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JAL-1619 AlignedCodonFrame in new alignment should references realigned
[jalview.git]
/
src
/
jalview
/
ws
/
AWSThread.java
diff --git
a/src/jalview/ws/AWSThread.java
b/src/jalview/ws/AWSThread.java
index
edb56a9
..
7f05e90
100644
(file)
--- a/
src/jalview/ws/AWSThread.java
+++ b/
src/jalview/ws/AWSThread.java
@@
-27,8
+27,8
@@
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.datamodel.AlignmentView;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
-import jalview.gui.WebserviceInfo;
import jalview.gui.FeatureRenderer.FeatureRendererSettings;
import jalview.gui.FeatureRenderer.FeatureRendererSettings;
+import jalview.gui.WebserviceInfo;
import jalview.util.MessageManager;
public abstract class AWSThread extends Thread
import jalview.util.MessageManager;
public abstract class AWSThread extends Thread
@@
-297,10
+297,11
@@
public abstract class AWSThread extends Thread
{
for (int i = 0; i < codonframe.length; i++)
{
{
for (int i = 0; i < codonframe.length; i++)
{
- if (codonframe[i] != null
- && codonframe[i].involvesSequence(alignment[sq]))
+ AlignedCodonFrame acf = codonframe[i];
+ final SequenceI seq = alignment[sq];
+ if (acf != null && acf.involvesSequence(seq))
{
{
- al.addCodonFrame(codonframe[i]);
+ al.addCodonFrame(new AlignedCodonFrame(acf, alignment));
codonframe[i] = null;
break;
}
codonframe[i] = null;
break;
}