*/
package jalview.datamodel;
-import java.awt.Color;
-
/**
* DOCUMENT ME!
*
*/
public class SequenceNode extends BinaryNode
{
- /** DOCUMENT ME!! */
- public double dist;
-
- /** DOCUMENT ME!! */
- public int count;
-
- /** DOCUMENT ME!! */
- public double height;
-
- /** DOCUMENT ME!! */
- public float ycount;
-
- /** DOCUMENT ME!! */
- public Color color = Color.black;
-
- /** DOCUMENT ME!! */
- public boolean dummy = false;
-
private boolean placeholder = false;
/**
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, double 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,
- double 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);
}
/*
/**
* 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!
*/
}
/**
- * 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
*