-package jalview.datamodel;\r
-\r
-import java.awt.Color;\r
-\r
-public class SequenceNode extends BinaryNode {\r
-\r
- public float dist;\r
- public int count;\r
- public float height;\r
- public float ycount;\r
- public Color color = Color.black;\r
- public boolean dummy = false;\r
- public SequenceNode() {\r
- super();\r
- }\r
-\r
- public SequenceNode(Object val, SequenceNode parent, float dist,String name) {\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
- 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
- return dummy;\r
- }\r
- public boolean setDummy(boolean newstate) {\r
- boolean oldstate = dummy;\r
- dummy = newstate;\r
- return oldstate;\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
-\r
- public SequenceNode AscendTree() {\r
- SequenceNode c = this;\r
- do {\r
- c = (SequenceNode) c.parent();\r
- } while (c!=null && c.dummy);\r
- return c;\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.datamodel;
+
+import java.awt.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SequenceNode
+ extends BinaryNode
+{
+ /** DOCUMENT ME!! */
+ public float dist;
+
+ /** DOCUMENT ME!! */
+ public int count;
+
+ /** DOCUMENT ME!! */
+ public float height;
+
+ /** DOCUMENT ME!! */
+ public float ycount;
+
+ /** DOCUMENT ME!! */
+ public Color color = Color.black;
+
+ /** DOCUMENT ME!! */
+ public boolean dummy = false;
+ private boolean placeholder = false;
+
+ /**
+ * Creates a new SequenceNode object.
+ */
+ public SequenceNode()
+ {
+ super();
+ }
+
+ /**
+ * Creates a new SequenceNode object.
+ *
+ * @param val DOCUMENT ME!
+ * @param parent DOCUMENT ME!
+ * @param dist DOCUMENT ME!
+ * @param name DOCUMENT ME!
+ */
+ public SequenceNode(Object val, SequenceNode parent, float dist, String name)
+ {
+ super(val, parent, name);
+ this.dist = dist;
+ }
+
+ /**
+ * Creates a new SequenceNode object.
+ *
+ * @param val DOCUMENT ME!
+ * @param parent DOCUMENT ME!
+ * @param name DOCUMENT ME!
+ * @param dist DOCUMENT ME!
+ * @param bootstrap DOCUMENT ME!
+ * @param dummy DOCUMENT ME!
+ */
+ public SequenceNode(Object val, SequenceNode parent, String name,
+ float dist, int bootstrap, boolean dummy)
+ {
+ super(val, parent, name);
+ this.dist = dist;
+ this.bootstrap = bootstrap;
+ this.dummy = dummy;
+ }
+
+ /**
+ * @param dummy true if node is created for the representation of polytomous trees
+ */
+ public boolean isDummy()
+ {
+ return dummy;
+ }
+
+ /* @param placeholder is true if the sequence refered to in the
+ * element node is not actually present in the associated alignment
+ */
+ public boolean isPlaceholder()
+ {
+ return placeholder;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param newstate DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setDummy(boolean newstate)
+ {
+ boolean oldstate = dummy;
+ dummy = newstate;
+
+ return oldstate;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param Placeholder DOCUMENT ME!
+ */
+ public void setPlaceholder(boolean Placeholder)
+ {
+ this.placeholder = Placeholder;
+ }
+
+ /**
+ * ascends the tree but doesn't stop until a non-dummy node is discovered.
+ * This will probably break if the tree is a mixture of BinaryNodes and SequenceNodes.
+ */
+ public SequenceNode AscendTree()
+ {
+ SequenceNode c = this;
+
+ do
+ {
+ c = (SequenceNode) c.parent();
+ }
+ while ( (c != null) && c.dummy);
+
+ return c;
+ }
+ /**
+ * test if this node has a name that might be a label rather than a bootstrap value
+ * @return true if node has a non-numeric label
+ */
+ public boolean isSequenceLabel()
+ {
+ if (name!=null && name.length()>0)
+ {
+ for (int c=0,s=name.length(); c<s; c++)
+ {
+ char q = name.charAt(c);
+ if ('0'<=q && q<='9')
+ continue;
+ return true;
+ }
+ }
+ return false;
+ }
+}