X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fworkers%2FStrucConsensusThread.java;h=61ec3d09b119e13cba7fa3b9ba107c52894df567;hb=a9177efb4097815d9a8031aa22700c61a7d6260a;hp=86c33365271338885f94f896d225d86facdd9652;hpb=3e7ebcfda0bc54b3b91905e21835142bfd1fe8a0;p=jalview.git
diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java
index 86c3336..61ec3d0 100644
--- a/src/jalview/workers/StrucConsensusThread.java
+++ b/src/jalview/workers/StrucConsensusThread.java
@@ -1,34 +1,36 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.workers;
-import java.util.Hashtable;
-
import jalview.analysis.StructureFrequency;
-import jalview.api.AlignCalcWorkerI;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+
+import java.util.Hashtable;
-public class StrucConsensusThread extends AlignCalcWorker implements
- AlignCalcWorkerI
+public class StrucConsensusThread extends AlignCalcWorker
{
public StrucConsensusThread(AlignViewportI alignViewport,
AlignmentViewPanel alignPanel)
@@ -40,6 +42,8 @@ public class StrucConsensusThread extends AlignCalcWorker implements
Hashtable[] hStrucConsensus;
+ private long nseq = -1;
+
@Override
public void run()
{
@@ -68,6 +72,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements
if (alignViewport.isClosed())
{
abortAndDestroy();
+ return;
}
AlignmentI alignment = alignViewport.getAlignment();
@@ -89,12 +94,15 @@ public class StrucConsensusThread extends AlignCalcWorker implements
.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
@@ -107,9 +115,10 @@ public class StrucConsensusThread extends AlignCalcWorker implements
try
{
- jalview.analysis.StructureFrequency.calculate(
- alignment.getSequencesArray(), 0, alignment.getWidth(),
- hStrucConsensus, true, rnaStruc);
+ final SequenceI[] arr = alignment.getSequencesArray();
+ nseq = arr.length;
+ jalview.analysis.StructureFrequency.calculate(arr, 0,
+ alignment.getWidth(), hStrucConsensus, true, rnaStruc);
} catch (ArrayIndexOutOfBoundsException x)
{
calcMan.workerComplete(this);
@@ -118,14 +127,9 @@ public class StrucConsensusThread extends AlignCalcWorker implements
alignViewport.setRnaStructureConsensusHash(hStrucConsensus);
// TODO AlignmentAnnotation rnaStruc!!!
updateResultAnnotation(true);
- if (alignViewport.getGlobalColourScheme() != null)
- {
- alignViewport.getGlobalColourScheme().setConsensus(hStrucConsensus);
- }
-
} catch (OutOfMemoryError error)
{
- calcMan.workerCannotRun(this);
+ calcMan.disableWorker(this);
// consensus = null;
// hconsensus = null;
@@ -135,7 +139,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements
calcMan.workerComplete(this);
if (ap != null)
{
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
}
@@ -158,8 +162,8 @@ public class StrucConsensusThread extends AlignCalcWorker implements
{
StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
0, hStrucConsensus.length,
- alignViewport.getIgnoreGapsConsensus(),
- alignViewport.isShowSequenceLogo());
+ alignViewport.isIgnoreGapsConsensus(),
+ alignViewport.isShowSequenceLogo(), nseq);
}
}