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JAL-2788 possible adjustments to sequence accesses
[jalview.git]
/
src
/
jalview
/
workers
/
StrucConsensusThread.java
diff --git
a/src/jalview/workers/StrucConsensusThread.java
b/src/jalview/workers/StrucConsensusThread.java
index
72d26ff
..
61ec3d0
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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-20,10
+20,7
@@
*/
package jalview.workers;
*/
package jalview.workers;
-import java.util.Hashtable;
-
import jalview.analysis.StructureFrequency;
import jalview.analysis.StructureFrequency;
-import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
@@
-31,8
+28,9
@@
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceI;
import jalview.datamodel.Annotation;
import jalview.datamodel.SequenceI;
-public class StrucConsensusThread extends AlignCalcWorker implements
- AlignCalcWorkerI
+import java.util.Hashtable;
+
+public class StrucConsensusThread extends AlignCalcWorker
{
public StrucConsensusThread(AlignViewportI alignViewport,
AlignmentViewPanel alignPanel)
{
public StrucConsensusThread(AlignViewportI alignViewport,
AlignmentViewPanel alignPanel)
@@
-74,6
+72,7
@@
public class StrucConsensusThread extends AlignCalcWorker implements
if (alignViewport.isClosed())
{
abortAndDestroy();
if (alignViewport.isClosed())
{
abortAndDestroy();
+ return;
}
AlignmentI alignment = alignViewport.getAlignment();
}
AlignmentI alignment = alignViewport.getAlignment();
@@
-95,12
+94,15
@@
public class StrucConsensusThread extends AlignCalcWorker implements
.getAlignmentAnnotation();
AlignmentAnnotation rnaStruc = null;
// select rna struct to use for calculation
.getAlignmentAnnotation();
AlignmentAnnotation rnaStruc = null;
// select rna struct to use for calculation
- for (int i = 0; i < aa.length; i++)
+ if (aa != null)
{
{
- if (aa[i].getRNAStruc() != null && aa[i].isValidStruc())
+ for (int i = 0; i < aa.length; i++)
{
{
- rnaStruc = aa[i];
- break;
+ if (aa[i].visible && aa[i].isRNA() && aa[i].isValidStruc())
+ {
+ rnaStruc = aa[i];
+ break;
+ }
}
}
// check to see if its valid
}
}
// check to see if its valid
@@
-125,14
+127,9
@@
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)
{
} catch (OutOfMemoryError error)
{
- calcMan.workerCannotRun(this);
+ calcMan.disableWorker(this);
// consensus = null;
// hconsensus = null;
// consensus = null;
// hconsensus = null;
@@
-142,7
+139,7
@@
public class StrucConsensusThread extends AlignCalcWorker implements
calcMan.workerComplete(this);
if (ap != null)
{
calcMan.workerComplete(this);
if (ap != null)
{
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
}
}
}
@@
-165,7
+162,7
@@
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);
}
}