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Merge branch 'develop' into features/JAL-4134_use_annotation_row_for_colours_and_groups
[jalview.git]
/
src
/
jalview
/
analysis
/
TreeModel.java
diff --git
a/src/jalview/analysis/TreeModel.java
b/src/jalview/analysis/TreeModel.java
index
703702a
..
0e57a58
100644
(file)
--- a/
src/jalview/analysis/TreeModel.java
+++ b/
src/jalview/analysis/TreeModel.java
@@
-20,7
+20,6
@@
*/
package jalview.analysis;
*/
package jalview.analysis;
-import jalview.bin.Cache;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.BinaryNode;
import jalview.datamodel.NodeTransformI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.BinaryNode;
import jalview.datamodel.NodeTransformI;
@@
-51,7
+50,7
@@
public class TreeModel
int noseqs;
int noseqs;
- SequenceNode top;
+ BinaryNode top;
double maxDistValue;
double maxDistValue;
@@
-59,7
+58,7
@@
public class TreeModel
int ycount;
int ycount;
- Vector<SequenceNode> node;
+ Vector<BinaryNode> node;
boolean hasDistances = true; // normal case for jalview trees
boolean hasDistances = true; // normal case for jalview trees
@@
-95,7
+94,7
@@
public class TreeModel
*/
public TreeModel(TreeBuilder tree)
{
*/
public TreeModel(TreeBuilder tree)
{
- this(tree.getSequences(), (SequenceNode) tree.getTopNode(), tree.hasDistances(),
+ this(tree.getSequences(), tree.getTopNode(), tree.hasDistances(),
tree.hasBootstrap(), tree.hasRootDistance());
seqData = tree.getOriginalData();
}
tree.hasBootstrap(), tree.hasRootDistance());
seqData = tree.getOriginalData();
}
@@
-109,7
+108,7
@@
public class TreeModel
* @param hasBoot
* @param hasRootDist
*/
* @param hasBoot
* @param hasRootDist
*/
- public TreeModel(SequenceI[] seqs, SequenceNode root, boolean hasDist,
+ public TreeModel(SequenceI[] seqs, BinaryNode root, boolean hasDist,
boolean hasBoot, boolean hasRootDist)
{
this.sequences = seqs;
boolean hasBoot, boolean hasRootDist)
{
this.sequences = seqs;
@@
-129,7
+128,7
@@
public class TreeModel
{
SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
{
SequenceIdMatcher algnIds = new SequenceIdMatcher(seqs);
- Vector<SequenceNode> leaves = findLeaves(top);
+ Vector<BinaryNode> leaves = findLeaves(top);
int i = 0;
int namesleft = seqs.length;
int i = 0;
int namesleft = seqs.length;
@@
-141,7
+140,8
@@
public class TreeModel
// int countOne2Many = 0;
while (i < leaves.size())
{
// int countOne2Many = 0;
while (i < leaves.size())
{
- j = leaves.elementAt(i++);
+ // TODO - decide if we get rid of the polymorphism here ?
+ j = (SequenceNode) leaves.elementAt(i++);
realnam = j.getName();
nam = null;
realnam = j.getName();
nam = null;
@@
-206,7
+206,7
@@
public class TreeModel
*/
public void updatePlaceHolders(List<SequenceI> list)
{
*/
public void updatePlaceHolders(List<SequenceI> list)
{
- Vector<SequenceNode> leaves = findLeaves(top);
+ Vector<BinaryNode> leaves = findLeaves(top);
int sz = leaves.size();
SequenceIdMatcher seqmatcher = null;
int sz = leaves.size();
SequenceIdMatcher seqmatcher = null;
@@
-214,7
+214,7
@@
public class TreeModel
while (i < sz)
{
while (i < sz)
{
- SequenceNode leaf = leaves.elementAt(i++);
+ SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);
if (list.contains(leaf.element()))
{
if (list.contains(leaf.element()))
{
@@
-289,15
+289,15
@@
public class TreeModel
/**
* Search for leaf nodes below (or at) the given node
*
/**
* Search for leaf nodes below (or at) the given node
*
- * @param nd
+ * @param top2
* root node to search from
*
* @return
*/
* root node to search from
*
* @return
*/
- public Vector<SequenceNode> findLeaves(SequenceNode nd)
+ public Vector<BinaryNode> findLeaves(BinaryNode top2)
{
{
- Vector<SequenceNode> leaves = new Vector<SequenceNode>();
- findLeaves(nd, leaves);
+ Vector<BinaryNode> leaves = new Vector<BinaryNode>();
+ findLeaves(top2, leaves);
return leaves;
}
return leaves;
}
@@
-311,8
+311,7
@@
public class TreeModel
*
* @return Vector of leaf nodes on binary tree
*/
*
* @return Vector of leaf nodes on binary tree
*/
- Vector<SequenceNode> findLeaves(SequenceNode nd,
- Vector<SequenceNode> leaves)
+ Vector<BinaryNode> findLeaves(BinaryNode nd, Vector<BinaryNode> leaves)
{
if (nd == null)
{
{
if (nd == null)
{
@@
-332,8
+331,8
@@
public class TreeModel
* TODO: Identify internal nodes... if (node.isSequenceLabel()) {
* leaves.addElement(node); }
*/
* TODO: Identify internal nodes... if (node.isSequenceLabel()) {
* leaves.addElement(node); }
*/
- findLeaves((SequenceNode) nd.left(), leaves);
- findLeaves((SequenceNode) nd.right(), leaves);
+ findLeaves(nd.left(), leaves);
+ findLeaves(nd.right(), leaves);
}
return leaves;
}
return leaves;
@@
-388,14
+387,14
@@
public class TreeModel
* @param threshold
* @see #getGroups()
*/
* @param threshold
* @see #getGroups()
*/
- public List<SequenceNode> groupNodes(float threshold)
+ public List<BinaryNode> groupNodes(float threshold)
{
{
- List<SequenceNode> groups = new ArrayList<SequenceNode>();
+ List<BinaryNode> groups = new ArrayList<BinaryNode>();
_groupNodes(groups, getTopNode(), threshold);
return groups;
}
_groupNodes(groups, getTopNode(), threshold);
return groups;
}
- protected void _groupNodes(List<SequenceNode> groups, SequenceNode nd,
+ protected void _groupNodes(List<BinaryNode> groups, BinaryNode nd,
float threshold)
{
if (nd == null)
float threshold)
{
if (nd == null)
@@
-409,8
+408,8
@@
public class TreeModel
}
else
{
}
else
{
- _groupNodes(groups, (SequenceNode) nd.left(), threshold);
- _groupNodes(groups, (SequenceNode) nd.right(), threshold);
+ _groupNodes(groups, nd.left(), threshold);
+ _groupNodes(groups, nd.right(), threshold);
}
}
}
}
@@
-630,7
+629,7
@@
public class TreeModel
*
* @return DOCUMENT ME!
*/
*
* @return DOCUMENT ME!
*/
- public SequenceNode getTopNode()
+ public BinaryNode getTopNode()
{
return top;
}
{
return top;
}
@@
-665,7
+664,7
@@
public class TreeModel
*/
public void applyToNodes(NodeTransformI nodeTransformI)
{
*/
public void applyToNodes(NodeTransformI nodeTransformI)
{
- for (Enumeration<SequenceNode> nodes = node.elements(); nodes
+ for (Enumeration<BinaryNode> nodes = node.elements(); nodes
.hasMoreElements(); nodeTransformI
.transform(nodes.nextElement()))
{
.hasMoreElements(); nodeTransformI
.transform(nodes.nextElement()))
{