X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FComplementConsensusThread.java;h=aca8ed0354492fc3fdcbe5ad080b74506c4e49a3;hb=bc1a3842b31a35a7794f4afec4911ad421c7c3e4;hp=2e4424e31d905af47554cf222f3538bb324a85c7;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git
diff --git a/src/jalview/workers/ComplementConsensusThread.java b/src/jalview/workers/ComplementConsensusThread.java
index 2e4424e..aca8ed0 100644
--- a/src/jalview/workers/ComplementConsensusThread.java
+++ b/src/jalview/workers/ComplementConsensusThread.java
@@ -1,13 +1,33 @@
+/*
+ * 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.
+ *
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.workers;
-import java.util.Hashtable;
-
import jalview.analysis.AAFrequency;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
+
+import java.util.ConcurrentModificationException;
+import java.util.Hashtable;
/**
* A thread to recompute the consensus of the cDNA complement for a linked
@@ -32,18 +52,38 @@ public class ComplementConsensusThread extends ConsensusThread
}
@Override
- protected Hashtable[] getViewportConsensus()
+ protected Hashtable[] getViewportConsensus()
{
return alignViewport.getComplementConsensusHash();
}
+ /**
+ * Calculate the cDNA consensus and store it on the Viewport
+ */
@Override
protected void computeConsensus(AlignmentI alignment)
{
- Hashtable[] hconsensus = new Hashtable[alignment.getWidth()];
+ @SuppressWarnings("unchecked")
+ Hashtable[] hconsensus = new Hashtable[alignment
+ .getWidth()];
- SequenceI[] aseqs = getSequences();
- AAFrequency.calculateCdna(alignment, hconsensus);
+ // SequenceI[] aseqs = getSequences();
+
+ /*
+ * Allow 3 tries at this, since this thread can start up while we are still
+ * modifying protein-codon mappings on the alignment
+ */
+ for (int i = 0; i < 3; i++)
+ {
+ try
+ {
+ AAFrequency.calculateCdna(alignment, hconsensus);
+ break;
+ } catch (ConcurrentModificationException e)
+ {
+ // try again
+ }
+ }
alignViewport.setComplementConsensusHash(hconsensus);
}
@@ -57,12 +97,23 @@ public class ComplementConsensusThread extends ConsensusThread
* @param consensusData
* the computed consensus data
*/
- @Override
protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
- Hashtable[] consensusData)
+ Hashtable[] consensusData)
{
AAFrequency.completeCdnaConsensus(consensusAnnotation, consensusData,
alignViewport.isShowSequenceLogo(), getSequences().length);
}
+ @Override
+ public void updateResultAnnotation(boolean immediate)
+ {
+ AlignmentAnnotation consensus = getConsensusAnnotation();
+ Hashtable[] hconsensus = getViewportConsensus();
+ if (immediate || !calcMan.isWorking(this) && consensus != null
+ && hconsensus != null)
+ {
+ deriveConsensus(consensus, hconsensus);
+ }
+ }
+
}