git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-4366 JAL-728 simple hack to use 3di matrix when gecos-3di is enabled
[jalview.git]
/
src
/
jalview
/
workers
/
ConservationThread.java
diff --git
a/src/jalview/workers/ConservationThread.java
b/src/jalview/workers/ConservationThread.java
index
54b0191
..
0afa711
100644
(file)
--- a/
src/jalview/workers/ConservationThread.java
+++ b/
src/jalview/workers/ConservationThread.java
@@
-21,6
+21,7
@@
package jalview.workers;
import jalview.analysis.Conservation;
package jalview.workers;
import jalview.analysis.Conservation;
+import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
@@
-95,9
+96,10
@@
public class ConservationThread extends AlignCalcWorker
}
try
{
}
try
{
+ // TODO - TDI is there a conservation measure ?
cons = Conservation.calculateConservation("All",
alignment.getSequences(), 0, alWidth - 1, false,
cons = Conservation.calculateConservation("All",
alignment.getSequences(), 0, alWidth - 1, false,
- ConsPercGaps, quality != null);
+ ConsPercGaps, quality != null, alignViewport.is3di() ? ScoreModels.getInstance().getFOLDSEEK3DI():ScoreModels.getInstance().getDefaultModel(true));
} catch (IndexOutOfBoundsException x)
{
// probable race condition. just finish and return without any fuss.
} catch (IndexOutOfBoundsException x)
{
// probable race condition. just finish and return without any fuss.