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JAL-4134 - refactor tree calculation code to work with binaryNode base type.
[jalview.git]
/
src
/
jalview
/
analysis
/
TreeModel.java
diff --git
a/src/jalview/analysis/TreeModel.java
b/src/jalview/analysis/TreeModel.java
index
4d5e4b2
..
703702a
100644
(file)
--- a/
src/jalview/analysis/TreeModel.java
+++ b/
src/jalview/analysis/TreeModel.java
@@
-95,7
+95,7
@@
public class TreeModel
*/
public TreeModel(TreeBuilder tree)
{
*/
public TreeModel(TreeBuilder tree)
{
- this(tree.getSequences(), tree.getTopNode(), tree.hasDistances(),
+ this(tree.getSequences(), (SequenceNode) tree.getTopNode(), tree.hasDistances(),
tree.hasBootstrap(), tree.hasRootDistance());
seqData = tree.getOriginalData();
}
tree.hasBootstrap(), tree.hasRootDistance());
seqData = tree.getOriginalData();
}
@@
-345,7
+345,7
@@
public class TreeModel
* @param nd
* SequenceNode
*/
* @param nd
* SequenceNode
*/
- void printNode(SequenceNode nd)
+ void printNode(BinaryNode nd)
{
if (nd == null)
{
{
if (nd == null)
{
@@
-361,8
+361,8
@@
public class TreeModel
else
{
System.out.println("Dist " + nd.dist);
else
{
System.out.println("Dist " + nd.dist);
- printNode((SequenceNode) nd.left());
- printNode((SequenceNode) nd.right());
+ printNode((BinaryNode) nd.left());
+ printNode((BinaryNode) nd.right());
}
}
}
}
@@
-422,7
+422,7
@@
public class TreeModel
*
* @return DOCUMENT ME!
*/
*
* @return DOCUMENT ME!
*/
- public double findHeight(SequenceNode nd)
+ public double findHeight(BinaryNode nd)
{
if (nd == null)
{
{
if (nd == null)
{
@@
-431,7
+431,7
@@
public class TreeModel
if ((nd.left() == null) && (nd.right() == null))
{
if ((nd.left() == null) && (nd.right() == null))
{
- nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
+ nd.height = ((BinaryNode) nd.parent()).height + nd.dist;
if (nd.height > maxheight)
{
if (nd.height > maxheight)
{
@@
-446,7
+446,7
@@
public class TreeModel
{
if (nd.parent() != null)
{
{
if (nd.parent() != null)
{
- nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
+ nd.height = ((BinaryNode) nd.parent()).height + nd.dist;
}
else
{
}
else
{
@@
-454,8
+454,8
@@
public class TreeModel
nd.height = (float) 0.0;
}
nd.height = (float) 0.0;
}
- maxheight = findHeight((SequenceNode) (nd.left()));
- maxheight = findHeight((SequenceNode) (nd.right()));
+ maxheight = findHeight((BinaryNode) (nd.left()));
+ maxheight = findHeight((BinaryNode) (nd.right()));
}
return maxheight;
}
return maxheight;
@@
-467,7
+467,7
@@
public class TreeModel
* @param nd
* DOCUMENT ME!
*/
* @param nd
* DOCUMENT ME!
*/
- void printN(SequenceNode nd)
+ void printN(BinaryNode nd)
{
if (nd == null)
{
{
if (nd == null)
{
@@
-476,8
+476,8
@@
public class TreeModel
if ((nd.left() != null) && (nd.right() != null))
{
if ((nd.left() != null) && (nd.right() != null))
{
- printN((SequenceNode) nd.left());
- printN((SequenceNode) nd.right());
+ printN((BinaryNode) nd.left());
+ printN((BinaryNode) nd.right());
}
else
{
}
else
{
@@
-494,7
+494,7
@@
public class TreeModel
* @param nd
* DOCUMENT ME!
*/
* @param nd
* DOCUMENT ME!
*/
- public void reCount(SequenceNode nd)
+ public void reCount(BinaryNode nd)
{
ycount = 0;
// _lycount = 0;
{
ycount = 0;
// _lycount = 0;
@@
-510,7
+510,7
@@
public class TreeModel
* @param nd
* DOCUMENT ME!
*/
* @param nd
* DOCUMENT ME!
*/
- void _reCount(SequenceNode nd)
+ void _reCount(BinaryNode nd)
{
// if (_lycount<_lylimit)
// {
{
// if (_lycount<_lylimit)
// {
@@
-526,11
+526,11
@@
public class TreeModel
if ((nd.left() != null) && (nd.right() != null))
{
if ((nd.left() != null) && (nd.right() != null))
{
- _reCount((SequenceNode) nd.left());
- _reCount((SequenceNode) nd.right());
+ _reCount((BinaryNode) nd.left());
+ _reCount((BinaryNode) nd.right());
- SequenceNode l = (SequenceNode) nd.left();
- SequenceNode r = (SequenceNode) nd.right();
+ BinaryNode l = (BinaryNode) nd.left();
+ BinaryNode r = (BinaryNode) nd.right();
nd.count = l.count + r.count;
nd.ycount = (l.ycount + r.ycount) / 2;
nd.count = l.count + r.count;
nd.ycount = (l.ycount + r.ycount) / 2;
@@
-549,14
+549,14
@@
public class TreeModel
* @param nd
* DOCUMENT ME!
*/
* @param nd
* DOCUMENT ME!
*/
- public void swapNodes(SequenceNode nd)
+ public void swapNodes(BinaryNode nd)
{
if (nd == null)
{
return;
}
{
if (nd == null)
{
return;
}
- SequenceNode tmp = (SequenceNode) nd.left();
+ BinaryNode tmp = (BinaryNode) nd.left();
nd.setLeft(nd.right());
nd.setRight(tmp);
nd.setLeft(nd.right());
nd.setRight(tmp);
@@
-570,7
+570,7
@@
public class TreeModel
* @param dir
* DOCUMENT ME!
*/
* @param dir
* DOCUMENT ME!
*/
- void changeDirection(SequenceNode nd, SequenceNode dir)
+ void changeDirection(BinaryNode nd, BinaryNode dir)
{
if (nd == null)
{
{
if (nd == null)
{
@@
-579,9
+579,9
@@
public class TreeModel
if (nd.parent() != top)
{
if (nd.parent() != top)
{
- changeDirection((SequenceNode) nd.parent(), nd);
+ changeDirection((BinaryNode) nd.parent(), nd);
- SequenceNode tmp = (SequenceNode) nd.parent();
+ BinaryNode tmp = (BinaryNode) nd.parent();
if (dir == nd.left())
{
if (dir == nd.left())
{