/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
- * Schema.\r
- * $Id$\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
-\r
package jalview.schemabinding.version2;\r
\r
- //---------------------------------/\r
- //- Imported classes and packages -/\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
* @version $Revision$ $Date$\r
*/\r
-public class JalviewModelSequence implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _JSeqList.\r
- */\r
- private java.util.Vector _JSeqList;\r
-\r
- /**\r
- * Field _JGroupList.\r
- */\r
- private java.util.Vector _JGroupList;\r
-\r
- /**\r
- * Field _viewportList.\r
- */\r
- private java.util.Vector _viewportList;\r
-\r
- /**\r
- * Field _userColoursList.\r
- */\r
- private java.util.Vector _userColoursList;\r
-\r
- /**\r
- * Field _treeList.\r
- */\r
- private java.util.Vector _treeList;\r
-\r
- /**\r
- * Field _featureSettings.\r
- */\r
- private jalview.schemabinding.version2.FeatureSettings _featureSettings;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public JalviewModelSequence() {\r
- super();\r
- this._JSeqList = new java.util.Vector();\r
- this._JGroupList = new java.util.Vector();\r
- this._viewportList = new java.util.Vector();\r
- this._userColoursList = new java.util.Vector();\r
- this._treeList = new java.util.Vector();\r
- }\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vJGroup\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addJGroup(\r
- final jalview.schemabinding.version2.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._JGroupList.addElement(vJGroup);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vJGroup\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addJGroup(\r
- final int index,\r
- final jalview.schemabinding.version2.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._JGroupList.add(index, vJGroup);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vJSeq\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addJSeq(\r
- final jalview.schemabinding.version2.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._JSeqList.addElement(vJSeq);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vJSeq\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addJSeq(\r
- final int index,\r
- final jalview.schemabinding.version2.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._JSeqList.add(index, vJSeq);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vTree\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addTree(\r
- final jalview.schemabinding.version2.Tree vTree)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._treeList.addElement(vTree);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vTree\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addTree(\r
- final int index,\r
- final jalview.schemabinding.version2.Tree vTree)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._treeList.add(index, vTree);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vUserColours\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addUserColours(\r
- final jalview.schemabinding.version2.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._userColoursList.addElement(vUserColours);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vUserColours\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addUserColours(\r
- final int index,\r
- final jalview.schemabinding.version2.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._userColoursList.add(index, vUserColours);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vViewport\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addViewport(\r
- final jalview.schemabinding.version2.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._viewportList.addElement(vViewport);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vViewport\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void addViewport(\r
- final int index,\r
- final jalview.schemabinding.version2.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException {\r
- this._viewportList.add(index, vViewport);\r
- }\r
-\r
- /**\r
- * Method enumerateJGroup.\r
- * \r
- * @return an Enumeration over all\r
- * jalview.schemabinding.version2.JGroup elements\r
- */\r
- public java.util.Enumeration enumerateJGroup(\r
- ) {\r
- return this._JGroupList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateJSeq.\r
- * \r
- * @return an Enumeration over all\r
- * jalview.schemabinding.version2.JSeq elements\r
- */\r
- public java.util.Enumeration enumerateJSeq(\r
- ) {\r
- return this._JSeqList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateTree.\r
- * \r
- * @return an Enumeration over all\r
- * jalview.schemabinding.version2.Tree elements\r
- */\r
- public java.util.Enumeration enumerateTree(\r
- ) {\r
- return this._treeList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateUserColours.\r
- * \r
- * @return an Enumeration over all\r
- * jalview.schemabinding.version2.UserColours elements\r
- */\r
- public java.util.Enumeration enumerateUserColours(\r
- ) {\r
- return this._userColoursList.elements();\r
- }\r
-\r
- /**\r
- * Method enumerateViewport.\r
- * \r
- * @return an Enumeration over all\r
- * jalview.schemabinding.version2.Viewport elements\r
- */\r
- public java.util.Enumeration enumerateViewport(\r
- ) {\r
- return this._viewportList.elements();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'featureSettings'.\r
- * \r
- * @return the value of field 'FeatureSettings'.\r
- */\r
- public jalview.schemabinding.version2.FeatureSettings getFeatureSettings(\r
- ) {\r
- return this._featureSettings;\r
- }\r
-\r
- /**\r
- * Method getJGroup.\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.JGroup at the given index\r
- */\r
- public jalview.schemabinding.version2.JGroup getJGroup(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._JGroupList.size()) {\r
- throw new IndexOutOfBoundsException("getJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");\r
- }\r
- \r
- return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index);\r
- }\r
-\r
- /**\r
- * Method getJGroup.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.JGroup[] getJGroup(\r
- ) {\r
- jalview.schemabinding.version2.JGroup[] array = new jalview.schemabinding.version2.JGroup[0];\r
- return (jalview.schemabinding.version2.JGroup[]) this._JGroupList.toArray(array);\r
- }\r
-\r
- /**\r
- * Method getJGroupCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getJGroupCount(\r
- ) {\r
- return this._JGroupList.size();\r
- }\r
-\r
- /**\r
- * Method getJSeq.\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 jalview.schemabinding.version2.JSeq\r
- * at the given index\r
- */\r
- public jalview.schemabinding.version2.JSeq getJSeq(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._JSeqList.size()) {\r
- throw new IndexOutOfBoundsException("getJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");\r
- }\r
- \r
- return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index);\r
- }\r
-\r
- /**\r
- * Method getJSeq.Returns the contents of the collection in an\r
- * Array. <p>Note: Just in case the collection contents are\r
- * changing in another thread, we pass a 0-length Array of the\r
- * 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.JSeq[] getJSeq(\r
- ) {\r
- jalview.schemabinding.version2.JSeq[] array = new jalview.schemabinding.version2.JSeq[0];\r
- return (jalview.schemabinding.version2.JSeq[]) this._JSeqList.toArray(array);\r
- }\r
-\r
- /**\r
- * Method getJSeqCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getJSeqCount(\r
- ) {\r
- return this._JSeqList.size();\r
- }\r
-\r
- /**\r
- * Method getTree.\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 jalview.schemabinding.version2.Tree\r
- * at the given index\r
- */\r
- public jalview.schemabinding.version2.Tree getTree(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._treeList.size()) {\r
- throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");\r
- }\r
- \r
- return (jalview.schemabinding.version2.Tree) _treeList.get(index);\r
- }\r
-\r
- /**\r
- * Method getTree.Returns the contents of the collection in an\r
- * Array. <p>Note: Just in case the collection contents are\r
- * changing in another thread, we pass a 0-length Array of the\r
- * 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.Tree[] getTree(\r
- ) {\r
- jalview.schemabinding.version2.Tree[] array = new jalview.schemabinding.version2.Tree[0];\r
- return (jalview.schemabinding.version2.Tree[]) this._treeList.toArray(array);\r
- }\r
-\r
- /**\r
- * Method getTreeCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getTreeCount(\r
- ) {\r
- return this._treeList.size();\r
- }\r
-\r
- /**\r
- * Method getUserColours.\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.UserColours at the given index\r
- */\r
- public jalview.schemabinding.version2.UserColours getUserColours(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._userColoursList.size()) {\r
- throw new IndexOutOfBoundsException("getUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");\r
- }\r
- \r
- return (jalview.schemabinding.version2.UserColours) _userColoursList.get(index);\r
- }\r
-\r
- /**\r
- * Method getUserColours.Returns the contents of the collection\r
- * in 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.UserColours[] getUserColours(\r
- ) {\r
- jalview.schemabinding.version2.UserColours[] array = new jalview.schemabinding.version2.UserColours[0];\r
- return (jalview.schemabinding.version2.UserColours[]) this._userColoursList.toArray(array);\r
- }\r
-\r
- /**\r
- * Method getUserColoursCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getUserColoursCount(\r
- ) {\r
- return this._userColoursList.size();\r
- }\r
-\r
- /**\r
- * Method getViewport.\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.Viewport at the given index\r
- */\r
- public jalview.schemabinding.version2.Viewport getViewport(\r
- final int index)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._viewportList.size()) {\r
- throw new IndexOutOfBoundsException("getViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");\r
- }\r
- \r
- return (jalview.schemabinding.version2.Viewport) _viewportList.get(index);\r
- }\r
-\r
- /**\r
- * Method getViewport.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.Viewport[] getViewport(\r
- ) {\r
- jalview.schemabinding.version2.Viewport[] array = new jalview.schemabinding.version2.Viewport[0];\r
- return (jalview.schemabinding.version2.Viewport[]) this._viewportList.toArray(array);\r
- }\r
-\r
- /**\r
- * Method getViewportCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getViewportCount(\r
- ) {\r
- return this._viewportList.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 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
- */\r
- public void removeAllJGroup(\r
- ) {\r
- this._JGroupList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllJSeq(\r
- ) {\r
- this._JSeqList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllTree(\r
- ) {\r
- this._treeList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllUserColours(\r
- ) {\r
- this._userColoursList.clear();\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllViewport(\r
- ) {\r
- this._viewportList.clear();\r
- }\r
-\r
- /**\r
- * Method removeJGroup.\r
- * \r
- * @param vJGroup\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeJGroup(\r
- final jalview.schemabinding.version2.JGroup vJGroup) {\r
- boolean removed = _JGroupList.remove(vJGroup);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeJGroupAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.JGroup removeJGroupAt(\r
- final int index) {\r
- java.lang.Object obj = this._JGroupList.remove(index);\r
- return (jalview.schemabinding.version2.JGroup) obj;\r
- }\r
-\r
- /**\r
- * Method removeJSeq.\r
- * \r
- * @param vJSeq\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeJSeq(\r
- final jalview.schemabinding.version2.JSeq vJSeq) {\r
- boolean removed = _JSeqList.remove(vJSeq);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeJSeqAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.JSeq removeJSeqAt(\r
- final int index) {\r
- java.lang.Object obj = this._JSeqList.remove(index);\r
- return (jalview.schemabinding.version2.JSeq) obj;\r
- }\r
-\r
- /**\r
- * Method removeTree.\r
- * \r
- * @param vTree\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeTree(\r
- final jalview.schemabinding.version2.Tree vTree) {\r
- boolean removed = _treeList.remove(vTree);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeTreeAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.Tree removeTreeAt(\r
- final int index) {\r
- java.lang.Object obj = this._treeList.remove(index);\r
- return (jalview.schemabinding.version2.Tree) obj;\r
- }\r
-\r
- /**\r
- * Method removeUserColours.\r
- * \r
- * @param vUserColours\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeUserColours(\r
- final jalview.schemabinding.version2.UserColours vUserColours) {\r
- boolean removed = _userColoursList.remove(vUserColours);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeUserColoursAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.UserColours removeUserColoursAt(\r
- final int index) {\r
- java.lang.Object obj = this._userColoursList.remove(index);\r
- return (jalview.schemabinding.version2.UserColours) obj;\r
- }\r
-\r
- /**\r
- * Method removeViewport.\r
- * \r
- * @param vViewport\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeViewport(\r
- final jalview.schemabinding.version2.Viewport vViewport) {\r
- boolean removed = _viewportList.remove(vViewport);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeViewportAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.Viewport removeViewportAt(\r
- final int index) {\r
- java.lang.Object obj = this._viewportList.remove(index);\r
- return (jalview.schemabinding.version2.Viewport) obj;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'featureSettings'.\r
- * \r
- * @param featureSettings the value of field 'featureSettings'.\r
- */\r
- public void setFeatureSettings(\r
- final jalview.schemabinding.version2.FeatureSettings featureSettings) {\r
- this._featureSettings = featureSettings;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vJGroup\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void setJGroup(\r
- final int index,\r
- final jalview.schemabinding.version2.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._JGroupList.size()) {\r
- throw new IndexOutOfBoundsException("setJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");\r
- }\r
- \r
- this._JGroupList.set(index, vJGroup);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vJGroupArray\r
- */\r
- public void setJGroup(\r
- final jalview.schemabinding.version2.JGroup[] vJGroupArray) {\r
- //-- copy array\r
- _JGroupList.clear();\r
- \r
- for (int i = 0; i < vJGroupArray.length; i++) {\r
- this._JGroupList.add(vJGroupArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vJSeq\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void setJSeq(\r
- final int index,\r
- final jalview.schemabinding.version2.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._JSeqList.size()) {\r
- throw new IndexOutOfBoundsException("setJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");\r
- }\r
- \r
- this._JSeqList.set(index, vJSeq);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vJSeqArray\r
- */\r
- public void setJSeq(\r
- final jalview.schemabinding.version2.JSeq[] vJSeqArray) {\r
- //-- copy array\r
- _JSeqList.clear();\r
- \r
- for (int i = 0; i < vJSeqArray.length; i++) {\r
- this._JSeqList.add(vJSeqArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vTree\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void setTree(\r
- final int index,\r
- final jalview.schemabinding.version2.Tree vTree)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._treeList.size()) {\r
- throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");\r
- }\r
- \r
- this._treeList.set(index, vTree);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vTreeArray\r
- */\r
- public void setTree(\r
- final jalview.schemabinding.version2.Tree[] vTreeArray) {\r
- //-- copy array\r
- _treeList.clear();\r
- \r
- for (int i = 0; i < vTreeArray.length; i++) {\r
- this._treeList.add(vTreeArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vUserColours\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void setUserColours(\r
- final int index,\r
- final jalview.schemabinding.version2.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._userColoursList.size()) {\r
- throw new IndexOutOfBoundsException("setUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");\r
- }\r
- \r
- this._userColoursList.set(index, vUserColours);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vUserColoursArray\r
- */\r
- public void setUserColours(\r
- final jalview.schemabinding.version2.UserColours[] vUserColoursArray) {\r
- //-- copy array\r
- _userColoursList.clear();\r
- \r
- for (int i = 0; i < vUserColoursArray.length; i++) {\r
- this._userColoursList.add(vUserColoursArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vViewport\r
- * @throws java.lang.IndexOutOfBoundsException if the index\r
- * given is outside the bounds of the collection\r
- */\r
- public void setViewport(\r
- final int index,\r
- final jalview.schemabinding.version2.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException {\r
- // check bounds for index\r
- if (index < 0 || index >= this._viewportList.size()) {\r
- throw new IndexOutOfBoundsException("setViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");\r
- }\r
- \r
- this._viewportList.set(index, vViewport);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vViewportArray\r
- */\r
- public void setViewport(\r
- final jalview.schemabinding.version2.Viewport[] vViewportArray) {\r
- //-- copy array\r
- _viewportList.clear();\r
- \r
- for (int i = 0; i < vViewportArray.length; i++) {\r
- this._viewportList.add(vViewportArray[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.JalviewModelSequence\r
- */\r
- public static jalview.schemabinding.version2.JalviewModelSequence unmarshal(\r
- final java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
- return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewModelSequence.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
- }\r
+public class JalviewModelSequence implements java.io.Serializable\r
+{\r
+\r
+ // --------------------------/\r
+ // - Class/Member Variables -/\r
+ // --------------------------/\r
+\r
+ /**\r
+ * Field _JSeqList.\r
+ */\r
+ private java.util.Vector _JSeqList;\r
+\r
+ /**\r
+ * Field _JGroupList.\r
+ */\r
+ private java.util.Vector _JGroupList;\r
+\r
+ /**\r
+ * Field _viewportList.\r
+ */\r
+ private java.util.Vector _viewportList;\r
+\r
+ /**\r
+ * Field _userColoursList.\r
+ */\r
+ private java.util.Vector _userColoursList;\r
+\r
+ /**\r
+ * Field _treeList.\r
+ */\r
+ private java.util.Vector _treeList;\r
+\r
+ /**\r
+ * Field _featureSettings.\r
+ */\r
+ private jalview.schemabinding.version2.FeatureSettings _featureSettings;\r
+\r
+ // ----------------/\r
+ // - Constructors -/\r
+ // ----------------/\r
+\r
+ public JalviewModelSequence()\r
+ {\r
+ super();\r
+ this._JSeqList = new java.util.Vector();\r
+ this._JGroupList = new java.util.Vector();\r
+ this._viewportList = new java.util.Vector();\r
+ this._userColoursList = new java.util.Vector();\r
+ this._treeList = new java.util.Vector();\r
+ }\r
+\r
+ // -----------/\r
+ // - Methods -/\r
+ // -----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vJGroup\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addJGroup(final jalview.schemabinding.version2.JGroup vJGroup)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._JGroupList.addElement(vJGroup);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vJGroup\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addJGroup(final int index,\r
+ final jalview.schemabinding.version2.JGroup vJGroup)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._JGroupList.add(index, vJGroup);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vJSeq\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addJSeq(final jalview.schemabinding.version2.JSeq vJSeq)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._JSeqList.addElement(vJSeq);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vJSeq\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addJSeq(final int index,\r
+ final jalview.schemabinding.version2.JSeq vJSeq)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._JSeqList.add(index, vJSeq);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vTree\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addTree(final jalview.schemabinding.version2.Tree vTree)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._treeList.addElement(vTree);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vTree\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addTree(final int index,\r
+ final jalview.schemabinding.version2.Tree vTree)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._treeList.add(index, vTree);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vUserColours\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addUserColours(\r
+ final jalview.schemabinding.version2.UserColours vUserColours)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._userColoursList.addElement(vUserColours);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vUserColours\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addUserColours(final int index,\r
+ final jalview.schemabinding.version2.UserColours vUserColours)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._userColoursList.add(index, vUserColours);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vViewport\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addViewport(\r
+ final jalview.schemabinding.version2.Viewport vViewport)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._viewportList.addElement(vViewport);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vViewport\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void addViewport(final int index,\r
+ final jalview.schemabinding.version2.Viewport vViewport)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ this._viewportList.add(index, vViewport);\r
+ }\r
+\r
+ /**\r
+ * Method enumerateJGroup.\r
+ * \r
+ * @return an Enumeration over all jalview.schemabinding.version2.JGroup\r
+ * elements\r
+ */\r
+ public java.util.Enumeration enumerateJGroup()\r
+ {\r
+ return this._JGroupList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumerateJSeq.\r
+ * \r
+ * @return an Enumeration over all jalview.schemabinding.version2.JSeq\r
+ * elements\r
+ */\r
+ public java.util.Enumeration enumerateJSeq()\r
+ {\r
+ return this._JSeqList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumerateTree.\r
+ * \r
+ * @return an Enumeration over all jalview.schemabinding.version2.Tree\r
+ * elements\r
+ */\r
+ public java.util.Enumeration enumerateTree()\r
+ {\r
+ return this._treeList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumerateUserColours.\r
+ * \r
+ * @return an Enumeration over all jalview.schemabinding.version2.UserColours\r
+ * elements\r
+ */\r
+ public java.util.Enumeration enumerateUserColours()\r
+ {\r
+ return this._userColoursList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumerateViewport.\r
+ * \r
+ * @return an Enumeration over all jalview.schemabinding.version2.Viewport\r
+ * elements\r
+ */\r
+ public java.util.Enumeration enumerateViewport()\r
+ {\r
+ return this._viewportList.elements();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'featureSettings'.\r
+ * \r
+ * @return the value of field 'FeatureSettings'.\r
+ */\r
+ public jalview.schemabinding.version2.FeatureSettings getFeatureSettings()\r
+ {\r
+ return this._featureSettings;\r
+ }\r
+\r
+ /**\r
+ * Method getJGroup.\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.JGroup at the given\r
+ * index\r
+ */\r
+ public jalview.schemabinding.version2.JGroup getJGroup(final int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._JGroupList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException("getJGroup: Index value '"\r
+ + index + "' not in range [0.."\r
+ + (this._JGroupList.size() - 1) + "]");\r
+ }\r
+\r
+ return (jalview.schemabinding.version2.JGroup) _JGroupList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getJGroup.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.JGroup[] getJGroup()\r
+ {\r
+ jalview.schemabinding.version2.JGroup[] array = new jalview.schemabinding.version2.JGroup[0];\r
+ return (jalview.schemabinding.version2.JGroup[]) this._JGroupList\r
+ .toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getJGroupCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getJGroupCount()\r
+ {\r
+ return this._JGroupList.size();\r
+ }\r
+\r
+ /**\r
+ * Method getJSeq.\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.JSeq at the given\r
+ * index\r
+ */\r
+ public jalview.schemabinding.version2.JSeq getJSeq(final int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._JSeqList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException("getJSeq: Index value '" + index\r
+ + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");\r
+ }\r
+\r
+ return (jalview.schemabinding.version2.JSeq) _JSeqList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getJSeq.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.JSeq[] getJSeq()\r
+ {\r
+ jalview.schemabinding.version2.JSeq[] array = new jalview.schemabinding.version2.JSeq[0];\r
+ return (jalview.schemabinding.version2.JSeq[]) this._JSeqList\r
+ .toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getJSeqCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getJSeqCount()\r
+ {\r
+ return this._JSeqList.size();\r
+ }\r
+\r
+ /**\r
+ * Method getTree.\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.Tree at the given\r
+ * index\r
+ */\r
+ public jalview.schemabinding.version2.Tree getTree(final int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._treeList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException("getTree: Index value '" + index\r
+ + "' not in range [0.." + (this._treeList.size() - 1) + "]");\r
+ }\r
+\r
+ return (jalview.schemabinding.version2.Tree) _treeList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getTree.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.Tree[] getTree()\r
+ {\r
+ jalview.schemabinding.version2.Tree[] array = new jalview.schemabinding.version2.Tree[0];\r
+ return (jalview.schemabinding.version2.Tree[]) this._treeList\r
+ .toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getTreeCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getTreeCount()\r
+ {\r
+ return this._treeList.size();\r
+ }\r
+\r
+ /**\r
+ * Method getUserColours.\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.UserColours at the\r
+ * given index\r
+ */\r
+ public jalview.schemabinding.version2.UserColours getUserColours(\r
+ final int index) throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._userColoursList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException("getUserColours: Index value '"\r
+ + index + "' not in range [0.."\r
+ + (this._userColoursList.size() - 1) + "]");\r
+ }\r
+\r
+ return (jalview.schemabinding.version2.UserColours) _userColoursList\r
+ .get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getUserColours.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.UserColours[] getUserColours()\r
+ {\r
+ jalview.schemabinding.version2.UserColours[] array = new jalview.schemabinding.version2.UserColours[0];\r
+ return (jalview.schemabinding.version2.UserColours[]) this._userColoursList\r
+ .toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getUserColoursCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getUserColoursCount()\r
+ {\r
+ return this._userColoursList.size();\r
+ }\r
+\r
+ /**\r
+ * Method getViewport.\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.Viewport at the\r
+ * given index\r
+ */\r
+ public jalview.schemabinding.version2.Viewport getViewport(final int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._viewportList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException("getViewport: Index value '"\r
+ + index + "' not in range [0.."\r
+ + (this._viewportList.size() - 1) + "]");\r
+ }\r
+\r
+ return (jalview.schemabinding.version2.Viewport) _viewportList\r
+ .get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getViewport.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.Viewport[] getViewport()\r
+ {\r
+ jalview.schemabinding.version2.Viewport[] array = new jalview.schemabinding.version2.Viewport[0];\r
+ return (jalview.schemabinding.version2.Viewport[]) this._viewportList\r
+ .toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getViewportCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getViewportCount()\r
+ {\r
+ return this._viewportList.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
+ */\r
+ public void removeAllJGroup()\r
+ {\r
+ this._JGroupList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllJSeq()\r
+ {\r
+ this._JSeqList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllTree()\r
+ {\r
+ this._treeList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllUserColours()\r
+ {\r
+ this._userColoursList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllViewport()\r
+ {\r
+ this._viewportList.clear();\r
+ }\r
+\r
+ /**\r
+ * Method removeJGroup.\r
+ * \r
+ * @param vJGroup\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeJGroup(\r
+ final jalview.schemabinding.version2.JGroup vJGroup)\r
+ {\r
+ boolean removed = _JGroupList.remove(vJGroup);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeJGroupAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.JGroup removeJGroupAt(\r
+ final int index)\r
+ {\r
+ java.lang.Object obj = this._JGroupList.remove(index);\r
+ return (jalview.schemabinding.version2.JGroup) obj;\r
+ }\r
+\r
+ /**\r
+ * Method removeJSeq.\r
+ * \r
+ * @param vJSeq\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeJSeq(final jalview.schemabinding.version2.JSeq vJSeq)\r
+ {\r
+ boolean removed = _JSeqList.remove(vJSeq);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeJSeqAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.JSeq removeJSeqAt(final int index)\r
+ {\r
+ java.lang.Object obj = this._JSeqList.remove(index);\r
+ return (jalview.schemabinding.version2.JSeq) obj;\r
+ }\r
+\r
+ /**\r
+ * Method removeTree.\r
+ * \r
+ * @param vTree\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeTree(final jalview.schemabinding.version2.Tree vTree)\r
+ {\r
+ boolean removed = _treeList.remove(vTree);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeTreeAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.Tree removeTreeAt(final int index)\r
+ {\r
+ java.lang.Object obj = this._treeList.remove(index);\r
+ return (jalview.schemabinding.version2.Tree) obj;\r
+ }\r
+\r
+ /**\r
+ * Method removeUserColours.\r
+ * \r
+ * @param vUserColours\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeUserColours(\r
+ final jalview.schemabinding.version2.UserColours vUserColours)\r
+ {\r
+ boolean removed = _userColoursList.remove(vUserColours);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeUserColoursAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.UserColours removeUserColoursAt(\r
+ final int index)\r
+ {\r
+ java.lang.Object obj = this._userColoursList.remove(index);\r
+ return (jalview.schemabinding.version2.UserColours) obj;\r
+ }\r
+\r
+ /**\r
+ * Method removeViewport.\r
+ * \r
+ * @param vViewport\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeViewport(\r
+ final jalview.schemabinding.version2.Viewport vViewport)\r
+ {\r
+ boolean removed = _viewportList.remove(vViewport);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeViewportAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.Viewport removeViewportAt(\r
+ final int index)\r
+ {\r
+ java.lang.Object obj = this._viewportList.remove(index);\r
+ return (jalview.schemabinding.version2.Viewport) obj;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'featureSettings'.\r
+ * \r
+ * @param featureSettings\r
+ * the value of field 'featureSettings'.\r
+ */\r
+ public void setFeatureSettings(\r
+ final jalview.schemabinding.version2.FeatureSettings featureSettings)\r
+ {\r
+ this._featureSettings = featureSettings;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vJGroup\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void setJGroup(final int index,\r
+ final jalview.schemabinding.version2.JGroup vJGroup)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._JGroupList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException("setJGroup: Index value '"\r
+ + index + "' not in range [0.."\r
+ + (this._JGroupList.size() - 1) + "]");\r
+ }\r
+\r
+ this._JGroupList.set(index, vJGroup);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vJGroupArray\r
+ */\r
+ public void setJGroup(\r
+ final jalview.schemabinding.version2.JGroup[] vJGroupArray)\r
+ {\r
+ // -- copy array\r
+ _JGroupList.clear();\r
+\r
+ for (int i = 0; i < vJGroupArray.length; i++)\r
+ {\r
+ this._JGroupList.add(vJGroupArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vJSeq\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void setJSeq(final int index,\r
+ final jalview.schemabinding.version2.JSeq vJSeq)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._JSeqList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException("setJSeq: Index value '" + index\r
+ + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");\r
+ }\r
+\r
+ this._JSeqList.set(index, vJSeq);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vJSeqArray\r
+ */\r
+ public void setJSeq(final jalview.schemabinding.version2.JSeq[] vJSeqArray)\r
+ {\r
+ // -- copy array\r
+ _JSeqList.clear();\r
+\r
+ for (int i = 0; i < vJSeqArray.length; i++)\r
+ {\r
+ this._JSeqList.add(vJSeqArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vTree\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void setTree(final int index,\r
+ final jalview.schemabinding.version2.Tree vTree)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._treeList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException("setTree: Index value '" + index\r
+ + "' not in range [0.." + (this._treeList.size() - 1) + "]");\r
+ }\r
+\r
+ this._treeList.set(index, vTree);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vTreeArray\r
+ */\r
+ public void setTree(final jalview.schemabinding.version2.Tree[] vTreeArray)\r
+ {\r
+ // -- copy array\r
+ _treeList.clear();\r
+\r
+ for (int i = 0; i < vTreeArray.length; i++)\r
+ {\r
+ this._treeList.add(vTreeArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vUserColours\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void setUserColours(final int index,\r
+ final jalview.schemabinding.version2.UserColours vUserColours)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._userColoursList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException("setUserColours: Index value '"\r
+ + index + "' not in range [0.."\r
+ + (this._userColoursList.size() - 1) + "]");\r
+ }\r
+\r
+ this._userColoursList.set(index, vUserColours);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vUserColoursArray\r
+ */\r
+ public void setUserColours(\r
+ final jalview.schemabinding.version2.UserColours[] vUserColoursArray)\r
+ {\r
+ // -- copy array\r
+ _userColoursList.clear();\r
+\r
+ for (int i = 0; i < vUserColoursArray.length; i++)\r
+ {\r
+ this._userColoursList.add(vUserColoursArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vViewport\r
+ * @throws java.lang.IndexOutOfBoundsException\r
+ * if the index given is outside the bounds of the collection\r
+ */\r
+ public void setViewport(final int index,\r
+ final jalview.schemabinding.version2.Viewport vViewport)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._viewportList.size())\r
+ {\r
+ throw new IndexOutOfBoundsException("setViewport: Index value '"\r
+ + index + "' not in range [0.."\r
+ + (this._viewportList.size() - 1) + "]");\r
+ }\r
+\r
+ this._viewportList.set(index, vViewport);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vViewportArray\r
+ */\r
+ public void setViewport(\r
+ final jalview.schemabinding.version2.Viewport[] vViewportArray)\r
+ {\r
+ // -- copy array\r
+ _viewportList.clear();\r
+\r
+ for (int i = 0; i < vViewportArray.length; i++)\r
+ {\r
+ this._viewportList.add(vViewportArray[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.JalviewModelSequence\r
+ */\r
+ public static jalview.schemabinding.version2.JalviewModelSequence 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.JalviewModelSequence) Unmarshaller\r
+ .unmarshal(\r
+ jalview.schemabinding.version2.JalviewModelSequence.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
git://source.jalview.org / jalview.git / blobdiff