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Merge branch 'develop' of https://source.jalview.org/git/jalview.git into develop
[jalview.git]
/
src
/
jalview
/
analysis
/
NJTree.java
diff --git
a/src/jalview/analysis/NJTree.java
b/src/jalview/analysis/NJTree.java
index
f08a436
..
3470dbc
100644
(file)
--- a/
src/jalview/analysis/NJTree.java
+++ b/
src/jalview/analysis/NJTree.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-867,12
+867,12
@@
public class NJTree
{
System.out
.println("Leaf = " + ((SequenceI) node.element()).getName());
{
System.out
.println("Leaf = " + ((SequenceI) node.element()).getName());
- System.out.println("Dist " + ((SequenceNode) node).dist);
+ System.out.println("Dist " + node.dist);
System.out.println("Boot " + node.getBootstrap());
}
else
{
System.out.println("Boot " + node.getBootstrap());
}
else
{
- System.out.println("Dist " + ((SequenceNode) node).dist);
+ System.out.println("Dist " + node.dist);
printNode((SequenceNode) node.left());
printNode((SequenceNode) node.right());
}
printNode((SequenceNode) node.left());
printNode((SequenceNode) node.right());
}
@@
-893,11
+893,11
@@
public class NJTree
if ((node.left() == null) && (node.right() == null))
{
if ((node.left() == null) && (node.right() == null))
{
- float dist = ((SequenceNode) node).dist;
+ float dist = node.dist;
if (dist > maxDistValue)
{
if (dist > maxDistValue)
{
- maxdist = (SequenceNode) node;
+ maxdist = node;
maxDistValue = dist;
}
}
maxDistValue = dist;
}
}
@@
-1099,9
+1099,9
@@
public class NJTree
+ ((SequenceI) node.element()).getName());
}
+ ((SequenceI) node.element()).getName());
}
- System.out.println(" dist = " + ((SequenceNode) node).dist + " "
- + ((SequenceNode) node).count + " "
- + ((SequenceNode) node).height);
+ System.out.println(" dist = " + node.dist + " "
+ + node.count + " "
+ + node.height);
}
/**
}
/**
@@
-1147,13
+1147,13
@@
public class NJTree
SequenceNode l = (SequenceNode) node.left();
SequenceNode r = (SequenceNode) node.right();
SequenceNode l = (SequenceNode) node.left();
SequenceNode r = (SequenceNode) node.right();
- ((SequenceNode) node).count = l.count + r.count;
- ((SequenceNode) node).ycount = (l.ycount + r.ycount) / 2;
+ node.count = l.count + r.count;
+ node.ycount = (l.ycount + r.ycount) / 2;
}
else
{
}
else
{
- ((SequenceNode) node).count = 1;
- ((SequenceNode) node).ycount = ycount++;
+ node.count = 1;
+ node.ycount = ycount++;
}
_lycount--;
}
}
_lycount--;
}
@@
-1292,7
+1292,9
@@
public class NJTree
{
for (Enumeration nodes = node.elements(); nodes.hasMoreElements(); nodeTransformI
.transform((BinaryNode) nodes.nextElement()))
{
for (Enumeration nodes = node.elements(); nodes.hasMoreElements(); nodeTransformI
.transform((BinaryNode) nodes.nextElement()))
+ {
;
;
+ }
}
}
}
}