*/\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
_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
} //-- 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
} //-- 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
} //-- 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
} //-- 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
} //-- 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
} //-- 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
} //-- 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
} //-- 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