-- copy array\r
- _alcodMapList.clear();\r
- \r
- for (int i = 0; i < vAlcodMapArray.length; i++) {\r
- this._alcodMapList.add(vAlcodMapArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vAlcodon\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void setAlcodon(\r
- final int index,\r
- final jalview.schemabinding.version2.Alcodon vAlcodon)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._alcodonList.size()) {\r
- throw new IndexOutOfBoundsException("setAlcodon: Index value '" + index + "' not in range [0.." + (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
- //-- copy array\r
- _alcodonList.clear();\r
- \r
- for (int i = 0; i < vAlcodonArray.length; i++) {\r
- this._alcodonList.add(vAlcodonArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * Method unmarshal.\r
- * \r
- * @param reader\r
- * @throws org.exolab.castor.xml.MarshalException if object is\r
- * null or if any SAXException is thrown during marshaling\r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- * @return the unmarshaled\r
- * 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, org.exolab.castor.xml.ValidationException {\r
- return (jalview.schemabinding.version2.AlcodonFrame) Unmarshaller.unmarshal(jalview.schemabinding.version2.AlcodonFrame.class, reader);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException if this\r
- * object is an invalid instance according to the schema\r
- */\r
- public void validate(\r
- )\r
- throws org.exolab.castor.xml.ValidationException {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\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 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 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
git://source.jalview.org / jalview.git / blobdiff