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Alignment might not have any annotations
[jalview.git]
/
src
/
jalview
/
analysis
/
NJTree.java
diff --git
a/src/jalview/analysis/NJTree.java
b/src/jalview/analysis/NJTree.java
index
99592f2
..
40dfc9b
100755
(executable)
--- a/
src/jalview/analysis/NJTree.java
+++ b/
src/jalview/analysis/NJTree.java
@@
-18,13
+18,16
@@
*/
\r
package jalview.analysis;
\r
\r
*/
\r
package jalview.analysis;
\r
\r
-import java.util.*;
\r
-
\r
import jalview.datamodel.*;
\r
import jalview.datamodel.*;
\r
-import jalview.io.*;
\r
-import jalview.schemes.*;
\r
+
\r
+import jalview.io.NewickFile;
\r
+
\r
+import jalview.schemes.ResidueProperties;
\r
+
\r
import jalview.util.*;
\r
\r
import jalview.util.*;
\r
\r
+import java.util.*;
\r
+
\r
\r
/**
\r
* DOCUMENT ME!
\r
\r
/**
\r
* DOCUMENT ME!
\r
@@
-58,9
+61,9
@@
public class NJTree
int start;
\r
int end;
\r
boolean hasDistances = true; // normal case for jalview trees
\r
int start;
\r
int end;
\r
boolean hasDistances = true; // normal case for jalview trees
\r
- boolean hasBootstrap = false; // normal case for jalview trees
\r
+ boolean hasBootstrap = false; // normal case for jalview trees
\r
\r
\r
- private boolean hasRootDistance = true;
\r
+ private boolean hasRootDistance = true;
\r
\r
/**
\r
* Creates a new NJTree object.
\r
\r
/**
\r
* Creates a new NJTree object.
\r
@@
-664,7
+667,7
@@
public class NJTree
AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");
\r
as.calcScoreMatrix();
\r
as.traceAlignment();
\r
AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");
\r
as.calcScoreMatrix();
\r
as.traceAlignment();
\r
- as.printAlignment();
\r
+ as.printAlignment(System.out);
\r
distance[i][j] = (float) as.maxscore;
\r
\r
if (max < distance[i][j])
\r
distance[i][j] = (float) as.maxscore;
\r
\r
if (max < distance[i][j])
\r