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JAL-1925 update source version in license
[jalview.git]
/
src
/
jalview
/
workers
/
StrucConsensusThread.java
diff --git
a/src/jalview/workers/StrucConsensusThread.java
b/src/jalview/workers/StrucConsensusThread.java
index
72d26ff
..
9694b37
100644
(file)
--- a/
src/jalview/workers/StrucConsensusThread.java
+++ b/
src/jalview/workers/StrucConsensusThread.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-20,8
+20,6
@@
*/
package jalview.workers;
*/
package jalview.workers;
-import java.util.Hashtable;
-
import jalview.analysis.StructureFrequency;
import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
import jalview.analysis.StructureFrequency;
import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
@@
-31,6
+29,8
@@
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceI;
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceI;
+import java.util.Hashtable;
+
public class StrucConsensusThread extends AlignCalcWorker implements
AlignCalcWorkerI
{
public class StrucConsensusThread extends AlignCalcWorker implements
AlignCalcWorkerI
{
@@
-74,6
+74,7
@@
public class StrucConsensusThread extends AlignCalcWorker implements
if (alignViewport.isClosed())
{
abortAndDestroy();
if (alignViewport.isClosed())
{
abortAndDestroy();
+ return;
}
AlignmentI alignment = alignViewport.getAlignment();
}
AlignmentI alignment = alignViewport.getAlignment();
@@
-97,7
+98,7
@@
public class StrucConsensusThread extends AlignCalcWorker implements
// select rna struct to use for calculation
for (int i = 0; i < aa.length; i++)
{
// select rna struct to use for calculation
for (int i = 0; i < aa.length; i++)
{
- if (aa[i].getRNAStruc() != null && aa[i].isValidStruc())
+ if (aa[i].visible && aa[i].isRNA() && aa[i].isValidStruc())
{
rnaStruc = aa[i];
break;
{
rnaStruc = aa[i];
break;
@@
-125,11
+126,6
@@
public class StrucConsensusThread extends AlignCalcWorker implements
alignViewport.setRnaStructureConsensusHash(hStrucConsensus);
// TODO AlignmentAnnotation rnaStruc!!!
updateResultAnnotation(true);
alignViewport.setRnaStructureConsensusHash(hStrucConsensus);
// TODO AlignmentAnnotation rnaStruc!!!
updateResultAnnotation(true);
- if (alignViewport.getGlobalColourScheme() != null)
- {
- alignViewport.getGlobalColourScheme().setConsensus(hStrucConsensus);
- }
-
} catch (OutOfMemoryError error)
{
calcMan.workerCannotRun(this);
} catch (OutOfMemoryError error)
{
calcMan.workerCannotRun(this);
@@
-165,7
+161,7
@@
public class StrucConsensusThread extends AlignCalcWorker implements
{
StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
0, hStrucConsensus.length,
{
StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
0, hStrucConsensus.length,
- alignViewport.getIgnoreGapsConsensus(),
+ alignViewport.isIgnoreGapsConsensus(),
alignViewport.isShowSequenceLogo(), nseq);
}
}
alignViewport.isShowSequenceLogo(), nseq);
}
}