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Merge branch 'kjvdh/features/PhylogenyViewer_tabbedsupport' into merge/2_11_2/kjvdh...
[jalview.git]
/
src
/
jalview
/
analysis
/
TreeModel.java
diff --git
a/src/jalview/analysis/TreeModel.java
b/src/jalview/analysis/TreeModel.java
index
4d5e4b2
..
11ca778
100644
(file)
--- a/
src/jalview/analysis/TreeModel.java
+++ b/
src/jalview/analysis/TreeModel.java
@@
-81,8
+81,8
@@
public class TreeModel
public TreeModel(SequenceI[] seqs, AlignmentView odata,
NewickFile treefile)
{
public TreeModel(SequenceI[] seqs, AlignmentView odata,
NewickFile treefile)
{
- this(seqs, treefile.getTree(), treefile.HasDistances(),
- treefile.HasBootstrap(), treefile.HasRootDistance());
+ this(seqs, treefile.getTree(), treefile.hasDistances(),
+ treefile.hasBootstrap(), treefile.hasRootDistance());
seqData = odata;
associateLeavesToSequences(seqs);
seqData = odata;
associateLeavesToSequences(seqs);
@@
-131,29
+131,27
@@
public class TreeModel
Vector<SequenceNode> leaves = findLeaves(top);
Vector<SequenceNode> leaves = findLeaves(top);
- int i = 0;
int namesleft = seqs.length;
int namesleft = seqs.length;
- SequenceNode j;
- SequenceI nam;
- String realnam;
- Vector<SequenceI> one2many = new Vector<SequenceI>();
+ SequenceI nodeSequence;
+ String nodeSequenceName;
+ Vector<SequenceI> one2many = new Vector<>();
// int countOne2Many = 0;
// int countOne2Many = 0;
- while (i < leaves.size())
+
+ for (SequenceNode sn : leaves)
{
{
- j = leaves.elementAt(i++);
- realnam = j.getName();
- nam = null;
+ nodeSequenceName = sn.getName();
+ nodeSequence = null;
if (namesleft > -1)
{
if (namesleft > -1)
{
- nam = algnIds.findIdMatch(realnam);
+ nodeSequence = algnIds.findIdMatch(nodeSequenceName);
}
}
- if (nam != null)
+ if (nodeSequence != null)
{
{
- j.setElement(nam);
- if (one2many.contains(nam))
+ sn.setElement(nodeSequence);
+ if (one2many.contains(nodeSequence))
{
// countOne2Many++;
// if (Cache.isDebugEnabled())
{
// countOne2Many++;
// if (Cache.isDebugEnabled())
@@
-162,14
+160,14
@@
public class TreeModel
}
else
{
}
else
{
- one2many.addElement(nam);
+ one2many.addElement(nodeSequence);
namesleft--;
}
}
else
{
namesleft--;
}
}
else
{
- j.setElement(new Sequence(realnam, "THISISAPLACEHLDER"));
- j.setPlaceholder(true);
+ sn.setElement(new Sequence(nodeSequenceName, "THISISAPLACEHLDER"));
+ sn.setPlaceholder(true);
}
}
// if (Cache.isDebugEnabled() && countOne2Many>0) {
}
}
// if (Cache.isDebugEnabled() && countOne2Many>0) {
@@
-296,7
+294,7
@@
public class TreeModel
*/
public Vector<SequenceNode> findLeaves(SequenceNode nd)
{
*/
public Vector<SequenceNode> findLeaves(SequenceNode nd)
{
- Vector<SequenceNode> leaves = new Vector<SequenceNode>();
+ Vector<SequenceNode> leaves = new Vector<>();
findLeaves(nd, leaves);
return leaves;
}
findLeaves(nd, leaves);
return leaves;
}
@@
-390,7
+388,7
@@
public class TreeModel
*/
public List<SequenceNode> groupNodes(float threshold)
{
*/
public List<SequenceNode> groupNodes(float threshold)
{
- List<SequenceNode> groups = new ArrayList<SequenceNode>();
+ List<SequenceNode> groups = new ArrayList<>();
_groupNodes(groups, getTopNode(), threshold);
return groups;
}
_groupNodes(groups, getTopNode(), threshold);
return groups;
}