+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.workers;
-import java.util.Hashtable;
-
-import jalview.analysis.AAFrequency;
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)
{
super(alignViewport, alignPanel);
}
+
+ AlignmentAnnotation strucConsensus;
+
+ Hashtable[] hStrucConsensus;
+
+ private long nseq = -1;
+
+ @Override
public void run()
{
try
{
+ if (calcMan.isPending(this))
+ {
+ return;
+ }
calcMan.notifyStart(this);
while (!calcMan.notifyWorking(this))
{
{
if (ap != null)
{
- ap.paintAlignment(false);
+ // ap.paintAlignment(false);
}
Thread.sleep(200);
if (alignViewport.isClosed())
{
abortAndDestroy();
+ return;
}
AlignmentI alignment = alignViewport.getAlignment();
calcMan.workerComplete(this);
return;
}
- AlignmentAnnotation strucConsensus=alignViewport.getAlignmentStrucConsensusAnnotation();
- Hashtable[] hStrucConsensus=alignViewport.getRnaStructureConsensusHash();
+ strucConsensus = alignViewport.getAlignmentStrucConsensusAnnotation();
+ hStrucConsensus = alignViewport.getRnaStructureConsensusHash();
strucConsensus.annotations = null;
strucConsensus.annotations = new Annotation[aWidth];
.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)
+ 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
-
- if (rnaStruc==null || !rnaStruc.isValidStruc())
+
+ if (rnaStruc == null || !rnaStruc.isValidStruc())
+ {
+ calcMan.workerComplete(this);
+ return;
+ }
+
+ try
+ {
+ 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);
return;
}
-
- jalview.analysis.StructureFrequency.calculate(alignment.getSequencesArray(), 0,
- alignment.getWidth(), hStrucConsensus, true, rnaStruc);
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;
ap.raiseOOMWarning("calculating RNA structure consensus", error);
- }
-
- calcMan.workerComplete(this);
- if (ap != null)
+ } finally
{
- ap.paintAlignment(true);
+ calcMan.workerComplete(this);
+ if (ap != null)
+ {
+ ap.paintAlignment(true);
+ }
}
}
+
/**
* update the consensus annotation from the sequence profile data using
* current visualization settings.
*/
+ @Override
public void updateAnnotation()
{
updateResultAnnotation(false);
public void updateResultAnnotation(boolean immediate)
{
- AlignmentAnnotation strucConsensus = alignViewport
- .getAlignmentStrucConsensusAnnotation();
- Hashtable[] hStrucConsensus = alignViewport.getRnaStructureConsensusHash();
- if (immediate || !calcMan.isWorking(this) && strucConsensus!=null && hStrucConsensus!=null)
+ if (immediate || !calcMan.isWorking(this) && strucConsensus != null
+ && hStrucConsensus != null)
{
- StructureFrequency.completeConsensus(strucConsensus,
- hStrucConsensus, 0, hStrucConsensus.length,
- alignViewport.getIgnoreGapsConsensus(),
- alignViewport.isShowSequenceLogo());
+ StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
+ 0, hStrucConsensus.length,
+ alignViewport.isIgnoreGapsConsensus(),
+ alignViewport.isShowSequenceLogo(), nseq);
}
}
-}
\ No newline at end of file
+}