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
Merge branch 'bug/JAL-2920_uniprotvariantfeature' into releases/Release_2_10_4_Branch
[jalview.git]
/
src
/
jalview
/
workers
/
ConsensusThread.java
diff --git
a/src/jalview/workers/ConsensusThread.java
b/src/jalview/workers/ConsensusThread.java
index
1cce3ff
..
335529c
100644
(file)
--- a/
src/jalview/workers/ConsensusThread.java
+++ b/
src/jalview/workers/ConsensusThread.java
@@
-28,7
+28,7
@@
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.ProfilesI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.Annotation;
import jalview.datamodel.ProfilesI;
import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
+import jalview.renderer.ResidueShaderI;
public class ConsensusThread extends AlignCalcWorker
{
public class ConsensusThread extends AlignCalcWorker
{
@@
-58,12
+58,13
@@
public class ConsensusThread extends AlignCalcWorker
}
while (!calcMan.notifyWorking(this))
{
}
while (!calcMan.notifyWorking(this))
{
- // System.err.println("Thread (Consensus"+Thread.currentThread().getName()+") Waiting around.");
+ // System.err.println("Thread
+ // (Consensus"+Thread.currentThread().getName()+") Waiting around.");
try
{
if (ap != null)
{
try
{
if (ap != null)
{
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
}
Thread.sleep(200);
} catch (Exception ex)
}
Thread.sleep(200);
} catch (Exception ex)
@@
-92,7
+93,7
@@
public class ConsensusThread extends AlignCalcWorker
if (ap != null)
{
if (ap != null)
{
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
} catch (OutOfMemoryError error)
{
}
} catch (OutOfMemoryError error)
{
@@
-153,11
+154,10
@@
public class ConsensusThread extends AlignCalcWorker
*/
protected void setColourSchemeConsensus(ProfilesI hconsensus)
{
*/
protected void setColourSchemeConsensus(ProfilesI hconsensus)
{
- ColourSchemeI globalColourScheme = alignViewport
- .getGlobalColourScheme();
- if (globalColourScheme != null)
+ ResidueShaderI cs = alignViewport.getResidueShading();
+ if (cs != null)
{
{
- globalColourScheme.setConsensus(hconsensus);
+ cs.setConsensus(hconsensus);
}
}
}
}