/*\r
- * This class was automatically generated with\r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\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
*/\r
\r
package jalview.schemabinding.version2;\r
\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
//---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.util.*;\r
\r
-import org.exolab.castor.xml.*;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
\r
/**\r
* Class JalviewModelSequence.\r
- *\r
+ * \r
* @version $Revision$ $Date$\r
*/\r
-public class JalviewModelSequence\r
- 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
- _JSeqList = new Vector();\r
- _JGroupList = new Vector();\r
- _viewportList = new Vector();\r
- _userColoursList = new Vector();\r
- _treeList = new Vector();\r
- } //-- jalview.schemabinding.version2.JalviewModelSequence()\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addJGroup\r
- *\r
- *\r
- *\r
- * @param vJGroup\r
- */\r
- public void addJGroup(jalview.schemabinding.version2.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _JGroupList.addElement(vJGroup);\r
- } //-- void addJGroup(jalview.schemabinding.version2.JGroup)\r
-\r
- /**\r
- * Method addJGroup\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vJGroup\r
- */\r
- public void addJGroup(int index,\r
- jalview.schemabinding.version2.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _JGroupList.insertElementAt(vJGroup, index);\r
- } //-- void addJGroup(int, jalview.schemabinding.version2.JGroup)\r
-\r
- /**\r
- * Method addJSeq\r
- *\r
- *\r
- *\r
- * @param vJSeq\r
- */\r
- public void addJSeq(jalview.schemabinding.version2.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _JSeqList.addElement(vJSeq);\r
- } //-- void addJSeq(jalview.schemabinding.version2.JSeq)\r
-\r
- /**\r
- * Method addJSeq\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vJSeq\r
- */\r
- public void addJSeq(int index, jalview.schemabinding.version2.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _JSeqList.insertElementAt(vJSeq, index);\r
- } //-- void addJSeq(int, jalview.schemabinding.version2.JSeq)\r
-\r
- /**\r
- * Method addTree\r
- *\r
- *\r
- *\r
- * @param vTree\r
- */\r
- public void addTree(jalview.schemabinding.version2.Tree vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _treeList.addElement(vTree);\r
- } //-- void addTree(jalview.schemabinding.version2.Tree)\r
-\r
- /**\r
- * Method addTree\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vTree\r
- */\r
- public void addTree(int index, jalview.schemabinding.version2.Tree vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _treeList.insertElementAt(vTree, index);\r
- } //-- void addTree(int, jalview.schemabinding.version2.Tree)\r
-\r
- /**\r
- * Method addUserColours\r
- *\r
- *\r
- *\r
- * @param vUserColours\r
- */\r
- public void addUserColours(jalview.schemabinding.version2.UserColours\r
- vUserColours)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _userColoursList.addElement(vUserColours);\r
- } //-- void addUserColours(jalview.schemabinding.version2.UserColours)\r
-\r
- /**\r
- * Method addUserColours\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vUserColours\r
- */\r
- public void addUserColours(int index,\r
- jalview.schemabinding.version2.UserColours\r
- vUserColours)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _userColoursList.insertElementAt(vUserColours, index);\r
- } //-- void addUserColours(int, jalview.schemabinding.version2.UserColours)\r
-\r
- /**\r
- * Method addViewport\r
- *\r
- *\r
- *\r
- * @param vViewport\r
- */\r
- public void addViewport(jalview.schemabinding.version2.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _viewportList.addElement(vViewport);\r
- } //-- void addViewport(jalview.schemabinding.version2.Viewport)\r
-\r
- /**\r
- * Method addViewport\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vViewport\r
- */\r
- public void addViewport(int index,\r
- jalview.schemabinding.version2.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _viewportList.insertElementAt(vViewport, index);\r
- } //-- void addViewport(int, jalview.schemabinding.version2.Viewport)\r
-\r
- /**\r
- * Method enumerateJGroup\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateJGroup()\r
- {\r
- return _JGroupList.elements();\r
- } //-- java.util.Enumeration enumerateJGroup()\r
-\r
- /**\r
- * Method enumerateJSeq\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateJSeq()\r
- {\r
- return _JSeqList.elements();\r
- } //-- java.util.Enumeration enumerateJSeq()\r
-\r
- /**\r
- * Method enumerateTree\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateTree()\r
- {\r
- return _treeList.elements();\r
- } //-- java.util.Enumeration enumerateTree()\r
-\r
- /**\r
- * Method enumerateUserColours\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateUserColours()\r
- {\r
- return _userColoursList.elements();\r
- } //-- java.util.Enumeration enumerateUserColours()\r
-\r
- /**\r
- * Method enumerateViewport\r
- *\r
- *\r
- *\r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateViewport()\r
- {\r
- return _viewportList.elements();\r
- } //-- java.util.Enumeration enumerateViewport()\r
-\r
- /**\r
- * Returns the value of field 'featureSettings'.\r
- *\r
- * @return FeatureSettings\r
- * @return the value of field 'featureSettings'.\r
- */\r
- public jalview.schemabinding.version2.FeatureSettings getFeatureSettings()\r
- {\r
- return this._featureSettings;\r
- } //-- jalview.schemabinding.version2.FeatureSettings getFeatureSettings()\r
-\r
- /**\r
- * Method getJGroup\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return JGroup\r
- */\r
- public jalview.schemabinding.version2.JGroup getJGroup(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _JGroupList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
-\r
- return (jalview.schemabinding.version2.JGroup) _JGroupList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.JGroup getJGroup(int)\r
-\r
- /**\r
- * Method getJGroup\r
- *\r
- *\r
- *\r
- * @return JGroup\r
- */\r
- public jalview.schemabinding.version2.JGroup[] getJGroup()\r
- {\r
- int size = _JGroupList.size();\r
- jalview.schemabinding.version2.JGroup[] mArray = new jalview.schemabinding.\r
- version2.JGroup[size];\r
- for (int index = 0; index < size; index++)\r
- {\r
- mArray[index] = (jalview.schemabinding.version2.JGroup) _JGroupList.\r
- elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.JGroup[] getJGroup()\r
-\r
- /**\r
- * Method getJGroupCount\r
- *\r
- *\r
- *\r
- * @return int\r
- */\r
- public int getJGroupCount()\r
- {\r
- return _JGroupList.size();\r
- } //-- int getJGroupCount()\r
-\r
- /**\r
- * Method getJSeq\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return JSeq\r
- */\r
- public jalview.schemabinding.version2.JSeq getJSeq(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _JSeqList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
-\r
- return (jalview.schemabinding.version2.JSeq) _JSeqList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.JSeq getJSeq(int)\r
-\r
- /**\r
- * Method getJSeq\r
- *\r
- *\r
- *\r
- * @return JSeq\r
- */\r
- public jalview.schemabinding.version2.JSeq[] getJSeq()\r
- {\r
- int size = _JSeqList.size();\r
- jalview.schemabinding.version2.JSeq[] mArray = new jalview.schemabinding.\r
- version2.JSeq[size];\r
- for (int index = 0; index < size; index++)\r
- {\r
- mArray[index] = (jalview.schemabinding.version2.JSeq) _JSeqList.elementAt(\r
- index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.JSeq[] getJSeq()\r
-\r
- /**\r
- * Method getJSeqCount\r
- *\r
- *\r
- *\r
- * @return int\r
- */\r
- public int getJSeqCount()\r
- {\r
- return _JSeqList.size();\r
- } //-- int getJSeqCount()\r
-\r
- /**\r
- * Method getTree\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return Tree\r
- */\r
- public jalview.schemabinding.version2.Tree getTree(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _treeList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
-\r
- return (jalview.schemabinding.version2.Tree) _treeList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.Tree getTree(int)\r
-\r
- /**\r
- * Method getTree\r
- *\r
- *\r
- *\r
- * @return Tree\r
- */\r
- public jalview.schemabinding.version2.Tree[] getTree()\r
- {\r
- int size = _treeList.size();\r
- jalview.schemabinding.version2.Tree[] mArray = new jalview.schemabinding.\r
- version2.Tree[size];\r
- for (int index = 0; index < size; index++)\r
- {\r
- mArray[index] = (jalview.schemabinding.version2.Tree) _treeList.elementAt(\r
- index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.Tree[] getTree()\r
-\r
- /**\r
- * Method getTreeCount\r
- *\r
- *\r
- *\r
- * @return int\r
- */\r
- public int getTreeCount()\r
- {\r
- return _treeList.size();\r
- } //-- int getTreeCount()\r
-\r
- /**\r
- * Method getUserColours\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return UserColours\r
- */\r
- public jalview.schemabinding.version2.UserColours getUserColours(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _userColoursList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
-\r
- return (jalview.schemabinding.version2.UserColours) _userColoursList.\r
- elementAt(index);\r
- } //-- jalview.schemabinding.version2.UserColours getUserColours(int)\r
-\r
- /**\r
- * Method getUserColours\r
- *\r
- *\r
- *\r
- * @return UserColours\r
- */\r
- public jalview.schemabinding.version2.UserColours[] getUserColours()\r
- {\r
- int size = _userColoursList.size();\r
- jalview.schemabinding.version2.UserColours[] mArray = new jalview.\r
- schemabinding.version2.UserColours[size];\r
- for (int index = 0; index < size; index++)\r
- {\r
- mArray[index] = (jalview.schemabinding.version2.UserColours)\r
- _userColoursList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.UserColours[] getUserColours()\r
-\r
- /**\r
- * Method getUserColoursCount\r
- *\r
- *\r
- *\r
- * @return int\r
- */\r
- public int getUserColoursCount()\r
- {\r
- return _userColoursList.size();\r
- } //-- int getUserColoursCount()\r
-\r
- /**\r
- * Method getViewport\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return Viewport\r
- */\r
- public jalview.schemabinding.version2.Viewport getViewport(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _viewportList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
-\r
- return (jalview.schemabinding.version2.Viewport) _viewportList.elementAt(\r
- index);\r
- } //-- jalview.schemabinding.version2.Viewport getViewport(int)\r
-\r
- /**\r
- * Method getViewport\r
- *\r
- *\r
- *\r
- * @return Viewport\r
- */\r
- public jalview.schemabinding.version2.Viewport[] getViewport()\r
- {\r
- int size = _viewportList.size();\r
- jalview.schemabinding.version2.Viewport[] mArray = new jalview.\r
- schemabinding.version2.Viewport[size];\r
- for (int index = 0; index < size; index++)\r
- {\r
- mArray[index] = (jalview.schemabinding.version2.Viewport) _viewportList.\r
- elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.Viewport[] getViewport()\r
-\r
- /**\r
- * Method getViewportCount\r
- *\r
- *\r
- *\r
- * @return int\r
- */\r
- public int getViewportCount()\r
- {\r
- return _viewportList.size();\r
- } //-- int getViewportCount()\r
-\r
- /**\r
- * Method isValid\r
- *\r
- *\r
- *\r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try\r
- {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid()\r
-\r
- /**\r
- * Method marshal\r
- *\r
- *\r
- *\r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
- {\r
-\r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer)\r
-\r
- /**\r
- * Method marshal\r
- *\r
- *\r
- *\r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
- {\r
-\r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
- /**\r
- * Method removeAllJGroup\r
- *\r
- */\r
- public void removeAllJGroup()\r
- {\r
- _JGroupList.removeAllElements();\r
- } //-- void removeAllJGroup()\r
-\r
- /**\r
- * Method removeAllJSeq\r
- *\r
- */\r
- public void removeAllJSeq()\r
- {\r
- _JSeqList.removeAllElements();\r
- } //-- void removeAllJSeq()\r
-\r
- /**\r
- * Method removeAllTree\r
- *\r
- */\r
- public void removeAllTree()\r
- {\r
- _treeList.removeAllElements();\r
- } //-- void removeAllTree()\r
-\r
- /**\r
- * Method removeAllUserColours\r
- *\r
- */\r
- public void removeAllUserColours()\r
- {\r
- _userColoursList.removeAllElements();\r
- } //-- void removeAllUserColours()\r
-\r
- /**\r
- * Method removeAllViewport\r
- *\r
- */\r
- public void removeAllViewport()\r
- {\r
- _viewportList.removeAllElements();\r
- } //-- void removeAllViewport()\r
-\r
- /**\r
- * Method removeJGroup\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return JGroup\r
- */\r
- public jalview.schemabinding.version2.JGroup removeJGroup(int index)\r
- {\r
- java.lang.Object obj = _JGroupList.elementAt(index);\r
- _JGroupList.removeElementAt(index);\r
- return (jalview.schemabinding.version2.JGroup) obj;\r
- } //-- jalview.schemabinding.version2.JGroup removeJGroup(int)\r
-\r
- /**\r
- * Method removeJSeq\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return JSeq\r
- */\r
- public jalview.schemabinding.version2.JSeq removeJSeq(int index)\r
- {\r
- java.lang.Object obj = _JSeqList.elementAt(index);\r
- _JSeqList.removeElementAt(index);\r
- return (jalview.schemabinding.version2.JSeq) obj;\r
- } //-- jalview.schemabinding.version2.JSeq removeJSeq(int)\r
-\r
- /**\r
- * Method removeTree\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return Tree\r
- */\r
- public jalview.schemabinding.version2.Tree removeTree(int index)\r
- {\r
- java.lang.Object obj = _treeList.elementAt(index);\r
- _treeList.removeElementAt(index);\r
- return (jalview.schemabinding.version2.Tree) obj;\r
- } //-- jalview.schemabinding.version2.Tree removeTree(int)\r
-\r
- /**\r
- * Method removeUserColours\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return UserColours\r
- */\r
- public jalview.schemabinding.version2.UserColours removeUserColours(int index)\r
- {\r
- java.lang.Object obj = _userColoursList.elementAt(index);\r
- _userColoursList.removeElementAt(index);\r
- return (jalview.schemabinding.version2.UserColours) obj;\r
- } //-- jalview.schemabinding.version2.UserColours removeUserColours(int)\r
-\r
- /**\r
- * Method removeViewport\r
- *\r
- *\r
- *\r
- * @param index\r
- * @return Viewport\r
- */\r
- public jalview.schemabinding.version2.Viewport removeViewport(int index)\r
- {\r
- java.lang.Object obj = _viewportList.elementAt(index);\r
- _viewportList.removeElementAt(index);\r
- return (jalview.schemabinding.version2.Viewport) obj;\r
- } //-- jalview.schemabinding.version2.Viewport removeViewport(int)\r
-\r
- /**\r
- * Sets the value of field 'featureSettings'.\r
- *\r
- * @param featureSettings the value of field 'featureSettings'.\r
- */\r
- public void setFeatureSettings(jalview.schemabinding.version2.FeatureSettings\r
- featureSettings)\r
- {\r
- this._featureSettings = featureSettings;\r
- } //-- void setFeatureSettings(jalview.schemabinding.version2.FeatureSettings)\r
-\r
- /**\r
- * Method setJGroup\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vJGroup\r
- */\r
- public void setJGroup(int index,\r
- jalview.schemabinding.version2.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _JGroupList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _JGroupList.setElementAt(vJGroup, index);\r
- } //-- void setJGroup(int, jalview.schemabinding.version2.JGroup)\r
-\r
- /**\r
- * Method setJGroup\r
- *\r
- *\r
- *\r
- * @param JGroupArray\r
- */\r
- public void setJGroup(jalview.schemabinding.version2.JGroup[] JGroupArray)\r
- {\r
- //-- copy array\r
- _JGroupList.removeAllElements();\r
- for (int i = 0; i < JGroupArray.length; i++)\r
- {\r
- _JGroupList.addElement(JGroupArray[i]);\r
- }\r
- } //-- void setJGroup(jalview.schemabinding.version2.JGroup)\r
-\r
- /**\r
- * Method setJSeq\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vJSeq\r
- */\r
- public void setJSeq(int index, jalview.schemabinding.version2.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _JSeqList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _JSeqList.setElementAt(vJSeq, index);\r
- } //-- void setJSeq(int, jalview.schemabinding.version2.JSeq)\r
-\r
- /**\r
- * Method setJSeq\r
- *\r
- *\r
- *\r
- * @param JSeqArray\r
- */\r
- public void setJSeq(jalview.schemabinding.version2.JSeq[] JSeqArray)\r
- {\r
- //-- copy array\r
- _JSeqList.removeAllElements();\r
- for (int i = 0; i < JSeqArray.length; i++)\r
- {\r
- _JSeqList.addElement(JSeqArray[i]);\r
- }\r
- } //-- void setJSeq(jalview.schemabinding.version2.JSeq)\r
-\r
- /**\r
- * Method setTree\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vTree\r
- */\r
- public void setTree(int index, jalview.schemabinding.version2.Tree vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _treeList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _treeList.setElementAt(vTree, index);\r
- } //-- void setTree(int, jalview.schemabinding.version2.Tree)\r
-\r
- /**\r
- * Method setTree\r
- *\r
- *\r
- *\r
- * @param treeArray\r
- */\r
- public void setTree(jalview.schemabinding.version2.Tree[] treeArray)\r
- {\r
- //-- copy array\r
- _treeList.removeAllElements();\r
- for (int i = 0; i < treeArray.length; i++)\r
- {\r
- _treeList.addElement(treeArray[i]);\r
- }\r
- } //-- void setTree(jalview.schemabinding.version2.Tree)\r
-\r
- /**\r
- * Method setUserColours\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vUserColours\r
- */\r
- public void setUserColours(int index,\r
- jalview.schemabinding.version2.UserColours\r
- vUserColours)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _userColoursList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _userColoursList.setElementAt(vUserColours, index);\r
- } //-- void setUserColours(int, jalview.schemabinding.version2.UserColours)\r
-\r
- /**\r
- * Method setUserColours\r
- *\r
- *\r
- *\r
- * @param userColoursArray\r
- */\r
- public void setUserColours(jalview.schemabinding.version2.UserColours[]\r
- userColoursArray)\r
- {\r
- //-- copy array\r
- _userColoursList.removeAllElements();\r
- for (int i = 0; i < userColoursArray.length; i++)\r
- {\r
- _userColoursList.addElement(userColoursArray[i]);\r
- }\r
- } //-- void setUserColours(jalview.schemabinding.version2.UserColours)\r
-\r
- /**\r
- * Method setViewport\r
- *\r
- *\r
- *\r
- * @param index\r
- * @param vViewport\r
- */\r
- public void setViewport(int index,\r
- jalview.schemabinding.version2.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ( (index < 0) || (index > _viewportList.size()))\r
- {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _viewportList.setElementAt(vViewport, index);\r
- } //-- void setViewport(int, jalview.schemabinding.version2.Viewport)\r
-\r
- /**\r
- * Method setViewport\r
- *\r
- *\r
- *\r
- * @param viewportArray\r
- */\r
- public void setViewport(jalview.schemabinding.version2.Viewport[]\r
- viewportArray)\r
- {\r
- //-- copy array\r
- _viewportList.removeAllElements();\r
- for (int i = 0; i < viewportArray.length; i++)\r
- {\r
- _viewportList.addElement(viewportArray[i]);\r
- }\r
- } //-- void setViewport(jalview.schemabinding.version2.Viewport)\r
-\r
- /**\r
- * Method unmarshal\r
- *\r
- *\r
- *\r
- * @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(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(jalview.schemabinding.version2.JalviewModelSequence.class,\r
- reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
- /**\r
- * Method validate\r
- *\r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
- Validator();\r
- validator.validate(this);\r
- } //-- void validate()\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
\r
}\r
git://source.jalview.org / jalview.git / blobdiff