-/*\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
-\r
-package jalview.binding;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\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
- * @version $Revision$ $Date$\r
- */\r
-public class JalviewModelSequence implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _JSeqList\r
- */\r
- private java.util.Vector _JSeqList;\r
-\r
- /**\r
- * Field _JGroupList\r
- */\r
- private java.util.Vector _JGroupList;\r
-\r
- /**\r
- * Field _viewportList\r
- */\r
- private java.util.Vector _viewportList;\r
-\r
- /**\r
- * Field _userColoursList\r
- */\r
- private java.util.Vector _userColoursList;\r
-\r
- /**\r
- * Field _treeList\r
- */\r
- private java.util.Vector _treeList;\r
-\r
- /**\r
- * Field _featureSettings\r
- */\r
- private jalview.binding.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.binding.JalviewModelSequence()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addJGroup\r
- * \r
- * \r
- * \r
- * @param vJGroup\r
- */\r
- public void addJGroup(jalview.binding.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _JGroupList.addElement(vJGroup);\r
- } //-- void addJGroup(jalview.binding.JGroup) \r
-\r
- /**\r
- * Method addJGroup\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vJGroup\r
- */\r
- public void addJGroup(int index, jalview.binding.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _JGroupList.insertElementAt(vJGroup, index);\r
- } //-- void addJGroup(int, jalview.binding.JGroup) \r
-\r
- /**\r
- * Method addJSeq\r
- * \r
- * \r
- * \r
- * @param vJSeq\r
- */\r
- public void addJSeq(jalview.binding.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _JSeqList.addElement(vJSeq);\r
- } //-- void addJSeq(jalview.binding.JSeq) \r
-\r
- /**\r
- * Method addJSeq\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vJSeq\r
- */\r
- public void addJSeq(int index, jalview.binding.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _JSeqList.insertElementAt(vJSeq, index);\r
- } //-- void addJSeq(int, jalview.binding.JSeq) \r
-\r
- /**\r
- * Method addTree\r
- * \r
- * \r
- * \r
- * @param vTree\r
- */\r
- public void addTree(jalview.binding.Tree vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _treeList.addElement(vTree);\r
- } //-- void addTree(jalview.binding.Tree) \r
-\r
- /**\r
- * Method addTree\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vTree\r
- */\r
- public void addTree(int index, jalview.binding.Tree vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _treeList.insertElementAt(vTree, index);\r
- } //-- void addTree(int, jalview.binding.Tree) \r
-\r
- /**\r
- * Method addUserColours\r
- * \r
- * \r
- * \r
- * @param vUserColours\r
- */\r
- public void addUserColours(jalview.binding.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _userColoursList.addElement(vUserColours);\r
- } //-- void addUserColours(jalview.binding.UserColours) \r
-\r
- /**\r
- * Method addUserColours\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vUserColours\r
- */\r
- public void addUserColours(int index, jalview.binding.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _userColoursList.insertElementAt(vUserColours, index);\r
- } //-- void addUserColours(int, jalview.binding.UserColours) \r
-\r
- /**\r
- * Method addViewport\r
- * \r
- * \r
- * \r
- * @param vViewport\r
- */\r
- public void addViewport(jalview.binding.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _viewportList.addElement(vViewport);\r
- } //-- void addViewport(jalview.binding.Viewport) \r
-\r
- /**\r
- * Method addViewport\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vViewport\r
- */\r
- public void addViewport(int index, jalview.binding.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _viewportList.insertElementAt(vViewport, index);\r
- } //-- void addViewport(int, jalview.binding.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.binding.FeatureSettings getFeatureSettings()\r
- {\r
- return this._featureSettings;\r
- } //-- jalview.binding.FeatureSettings getFeatureSettings() \r
-\r
- /**\r
- * Method getJGroup\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return JGroup\r
- */\r
- public jalview.binding.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.binding.JGroup) _JGroupList.elementAt(index);\r
- } //-- jalview.binding.JGroup getJGroup(int) \r
-\r
- /**\r
- * Method getJGroup\r
- * \r
- * \r
- * \r
- * @return JGroup\r
- */\r
- public jalview.binding.JGroup[] getJGroup()\r
- {\r
- int size = _JGroupList.size();\r
- jalview.binding.JGroup[] mArray = new jalview.binding.JGroup[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.binding.JGroup) _JGroupList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.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.binding.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.binding.JSeq) _JSeqList.elementAt(index);\r
- } //-- jalview.binding.JSeq getJSeq(int) \r
-\r
- /**\r
- * Method getJSeq\r
- * \r
- * \r
- * \r
- * @return JSeq\r
- */\r
- public jalview.binding.JSeq[] getJSeq()\r
- {\r
- int size = _JSeqList.size();\r
- jalview.binding.JSeq[] mArray = new jalview.binding.JSeq[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.binding.JSeq) _JSeqList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.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.binding.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.binding.Tree) _treeList.elementAt(index);\r
- } //-- jalview.binding.Tree getTree(int) \r
-\r
- /**\r
- * Method getTree\r
- * \r
- * \r
- * \r
- * @return Tree\r
- */\r
- public jalview.binding.Tree[] getTree()\r
- {\r
- int size = _treeList.size();\r
- jalview.binding.Tree[] mArray = new jalview.binding.Tree[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.binding.Tree) _treeList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.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.binding.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.binding.UserColours) _userColoursList.elementAt(index);\r
- } //-- jalview.binding.UserColours getUserColours(int) \r
-\r
- /**\r
- * Method getUserColours\r
- * \r
- * \r
- * \r
- * @return UserColours\r
- */\r
- public jalview.binding.UserColours[] getUserColours()\r
- {\r
- int size = _userColoursList.size();\r
- jalview.binding.UserColours[] mArray = new jalview.binding.UserColours[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.binding.UserColours) _userColoursList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.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.binding.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.binding.Viewport) _viewportList.elementAt(index);\r
- } //-- jalview.binding.Viewport getViewport(int) \r
-\r
- /**\r
- * Method getViewport\r
- * \r
- * \r
- * \r
- * @return Viewport\r
- */\r
- public jalview.binding.Viewport[] getViewport()\r
- {\r
- int size = _viewportList.size();\r
- jalview.binding.Viewport[] mArray = new jalview.binding.Viewport[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.binding.Viewport) _viewportList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.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.binding.JGroup removeJGroup(int index)\r
- {\r
- java.lang.Object obj = _JGroupList.elementAt(index);\r
- _JGroupList.removeElementAt(index);\r
- return (jalview.binding.JGroup) obj;\r
- } //-- jalview.binding.JGroup removeJGroup(int) \r
-\r
- /**\r
- * Method removeJSeq\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return JSeq\r
- */\r
- public jalview.binding.JSeq removeJSeq(int index)\r
- {\r
- java.lang.Object obj = _JSeqList.elementAt(index);\r
- _JSeqList.removeElementAt(index);\r
- return (jalview.binding.JSeq) obj;\r
- } //-- jalview.binding.JSeq removeJSeq(int) \r
-\r
- /**\r
- * Method removeTree\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Tree\r
- */\r
- public jalview.binding.Tree removeTree(int index)\r
- {\r
- java.lang.Object obj = _treeList.elementAt(index);\r
- _treeList.removeElementAt(index);\r
- return (jalview.binding.Tree) obj;\r
- } //-- jalview.binding.Tree removeTree(int) \r
-\r
- /**\r
- * Method removeUserColours\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return UserColours\r
- */\r
- public jalview.binding.UserColours removeUserColours(int index)\r
- {\r
- java.lang.Object obj = _userColoursList.elementAt(index);\r
- _userColoursList.removeElementAt(index);\r
- return (jalview.binding.UserColours) obj;\r
- } //-- jalview.binding.UserColours removeUserColours(int) \r
-\r
- /**\r
- * Method removeViewport\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Viewport\r
- */\r
- public jalview.binding.Viewport removeViewport(int index)\r
- {\r
- java.lang.Object obj = _viewportList.elementAt(index);\r
- _viewportList.removeElementAt(index);\r
- return (jalview.binding.Viewport) obj;\r
- } //-- jalview.binding.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.binding.FeatureSettings featureSettings)\r
- {\r
- this._featureSettings = featureSettings;\r
- } //-- void setFeatureSettings(jalview.binding.FeatureSettings) \r
-\r
- /**\r
- * Method setJGroup\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vJGroup\r
- */\r
- public void setJGroup(int index, jalview.binding.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.binding.JGroup) \r
-\r
- /**\r
- * Method setJGroup\r
- * \r
- * \r
- * \r
- * @param JGroupArray\r
- */\r
- public void setJGroup(jalview.binding.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.binding.JGroup) \r
-\r
- /**\r
- * Method setJSeq\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vJSeq\r
- */\r
- public void setJSeq(int index, jalview.binding.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.binding.JSeq) \r
-\r
- /**\r
- * Method setJSeq\r
- * \r
- * \r
- * \r
- * @param JSeqArray\r
- */\r
- public void setJSeq(jalview.binding.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.binding.JSeq) \r
-\r
- /**\r
- * Method setTree\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vTree\r
- */\r
- public void setTree(int index, jalview.binding.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.binding.Tree) \r
-\r
- /**\r
- * Method setTree\r
- * \r
- * \r
- * \r
- * @param treeArray\r
- */\r
- public void setTree(jalview.binding.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.binding.Tree) \r
-\r
- /**\r
- * Method setUserColours\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vUserColours\r
- */\r
- public void setUserColours(int index, jalview.binding.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.binding.UserColours) \r
-\r
- /**\r
- * Method setUserColours\r
- * \r
- * \r
- * \r
- * @param userColoursArray\r
- */\r
- public void setUserColours(jalview.binding.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.binding.UserColours) \r
-\r
- /**\r
- * Method setViewport\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vViewport\r
- */\r
- public void setViewport(int index, jalview.binding.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.binding.Viewport) \r
-\r
- /**\r
- * Method setViewport\r
- * \r
- * \r
- * \r
- * @param viewportArray\r
- */\r
- public void setViewport(jalview.binding.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.binding.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.binding.JalviewModelSequence) Unmarshaller.unmarshal(jalview.binding.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
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class JalviewModelSequence.
+ *
+ * @version $Revision$ $Date$
+ */
+public class JalviewModelSequence implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _JSeqList.
+ */
+ private java.util.Vector _JSeqList;
+
+ /**
+ * Field _JGroupList.
+ */
+ private java.util.Vector _JGroupList;
+
+ /**
+ * Field _viewportList.
+ */
+ private java.util.Vector _viewportList;
+
+ /**
+ * Field _userColoursList.
+ */
+ private java.util.Vector _userColoursList;
+
+ /**
+ * Field _treeList.
+ */
+ private java.util.Vector _treeList;
+
+ /**
+ * Field _featureSettings.
+ */
+ private jalview.binding.FeatureSettings _featureSettings;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public JalviewModelSequence() {
+ super();
+ this._JSeqList = new java.util.Vector();
+ this._JGroupList = new java.util.Vector();
+ this._viewportList = new java.util.Vector();
+ this._userColoursList = new java.util.Vector();
+ this._treeList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vJGroup
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addJGroup(
+ final jalview.binding.JGroup vJGroup)
+ throws java.lang.IndexOutOfBoundsException {
+ this._JGroupList.addElement(vJGroup);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJGroup
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addJGroup(
+ final int index,
+ final jalview.binding.JGroup vJGroup)
+ throws java.lang.IndexOutOfBoundsException {
+ this._JGroupList.add(index, vJGroup);
+ }
+
+ /**
+ *
+ *
+ * @param vJSeq
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addJSeq(
+ final jalview.binding.JSeq vJSeq)
+ throws java.lang.IndexOutOfBoundsException {
+ this._JSeqList.addElement(vJSeq);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJSeq
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addJSeq(
+ final int index,
+ final jalview.binding.JSeq vJSeq)
+ throws java.lang.IndexOutOfBoundsException {
+ this._JSeqList.add(index, vJSeq);
+ }
+
+ /**
+ *
+ *
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addTree(
+ final jalview.binding.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ this._treeList.addElement(vTree);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addTree(
+ final int index,
+ final jalview.binding.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ this._treeList.add(index, vTree);
+ }
+
+ /**
+ *
+ *
+ * @param vUserColours
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addUserColours(
+ final jalview.binding.UserColours vUserColours)
+ throws java.lang.IndexOutOfBoundsException {
+ this._userColoursList.addElement(vUserColours);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vUserColours
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addUserColours(
+ final int index,
+ final jalview.binding.UserColours vUserColours)
+ throws java.lang.IndexOutOfBoundsException {
+ this._userColoursList.add(index, vUserColours);
+ }
+
+ /**
+ *
+ *
+ * @param vViewport
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addViewport(
+ final jalview.binding.Viewport vViewport)
+ throws java.lang.IndexOutOfBoundsException {
+ this._viewportList.addElement(vViewport);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vViewport
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addViewport(
+ final int index,
+ final jalview.binding.Viewport vViewport)
+ throws java.lang.IndexOutOfBoundsException {
+ this._viewportList.add(index, vViewport);
+ }
+
+ /**
+ * Method enumerateJGroup.
+ *
+ * @return an Enumeration over all jalview.binding.JGroup
+ * elements
+ */
+ public java.util.Enumeration enumerateJGroup(
+ ) {
+ return this._JGroupList.elements();
+ }
+
+ /**
+ * Method enumerateJSeq.
+ *
+ * @return an Enumeration over all jalview.binding.JSeq elements
+ */
+ public java.util.Enumeration enumerateJSeq(
+ ) {
+ return this._JSeqList.elements();
+ }
+
+ /**
+ * Method enumerateTree.
+ *
+ * @return an Enumeration over all jalview.binding.Tree elements
+ */
+ public java.util.Enumeration enumerateTree(
+ ) {
+ return this._treeList.elements();
+ }
+
+ /**
+ * Method enumerateUserColours.
+ *
+ * @return an Enumeration over all jalview.binding.UserColours
+ * elements
+ */
+ public java.util.Enumeration enumerateUserColours(
+ ) {
+ return this._userColoursList.elements();
+ }
+
+ /**
+ * Method enumerateViewport.
+ *
+ * @return an Enumeration over all jalview.binding.Viewport
+ * elements
+ */
+ public java.util.Enumeration enumerateViewport(
+ ) {
+ return this._viewportList.elements();
+ }
+
+ /**
+ * Returns the value of field 'featureSettings'.
+ *
+ * @return the value of field 'FeatureSettings'.
+ */
+ public jalview.binding.FeatureSettings getFeatureSettings(
+ ) {
+ return this._featureSettings;
+ }
+
+ /**
+ * Method getJGroup.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.JGroup at the given
+ * index
+ */
+ public jalview.binding.JGroup getJGroup(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._JGroupList.size()) {
+ throw new IndexOutOfBoundsException("getJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.JGroup) _JGroupList.get(index);
+ }
+
+ /**
+ * Method getJGroup.Returns the contents of the collection in
+ * an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.JGroup[] getJGroup(
+ ) {
+ jalview.binding.JGroup[] array = new jalview.binding.JGroup[0];
+ return (jalview.binding.JGroup[]) this._JGroupList.toArray(array);
+ }
+
+ /**
+ * Method getJGroupCount.
+ *
+ * @return the size of this collection
+ */
+ public int getJGroupCount(
+ ) {
+ return this._JGroupList.size();
+ }
+
+ /**
+ * Method getJSeq.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.JSeq at the given
+ * index
+ */
+ public jalview.binding.JSeq getJSeq(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._JSeqList.size()) {
+ throw new IndexOutOfBoundsException("getJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.JSeq) _JSeqList.get(index);
+ }
+
+ /**
+ * Method getJSeq.Returns the contents of the collection in an
+ * Array. <p>Note: Just in case the collection contents are
+ * changing in another thread, we pass a 0-length Array of the
+ * correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.JSeq[] getJSeq(
+ ) {
+ jalview.binding.JSeq[] array = new jalview.binding.JSeq[0];
+ return (jalview.binding.JSeq[]) this._JSeqList.toArray(array);
+ }
+
+ /**
+ * Method getJSeqCount.
+ *
+ * @return the size of this collection
+ */
+ public int getJSeqCount(
+ ) {
+ return this._JSeqList.size();
+ }
+
+ /**
+ * Method getTree.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Tree at the given
+ * index
+ */
+ public jalview.binding.Tree getTree(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size()) {
+ throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Tree) _treeList.get(index);
+ }
+
+ /**
+ * Method getTree.Returns the contents of the collection in an
+ * Array. <p>Note: Just in case the collection contents are
+ * changing in another thread, we pass a 0-length Array of the
+ * correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.Tree[] getTree(
+ ) {
+ jalview.binding.Tree[] array = new jalview.binding.Tree[0];
+ return (jalview.binding.Tree[]) this._treeList.toArray(array);
+ }
+
+ /**
+ * Method getTreeCount.
+ *
+ * @return the size of this collection
+ */
+ public int getTreeCount(
+ ) {
+ return this._treeList.size();
+ }
+
+ /**
+ * Method getUserColours.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.UserColours at the
+ * given index
+ */
+ public jalview.binding.UserColours getUserColours(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._userColoursList.size()) {
+ throw new IndexOutOfBoundsException("getUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.UserColours) _userColoursList.get(index);
+ }
+
+ /**
+ * Method getUserColours.Returns the contents of the collection
+ * in an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.UserColours[] getUserColours(
+ ) {
+ jalview.binding.UserColours[] array = new jalview.binding.UserColours[0];
+ return (jalview.binding.UserColours[]) this._userColoursList.toArray(array);
+ }
+
+ /**
+ * Method getUserColoursCount.
+ *
+ * @return the size of this collection
+ */
+ public int getUserColoursCount(
+ ) {
+ return this._userColoursList.size();
+ }
+
+ /**
+ * Method getViewport.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Viewport at the
+ * given index
+ */
+ public jalview.binding.Viewport getViewport(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._viewportList.size()) {
+ throw new IndexOutOfBoundsException("getViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Viewport) _viewportList.get(index);
+ }
+
+ /**
+ * Method getViewport.Returns the contents of the collection in
+ * an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.Viewport[] getViewport(
+ ) {
+ jalview.binding.Viewport[] array = new jalview.binding.Viewport[0];
+ return (jalview.binding.Viewport[]) this._viewportList.toArray(array);
+ }
+
+ /**
+ * Method getViewportCount.
+ *
+ * @return the size of this collection
+ */
+ public int getViewportCount(
+ ) {
+ return this._viewportList.size();
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllJGroup(
+ ) {
+ this._JGroupList.clear();
+ }
+
+ /**
+ */
+ public void removeAllJSeq(
+ ) {
+ this._JSeqList.clear();
+ }
+
+ /**
+ */
+ public void removeAllTree(
+ ) {
+ this._treeList.clear();
+ }
+
+ /**
+ */
+ public void removeAllUserColours(
+ ) {
+ this._userColoursList.clear();
+ }
+
+ /**
+ */
+ public void removeAllViewport(
+ ) {
+ this._viewportList.clear();
+ }
+
+ /**
+ * Method removeJGroup.
+ *
+ * @param vJGroup
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeJGroup(
+ final jalview.binding.JGroup vJGroup) {
+ boolean removed = _JGroupList.remove(vJGroup);
+ return removed;
+ }
+
+ /**
+ * Method removeJGroupAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.JGroup removeJGroupAt(
+ final int index) {
+ java.lang.Object obj = this._JGroupList.remove(index);
+ return (jalview.binding.JGroup) obj;
+ }
+
+ /**
+ * Method removeJSeq.
+ *
+ * @param vJSeq
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeJSeq(
+ final jalview.binding.JSeq vJSeq) {
+ boolean removed = _JSeqList.remove(vJSeq);
+ return removed;
+ }
+
+ /**
+ * Method removeJSeqAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.JSeq removeJSeqAt(
+ final int index) {
+ java.lang.Object obj = this._JSeqList.remove(index);
+ return (jalview.binding.JSeq) obj;
+ }
+
+ /**
+ * Method removeTree.
+ *
+ * @param vTree
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeTree(
+ final jalview.binding.Tree vTree) {
+ boolean removed = _treeList.remove(vTree);
+ return removed;
+ }
+
+ /**
+ * Method removeTreeAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Tree removeTreeAt(
+ final int index) {
+ java.lang.Object obj = this._treeList.remove(index);
+ return (jalview.binding.Tree) obj;
+ }
+
+ /**
+ * Method removeUserColours.
+ *
+ * @param vUserColours
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeUserColours(
+ final jalview.binding.UserColours vUserColours) {
+ boolean removed = _userColoursList.remove(vUserColours);
+ return removed;
+ }
+
+ /**
+ * Method removeUserColoursAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.UserColours removeUserColoursAt(
+ final int index) {
+ java.lang.Object obj = this._userColoursList.remove(index);
+ return (jalview.binding.UserColours) obj;
+ }
+
+ /**
+ * Method removeViewport.
+ *
+ * @param vViewport
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeViewport(
+ final jalview.binding.Viewport vViewport) {
+ boolean removed = _viewportList.remove(vViewport);
+ return removed;
+ }
+
+ /**
+ * Method removeViewportAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Viewport removeViewportAt(
+ final int index) {
+ java.lang.Object obj = this._viewportList.remove(index);
+ return (jalview.binding.Viewport) obj;
+ }
+
+ /**
+ * Sets the value of field 'featureSettings'.
+ *
+ * @param featureSettings the value of field 'featureSettings'.
+ */
+ public void setFeatureSettings(
+ final jalview.binding.FeatureSettings featureSettings) {
+ this._featureSettings = featureSettings;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJGroup
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setJGroup(
+ final int index,
+ final jalview.binding.JGroup vJGroup)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._JGroupList.size()) {
+ throw new IndexOutOfBoundsException("setJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");
+ }
+
+ this._JGroupList.set(index, vJGroup);
+ }
+
+ /**
+ *
+ *
+ * @param vJGroupArray
+ */
+ public void setJGroup(
+ final jalview.binding.JGroup[] vJGroupArray) {
+ //-- copy array
+ _JGroupList.clear();
+
+ for (int i = 0; i < vJGroupArray.length; i++) {
+ this._JGroupList.add(vJGroupArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJSeq
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setJSeq(
+ final int index,
+ final jalview.binding.JSeq vJSeq)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._JSeqList.size()) {
+ throw new IndexOutOfBoundsException("setJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+ }
+
+ this._JSeqList.set(index, vJSeq);
+ }
+
+ /**
+ *
+ *
+ * @param vJSeqArray
+ */
+ public void setJSeq(
+ final jalview.binding.JSeq[] vJSeqArray) {
+ //-- copy array
+ _JSeqList.clear();
+
+ for (int i = 0; i < vJSeqArray.length; i++) {
+ this._JSeqList.add(vJSeqArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setTree(
+ final int index,
+ final jalview.binding.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size()) {
+ throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ this._treeList.set(index, vTree);
+ }
+
+ /**
+ *
+ *
+ * @param vTreeArray
+ */
+ public void setTree(
+ final jalview.binding.Tree[] vTreeArray) {
+ //-- copy array
+ _treeList.clear();
+
+ for (int i = 0; i < vTreeArray.length; i++) {
+ this._treeList.add(vTreeArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vUserColours
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setUserColours(
+ final int index,
+ final jalview.binding.UserColours vUserColours)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._userColoursList.size()) {
+ throw new IndexOutOfBoundsException("setUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");
+ }
+
+ this._userColoursList.set(index, vUserColours);
+ }
+
+ /**
+ *
+ *
+ * @param vUserColoursArray
+ */
+ public void setUserColours(
+ final jalview.binding.UserColours[] vUserColoursArray) {
+ //-- copy array
+ _userColoursList.clear();
+
+ for (int i = 0; i < vUserColoursArray.length; i++) {
+ this._userColoursList.add(vUserColoursArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vViewport
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setViewport(
+ final int index,
+ final jalview.binding.Viewport vViewport)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._viewportList.size()) {
+ throw new IndexOutOfBoundsException("setViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");
+ }
+
+ this._viewportList.set(index, vViewport);
+ }
+
+ /**
+ *
+ *
+ * @param vViewportArray
+ */
+ public void setViewport(
+ final jalview.binding.Viewport[] vViewportArray) {
+ //-- copy array
+ _viewportList.clear();
+
+ for (int i = 0; i < vViewportArray.length; i++) {
+ this._viewportList.add(vViewportArray[i]);
+ }
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.JalviewModelSequence
+ */
+ public static jalview.binding.JalviewModelSequence unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff