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JAL-1551 spotlessApply
[jalview.git]
/
src
/
jalview
/
datamodel
/
BinaryNode.java
diff --git
a/src/jalview/datamodel/BinaryNode.java
b/src/jalview/datamodel/BinaryNode.java
index
6d392d4
..
5b55594
100755
(executable)
--- a/
src/jalview/datamodel/BinaryNode.java
+++ b/
src/jalview/datamodel/BinaryNode.java
@@
-40,7
+40,7
@@
public class BinaryNode
BinaryNode parent;
BinaryNode parent;
- /** DOCUMENT ME!! */
+ /** Bootstrap value */
public int bootstrap;
/** DOCUMENT ME!! */
public int bootstrap;
/** DOCUMENT ME!! */
@@
-68,6
+68,7
@@
public class BinaryNode
{
left = right = parent = null;
bootstrap = 0;
{
left = right = parent = null;
bootstrap = 0;
+ dist = 0;
}
/**
}
/**
@@
-80,13
+81,28
@@
public class BinaryNode
* @param name
* DOCUMENT ME!
*/
* @param name
* DOCUMENT ME!
*/
- public BinaryNode(Object element, BinaryNode parent, String name)
+ public BinaryNode(Object element, BinaryNode parent, String name,
+ double dist)
{
{
+ this();
this.element = element;
this.parent = parent;
this.name = name;
this.element = element;
this.parent = parent;
this.name = name;
+ this.dist = dist;
+ }
+
+ public BinaryNode(Object element, BinaryNode parent, String name,
+ double dist, int bootstrap)
+ {
+ this(element, parent, name, dist);
+ this.bootstrap = bootstrap;
+ }
- left = right = null;
+ public BinaryNode(Object val, BinaryNode parent, String name, double dist,
+ int bootstrap, boolean dummy)
+ {
+ this(val, parent, name, dist, bootstrap);
+ this.dummy = dummy;
}
/**
}
/**
@@
-322,18
+338,43
@@
public class BinaryNode
}
/**
}
/**
+ * @param dummy
+ * true if node is created for the representation of polytomous trees
+ */
+ public boolean isDummy()
+ {
+ return dummy;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param newstate
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean setDummy(boolean newstate)
+ {
+ boolean oldstate = dummy;
+ dummy = newstate;
+
+ return oldstate;
+ }
+
+ /**
* ascends the tree but doesn't stop until a non-dummy node is discovered.
*
*/
public BinaryNode AscendTree()
{
BinaryNode c = this;
* ascends the tree but doesn't stop until a non-dummy node is discovered.
*
*/
public BinaryNode AscendTree()
{
BinaryNode c = this;
-
+
do
{
c = c.parent();
} while ((c != null) && c.dummy);
do
{
c = c.parent();
} while ((c != null) && c.dummy);
-
+
return c;
}
}
return c;
}
}