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Added order-preservation for clustalW alignment. No support for
author
jprocter
<Jim Procter>
Wed, 13 Apr 2005 16:39:13 +0000
(16:39 +0000)
committer
jprocter
<Jim Procter>
Wed, 13 Apr 2005 16:39:13 +0000
(16:39 +0000)
recovering order yet.
src/jalview/ws/Jemboss.java
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diff --git
a/src/jalview/ws/Jemboss.java
b/src/jalview/ws/Jemboss.java
index
a8bf163
..
7983262
100755
(executable)
--- a/
src/jalview/ws/Jemboss.java
+++ b/
src/jalview/ws/Jemboss.java
@@
-83,8
+83,11
@@
public class Jemboss
}
return allfound;
}
}
return allfound;
}
-
- public SequenceI[] clustalW(SequenceI[] sequences)
+ public SequenceI[] clustalW(SequenceI[] sequences) {
+ // Does the same as below but keeps initial sequence order.
+ return (this.clustalW(sequences, true));
+ }
+ public SequenceI[] clustalW(SequenceI[] sequences, boolean PreserveOrder)
{
// Simplest client call - with gumph from jemboss.server.TestPrivateServer
{
// Simplest client call - with gumph from jemboss.server.TestPrivateServer
@@
-172,6
+175,12
@@
public class Jemboss
System.out.println("jalview.Jemboss: Couldn't read response:\n"
+ alfile + "\n---EOF\n");
else {
System.out.println("jalview.Jemboss: Couldn't read response:\n"
+ alfile + "\n---EOF\n");
else {
+ if (PreserveOrder) {
+ float[] ids = new float[alignment.length];
+ for (int i=0; i<alignment.length; i++)
+ ids[i] = (new Float(alignment[i].getName().substring(8))).floatValue();
+ jalview.util.QuickSort.sort(ids, alignment);
+ }
if (!deuniquify(namemap, alignment)) {
System.out.println("jalview.Jemboss: Warning: Some of the "
+"original sequence names have not been recovered!\n");
if (!deuniquify(namemap, alignment)) {
System.out.println("jalview.Jemboss: Warning: Some of the "
+"original sequence names have not been recovered!\n");