/*\r
- * This class was automatically generated with\r
+ * This class was automatically generated with \r
* <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
* Schema.\r
* $Id$\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 java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\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
+ _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
+ //-----------/\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, 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 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, jalview.schemabinding.version2.UserColours 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, 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
+ 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.version2.JGroup[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.schemabinding.version2.JGroup) _JGroupList.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
+ 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.version2.JSeq[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.schemabinding.version2.JSeq) _JSeqList.elementAt(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
+ 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.version2.Tree[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.schemabinding.version2.Tree) _treeList.elementAt(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
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.UserColours) _userColoursList.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.schemabinding.version2.UserColours[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.schemabinding.version2.UserColours) _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
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.Viewport) _viewportList.elementAt(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.schemabinding.version2.Viewport[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.schemabinding.version2.Viewport) _viewportList.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
+ validate();\r
+ }\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\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, 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, 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 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, jalview.schemabinding.version2.JGroup vJGroup)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _JGroupList.size())) {\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
+ _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
+ 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
+ _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
+ 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
+ _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, jalview.schemabinding.version2.UserColours vUserColours)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _userColoursList.size())) {\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[] userColoursArray)\r
+ {\r
+ //-- copy array\r
+ _userColoursList.removeAllElements();\r
+ for (int i = 0; i < userColoursArray.length; i++) {\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, jalview.schemabinding.version2.Viewport vViewport)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _viewportList.size())) {\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[] viewportArray)\r
+ {\r
+ //-- copy array\r
+ _viewportList.removeAllElements();\r
+ for (int i = 0; i < viewportArray.length; i++) {\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, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller.unmarshal(jalview.schemabinding.version2.JalviewModelSequence.class, 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.Validator();\r
+ validator.validate(this);\r
+ } //-- void validate() \r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff