/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 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.
*
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
import java.util.ConcurrentModificationException;
import java.util.Hashtable;
}
@Override
- protected Hashtable[] getViewportConsensus()
+ protected Hashtable<String, Object>[] getViewportConsensus()
{
return alignViewport.getComplementConsensusHash();
}
@Override
protected void computeConsensus(AlignmentI alignment)
{
- Hashtable[] hconsensus = new Hashtable[alignment.getWidth()];
+ @SuppressWarnings("unchecked")
+ Hashtable<String, Object>[] hconsensus = new Hashtable[alignment
+ .getWidth()];
- SequenceI[] aseqs = getSequences();
+ // SequenceI[] aseqs = getSequences();
/*
* Allow 3 tries at this, since this thread can start up while we are still
* @param consensusData
* the computed consensus data
*/
- @Override
protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
- Hashtable[] consensusData)
+ Hashtable<String, Object>[] consensusData)
{
AAFrequency.completeCdnaConsensus(consensusAnnotation, consensusData,
alignViewport.isShowSequenceLogo(), getSequences().length);
}
+ @Override
+ public void updateResultAnnotation(boolean immediate)
+ {
+ AlignmentAnnotation consensus = getConsensusAnnotation();
+ Hashtable<String, Object>[] hconsensus = getViewportConsensus();
+ if (immediate || !calcMan.isWorking(this) && consensus != null
+ && hconsensus != null)
+ {
+ deriveConsensus(consensus, hconsensus);
+ }
+ }
+
}