X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceNode.java;h=9d00fa5ac820c0adcc6fdb9304229cc31c344ac4;hb=beb2fee66dde629e3bbb7febb38d0116e1a64df2;hp=e81c43b5a300497b56b79ae8024ff6c31970fcd7;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java
index e81c43b..9d00fa5 100755
--- a/src/jalview/datamodel/SequenceNode.java
+++ b/src/jalview/datamodel/SequenceNode.java
@@ -1,50 +1,33 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview 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 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview 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 Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-import java.awt.*;
-
/**
* DOCUMENT ME!
*
* @author $author$
* @version $Revision$
*/
-public class SequenceNode extends BinaryNode
+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;
/**
@@ -55,57 +38,22 @@ public class SequenceNode extends BinaryNode
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)
+ public SequenceNode(SequenceI val, BinaryNode parent,
+ String name, double dist, int bootstrap, boolean dummy)
{
- super(val, parent, name);
- this.dist = dist;
+ super(val, parent, name, dist, bootstrap, dummy);
}
- /**
- * 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)
+ public SequenceNode(SequenceI element, BinaryNode parent,
+ String name, double dist, int bootstrap)
{
- super(val, parent, name);
- this.dist = dist;
- this.bootstrap = bootstrap;
- this.dummy = dummy;
+ super(element, parent, name, dist, bootstrap);
}
- /**
- * @param dummy
- * true if node is created for the representation of polytomous trees
- */
- public boolean isDummy()
+ public SequenceNode(SequenceI element, BinaryNode parent,
+ String name, double dist)
{
- return dummy;
+ super(element, parent, name, dist);
}
/*
@@ -120,22 +68,6 @@ public class SequenceNode extends BinaryNode
/**
* 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!
*/
@@ -145,23 +77,6 @@ public class SequenceNode extends BinaryNode
}
/**
- * 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
*
@@ -175,7 +90,9 @@ public class SequenceNode extends BinaryNode
{
char q = name.charAt(c);
if ('0' <= q && q <= '9')
+ {
continue;
+ }
return true;
}
}