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Merge remote-tracking branch 'origin/tasks/JAL-3035_remove_dasobert_dependency' into...
[jalview.git]
/
src
/
jalview
/
analysis
/
TreeModel.java
diff --git
a/src/jalview/analysis/TreeModel.java
b/src/jalview/analysis/TreeModel.java
index
5a41802
..
a50634e
100644
(file)
--- a/
src/jalview/analysis/TreeModel.java
+++ b/
src/jalview/analysis/TreeModel.java
@@
-77,10
+77,11
@@
public class TreeModel
* @param treefile
* NewickFile
*/
* @param treefile
* NewickFile
*/
- 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);
@@
-93,8
+94,8
@@
public class TreeModel
*/
public TreeModel(TreeBuilder tree)
{
*/
public TreeModel(TreeBuilder tree)
{
- this(tree.getSequences(), tree.getTopNode(), tree.hasDistances(), tree
- .hasBootstrap(), tree.hasRootDistance());
+ this(tree.getSequences(), tree.getTopNode(), tree.hasDistances(),
+ tree.hasBootstrap(), tree.hasRootDistance());
seqData = tree.getOriginalData();
}
seqData = tree.getOriginalData();
}
@@
-187,8
+188,12
@@
public class TreeModel
{
NewickFile fout = new NewickFile(getTopNode());
{
NewickFile fout = new NewickFile(getTopNode());
- return fout.print(hasBootstrap(), hasDistances(),
- hasRootDistance()); // output all data available for tree
+ return fout.print(hasBootstrap(), hasDistances(), hasRootDistance()); // output
+ // all
+ // data
+ // available
+ // for
+ // tree
}
/**
}
/**
@@
-248,8
+253,8
@@
public class TreeModel
if (!leaf.isPlaceholder())
{
// Construct a new placeholder sequence object for this leaf
if (!leaf.isPlaceholder())
{
// Construct a new placeholder sequence object for this leaf
- leaf.setElement(new Sequence(leaf.getName(),
- "THISISAPLACEHLDER"));
+ leaf.setElement(
+ new Sequence(leaf.getName(), "THISISAPLACEHLDER"));
}
leaf.setPlaceholder(true);
}
leaf.setPlaceholder(true);
@@
-478,8
+483,8
@@
public class TreeModel
System.out.println(" name = " + ((SequenceI) nd.element()).getName());
}
System.out.println(" name = " + ((SequenceI) nd.element()).getName());
}
- System.out.println(" dist = " + nd.dist + " " + nd.count + " "
- + nd.height);
+ System.out.println(
+ " dist = " + nd.dist + " " + nd.count + " " + nd.height);
}
/**
}
/**
@@
-508,7
+513,8
@@
public class TreeModel
{
// if (_lycount<_lylimit)
// {
{
// if (_lycount<_lylimit)
// {
- // System.err.println("Warning: depth of _recount greater than number of nodes.");
+ // System.err.println("Warning: depth of _recount greater than number of
+ // nodes.");
// }
if (nd == null)
{
// }
if (nd == null)
{
@@
-659,8
+665,8
@@
public class TreeModel
public void applyToNodes(NodeTransformI nodeTransformI)
{
for (Enumeration<SequenceNode> nodes = node.elements(); nodes
public void applyToNodes(NodeTransformI nodeTransformI)
{
for (Enumeration<SequenceNode> nodes = node.elements(); nodes
- .hasMoreElements(); nodeTransformI.transform(nodes
- .nextElement()))
+ .hasMoreElements(); nodeTransformI
+ .transform(nodes.nextElement()))
{
;
}
{
;
}