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JAL-2937 hmmbuild input data generated via AlignmentView from alignment, not directly...
author
Jim Procter
<jprocter@issues.jalview.org>
Fri, 1 Jun 2018 14:00:49 +0000
(15:00 +0100)
committer
Jim Procter
<jprocter@issues.jalview.org>
Fri, 1 Jun 2018 14:00:49 +0000
(15:00 +0100)
src/jalview/hmmer/HMMBuild.java
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diff --git
a/src/jalview/hmmer/HMMBuild.java
b/src/jalview/hmmer/HMMBuild.java
index
6de7029
..
6fcd6db
100644
(file)
--- a/
src/jalview/hmmer/HMMBuild.java
+++ b/
src/jalview/hmmer/HMMBuild.java
@@
-4,6
+4,7
@@
import jalview.api.AlignViewportI;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
@@
-105,24
+106,29
@@
public class HMMBuild extends HmmerCommand
{
foundArg = true;
String value = arg.getValue();
{
foundArg = true;
String value = arg.getValue();
+
if (MessageManager.getString("label.alignment").equals(value))
{
if (MessageManager.getString("label.alignment").equals(value))
{
- runBuildFor.add(alignment);
+ runBuildFor.add(viewport.getAlignmentView(false)
+ .getVisibleAlignment('-'));
}
else if (MessageManager.getString("label.groups_and_alignment")
.equals(value))
{
}
else if (MessageManager.getString("label.groups_and_alignment")
.equals(value))
{
- runBuildFor.add(alignment);
- runBuildFor.addAll(viewport.getAlignment().getGroups());
+ AlignmentView av = viewport.getAlignmentView(true);
+ runBuildFor.add(av.getVisibleAlignment('-'));
+ runBuildFor.addAll(av.getVisibleGroups('-'));
}
else if (MessageManager.getString("label.groups").equals(value))
{
}
else if (MessageManager.getString("label.groups").equals(value))
{
- runBuildFor.addAll(viewport.getAlignment().getGroups());
+ AlignmentView av = viewport.getAlignmentView(false);
+ runBuildFor.addAll(av.getVisibleGroups('-'));
}
else if (MessageManager.getString("label.selected_group")
.equals(value))
{
}
else if (MessageManager.getString("label.selected_group")
.equals(value))
{
- runBuildFor.add(viewport.getSelectionGroup());
+ AlignmentView av = viewport.getAlignmentView(true);
+ runBuildFor.add(av.getVisibleAlignment('-'));
}
}
else if (MessageManager.getString("label.use_reference")
}
}
else if (MessageManager.getString("label.use_reference")
@@
-183,7
+189,8
@@
public class HMMBuild extends HmmerCommand
else
{
SequenceI[] sel = ((SequenceGroup) ac)
else
{
SequenceI[] sel = ((SequenceGroup) ac)
- .getSelectionAsNewSequences((AlignmentI) ac.getContext());
+ .getSelectionAsNewSequences((AlignmentI) ac.getContext(),
+ false);
for (SequenceI seq : sel)
{
copy.add(seq);
for (SequenceI seq : sel)
{
copy.add(seq);