git://source.jalview.org
/
jalview.git
/ commitdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
| commitdiff |
tree
raw
|
patch
|
inline
| side by side (parent:
7a4dfd9
)
fixed so that alignment percentage ID is used for distance calculation
author
jprocter
<Jim Procter>
Tue, 8 Mar 2005 16:44:11 +0000
(16:44 +0000)
committer
jprocter
<Jim Procter>
Tue, 8 Mar 2005 16:44:11 +0000
(16:44 +0000)
src/jalview/analysis/NJTree.java
patch
|
blob
|
history
diff --git
a/src/jalview/analysis/NJTree.java
b/src/jalview/analysis/NJTree.java
index
4aeee3d
..
7324b6c
100755
(executable)
--- a/
src/jalview/analysis/NJTree.java
+++ b/
src/jalview/analysis/NJTree.java
@@
-331,14
+331,13
@@
public class NJTree {
public float[][] findDistances() {
\r
\r
float[][] distance = new float[noseqs][noseqs];
\r
public float[][] findDistances() {
\r
\r
float[][] distance = new float[noseqs][noseqs];
\r
-
\r
if (pwtype.equals("PID")) {
\r
for (int i = 0; i < noseqs-1; i++) {
\r
for (int j = i; j < noseqs; j++) {
\r
if (j==i) {
\r
distance[i][i] = 0;
\r
} else {
\r
if (pwtype.equals("PID")) {
\r
for (int i = 0; i < noseqs-1; i++) {
\r
for (int j = i; j < noseqs; j++) {
\r
if (j==i) {
\r
distance[i][i] = 0;
\r
} else {
\r
- distance[i][j] = 100-Comparison.compare(sequence[i],sequence[j],start,end);
\r
+ distance[i][j] = 100-Comparison.PID(sequence[i], sequence[j]);
\r
distance[j][i] = distance[i][j];
\r
}
\r
}
\r
distance[j][i] = distance[i][j];
\r
}
\r
}
\r