- /** DOCUMENT ME!! */\r
- public float dist;\r
-\r
- /** DOCUMENT ME!! */\r
- public int count;\r
-\r
- /** DOCUMENT ME!! */\r
- public float height;\r
-\r
- /** DOCUMENT ME!! */\r
- public float ycount;\r
-\r
- /** DOCUMENT ME!! */\r
- public Color color = Color.black;\r
-\r
- /** DOCUMENT ME!! */\r
- public boolean dummy = false;\r
- private boolean placeholder = false;\r
-\r
- /**\r
- * Creates a new SequenceNode object.\r
- */\r
- public SequenceNode()\r
- {\r
- super();\r
- }\r
-\r
- /**\r
- * Creates a new SequenceNode object.\r
- *\r
- * @param val DOCUMENT ME!\r
- * @param parent DOCUMENT ME!\r
- * @param dist DOCUMENT ME!\r
- * @param name DOCUMENT ME!\r
- */\r
- public SequenceNode(Object val, SequenceNode parent, float dist, String name)\r
- {\r
- super(val, parent, name);\r
- this.dist = dist;\r
- }\r
-\r
- /**\r
- * Creates a new SequenceNode object.\r
- *\r
- * @param val DOCUMENT ME!\r
- * @param parent DOCUMENT ME!\r
- * @param name DOCUMENT ME!\r
- * @param dist DOCUMENT ME!\r
- * @param bootstrap DOCUMENT ME!\r
- * @param dummy DOCUMENT ME!\r
- */\r
- public SequenceNode(Object val, SequenceNode parent, String name,\r
- float dist, int bootstrap, boolean dummy)\r
- {\r
- super(val, parent, name);\r
- this.dist = dist;\r
- this.bootstrap = bootstrap;\r
- this.dummy = dummy;\r
- }\r
-\r
- /**\r
- * @param dummy true if node is created for the representation of polytomous trees\r
- */\r
- public boolean isDummy()\r
- {\r
- return dummy;\r
- }\r
-\r
- /* @param placeholder is true if the sequence refered to in the\r
- * element node is not actually present in the associated alignment\r
- */\r
- public boolean isPlaceholder()\r
+ /** DOCUMENT ME!! */\r
+ public float dist;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public int count;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public float height;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public float ycount;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public Color color = Color.black;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public boolean dummy = false;\r
+ private boolean placeholder = false;\r
+\r
+ /**\r
+ * Creates a new SequenceNode object.\r
+ */\r
+ public SequenceNode()\r
+ {\r
+ super();\r
+ }\r
+\r
+ /**\r
+ * Creates a new SequenceNode object.\r
+ *\r
+ * @param val DOCUMENT ME!\r
+ * @param parent DOCUMENT ME!\r
+ * @param dist DOCUMENT ME!\r
+ * @param name DOCUMENT ME!\r
+ */\r
+ public SequenceNode(Object val, SequenceNode parent, float dist, String name)\r
+ {\r
+ super(val, parent, name);\r
+ this.dist = dist;\r
+ }\r
+\r
+ /**\r
+ * Creates a new SequenceNode object.\r
+ *\r
+ * @param val DOCUMENT ME!\r
+ * @param parent DOCUMENT ME!\r
+ * @param name DOCUMENT ME!\r
+ * @param dist DOCUMENT ME!\r
+ * @param bootstrap DOCUMENT ME!\r
+ * @param dummy DOCUMENT ME!\r
+ */\r
+ public SequenceNode(Object val, SequenceNode parent, String name,\r
+ float dist, int bootstrap, boolean dummy)\r
+ {\r
+ super(val, parent, name);\r
+ this.dist = dist;\r
+ this.bootstrap = bootstrap;\r
+ this.dummy = dummy;\r
+ }\r
+\r
+ /**\r
+ * @param dummy true if node is created for the representation of polytomous trees\r
+ */\r
+ public boolean isDummy()\r
+ {\r
+ return dummy;\r
+ }\r
+\r
+ /* @param placeholder is true if the sequence refered to in the\r
+ * element node is not actually present in the associated alignment\r
+ */\r
+ public boolean isPlaceholder()\r
+ {\r
+ return placeholder;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param newstate DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean setDummy(boolean newstate)\r
+ {\r
+ boolean oldstate = dummy;\r
+ dummy = newstate;\r
+\r
+ return oldstate;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param Placeholder DOCUMENT ME!\r
+ */\r
+ public void setPlaceholder(boolean Placeholder)\r
+ {\r
+ this.placeholder = Placeholder;\r
+ }\r
+\r
+ /**\r
+ * ascends the tree but doesn't stop until a non-dummy node is discovered.\r
+ * This will probably break if the tree is a mixture of BinaryNodes and SequenceNodes.\r
+ */\r
+ public SequenceNode AscendTree()\r
+ {\r
+ SequenceNode c = this;\r
+\r
+ do\r