/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.datamodel;\r
\r
import java.awt.*;\r
\r
-public class SequenceNode extends BinaryNode {\r
-\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class SequenceNode\r
+ extends BinaryNode\r
+{\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
- public SequenceNode() {\r
+ /**\r
+ * Creates a new SequenceNode object.\r
+ */\r
+ public SequenceNode()\r
+ {\r
super();\r
}\r
\r
- public SequenceNode(Object val, SequenceNode parent, float dist,String name) {\r
- super(val,parent,name);\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
- public SequenceNode(Object val, SequenceNode parent, String name, float dist, int bootstrap, boolean dummy) {\r
- super(val,parent,name);\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
/**\r
* @param dummy true if node is created for the representation of polytomous trees\r
*/\r
-\r
- public boolean isDummy() {\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
return placeholder;\r
}\r
\r
- public boolean setDummy(boolean newstate) {\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
* 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
-\r
- public SequenceNode AscendTree() {\r
+ public SequenceNode AscendTree()\r
+ {\r
SequenceNode c = this;\r
- do {\r
+\r
+ do\r
+ {\r
c = (SequenceNode) c.parent();\r
- } while (c!=null && c.dummy);\r
+ }\r
+ while ( (c != null) && c.dummy);\r
+\r
return c;\r
}\r
}\r