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JAL-1807 explicit imports (jalview.viewmodel)
[jalview.git]
/
src
/
jalview
/
analysis
/
NJTree.java
diff --git
a/src/jalview/analysis/NJTree.java
b/src/jalview/analysis/NJTree.java
index
f08a436
..
3674be1
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.
*
@@
-31,6
+31,7
@@
import jalview.datamodel.SequenceI;
import jalview.datamodel.SequenceNode;
import jalview.io.NewickFile;
import jalview.schemes.ResidueProperties;
import jalview.datamodel.SequenceNode;
import jalview.io.NewickFile;
import jalview.schemes.ResidueProperties;
+import jalview.util.Format;
import java.util.Enumeration;
import java.util.List;
import java.util.Enumeration;
import java.util.List;
@@
-116,7
+117,7
@@
public class NJTree
}
/*
* sequenceString = new String[odata.length]; char gapChar =
}
/*
* sequenceString = new String[odata.length]; char gapChar =
- * jalview.util.Comparison.GapChars.charAt(0); for (int i = 0; i <
+ * Comparison.GapChars.charAt(0); for (int i = 0; i <
* odata.length; i++) { SequenceI oseq_aligned = odata[i].getSeq(gapChar);
* sequenceString[i] = oseq_aligned.getSequence(); }
*/
* odata.length; i++) { SequenceI oseq_aligned = odata[i].getSeq(gapChar);
* sequenceString[i] = oseq_aligned.getSequence(); }
*/
@@
-179,8
+180,8
@@
public class NJTree
if (one2many.contains(nam))
{
countOne2Many++;
if (one2many.contains(nam))
{
countOne2Many++;
- // if (jalview.bin.Cache.log.isDebugEnabled())
- // jalview.bin.Cache.log.debug("One 2 many relationship for
+ // if (Cache.log.isDebugEnabled())
+ // Cache.log.debug("One 2 many relationship for
// "+nam.getName());
}
else
// "+nam.getName());
}
else
@@
-195,8
+196,8
@@
public class NJTree
j.setPlaceholder(true);
}
}
j.setPlaceholder(true);
}
}
- // if (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many>0) {
- // jalview.bin.Cache.log.debug("There were "+countOne2Many+" alignment
+ // if (Cache.log.isDebugEnabled() && countOne2Many>0) {
+ // Cache.log.debug("There were "+countOne2Many+" alignment
// sequence ids (out of "+one2many.size()+" unique ids) linked to two or
// more leaves.");
// }
// sequence ids (out of "+one2many.size()+" unique ids) linked to two or
// more leaves.");
// }
@@
-284,7
+285,7
@@
public class NJTree
*/
public String toString()
{
*/
public String toString()
{
- jalview.io.NewickFile fout = new jalview.io.NewickFile(getTopNode());
+ NewickFile fout = new NewickFile(getTopNode());
return fout.print(isHasBootstrap(), isHasDistances(),
isHasRootDistance()); // output all data available for tree
return fout.print(isHasBootstrap(), isHasDistances(),
isHasRootDistance()); // output all data available for tree
@@
-867,12
+868,12
@@
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
+894,11
@@
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;
}
}
@@
-1068,8
+1069,7
@@
public class NJTree
String[] seqdatas = seqData.getSequenceStrings(gapChar);
for (int i = 0; i < seqdatas.length; i++)
{
String[] seqdatas = seqData.getSequenceStrings(gapChar);
for (int i = 0; i < seqdatas.length; i++)
{
- sb.append(new jalview.util.Format("%-" + 15 + "s").form(sequence[i]
- .getName()));
+ sb.append(new Format("%-" + 15 + "s").form(sequence[i].getName()));
sb.append(" " + seqdatas[i] + "\n");
}
return sb.toString();
sb.append(" " + seqdatas[i] + "\n");
}
return sb.toString();
@@
-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()))
+ {
;
;
+ }
}
}
}
}