/*
- * 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 <http://www.gnu.org/licenses/>.
+ * 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 jalview.analysis.AAFrequency;
-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.schemes.ColourSchemeI;
+import jalview.datamodel.ProfilesI;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.ResidueShaderI;
-import java.util.Hashtable;
-
-public class ConsensusThread extends AlignCalcWorker implements
- AlignCalcWorkerI
+public class ConsensusThread extends AlignCalcWorker
{
public ConsensusThread(AlignViewportI alignViewport,
AlignmentViewPanel alignPanel)
long started = System.currentTimeMillis();
try
{
- AlignmentAnnotation consensus = alignViewport
- .getAlignmentConsensusAnnotation();
- if (consensus == null || calcMan.isPending(this))
+ AlignmentAnnotation consensus = getConsensusAnnotation();
+ AlignmentAnnotation gap = getGapAnnotation();
+ if ((consensus == null && gap == null) || calcMan.isPending(this))
{
calcMan.workerComplete(this);
return;
}
while (!calcMan.notifyWorking(this))
{
- // System.err.println("Thread (Consensus"+Thread.currentThread().getName()+") Waiting around.");
+ // System.err.println("Thread
+ // (Consensus"+Thread.currentThread().getName()+") Waiting around.");
try
{
if (ap != null)
{
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
}
Thread.sleep(200);
} catch (Exception ex)
if (alignViewport.isClosed())
{
abortAndDestroy();
+ return;
}
AlignmentI alignment = alignViewport.getAlignment();
if (alignment == null || (aWidth = alignment.getWidth()) < 0)
{
calcMan.workerComplete(this);
- // .updatingConservation = false;
- // AlignViewport.UPDATING_CONSERVATION = false;
-
return;
}
- consensus = alignViewport.getAlignmentConsensusAnnotation();
- consensus.annotations = null;
- consensus.annotations = new Annotation[aWidth];
- Hashtable[] hconsensus = alignViewport.getSequenceConsensusHash();
- hconsensus = new Hashtable[aWidth];
- try
- {
- AAFrequency.calculate(alignment.getSequencesArray(), 0,
- alignment.getWidth(), hconsensus, true);
- } catch (ArrayIndexOutOfBoundsException x)
- {
- // this happens due to a race condition -
- // alignment was edited at same time as calculation was running
- //
- // calcMan.workerCannotRun(this);
- calcMan.workerComplete(this);
- return;
- }
- alignViewport.setSequenceConsensusHash(hconsensus);
+ eraseConsensus(aWidth);
+ computeConsensus(alignment);
updateResultAnnotation(true);
- ColourSchemeI globalColourScheme = alignViewport
- .getGlobalColourScheme();
- if (globalColourScheme != null)
+
+ if (ap != null)
{
- globalColourScheme.setConsensus(hconsensus);
+ ap.paintAlignment(true, true);
}
-
} catch (OutOfMemoryError error)
{
- calcMan.workerCannotRun(this);
-
- // consensus = null;
- // hconsensus = null;
+ calcMan.disableWorker(this);
ap.raiseOOMWarning("calculating consensus", error);
+ } finally
+ {
+ /*
+ * e.g. ArrayIndexOutOfBoundsException can happen due to a race condition
+ * - alignment was edited at same time as calculation was running
+ */
+ calcMan.workerComplete(this);
}
+ }
- calcMan.workerComplete(this);
- if (ap != null)
+ /**
+ * Clear out any existing consensus annotations
+ *
+ * @param aWidth
+ * the width (number of columns) of the annotated alignment
+ */
+ protected void eraseConsensus(int aWidth)
+ {
+ AlignmentAnnotation consensus = getConsensusAnnotation();
+ if (consensus != null)
{
- ap.paintAlignment(true);
+ consensus.annotations = new Annotation[aWidth];
+ }
+ AlignmentAnnotation gap = getGapAnnotation();
+ if (gap != null)
+ {
+ gap.annotations = new Annotation[aWidth];
}
}
/**
+ * @param alignment
+ */
+ protected void computeConsensus(AlignmentI alignment)
+ {
+
+ SequenceI[] aseqs = getSequences();
+ int width = alignment.getWidth();
+ ProfilesI hconsensus = AAFrequency.calculate(aseqs, width, 0, width,
+ true);
+
+ alignViewport.setSequenceConsensusHash(hconsensus);
+ setColourSchemeConsensus(hconsensus);
+ }
+
+ /**
+ * @return
+ */
+ protected SequenceI[] getSequences()
+ {
+ return alignViewport.getAlignment().getSequencesArray();
+ }
+
+ /**
+ * @param hconsensus
+ */
+ protected void setColourSchemeConsensus(ProfilesI hconsensus)
+ {
+ ResidueShaderI cs = alignViewport.getResidueShading();
+ if (cs != null)
+ {
+ cs.setConsensus(hconsensus);
+ }
+ }
+
+ /**
+ * Get the Consensus annotation for the alignment
+ *
+ * @return
+ */
+ protected AlignmentAnnotation getConsensusAnnotation()
+ {
+ return alignViewport.getAlignmentConsensusAnnotation();
+ }
+
+ /**
+ * Get the Gap annotation for the alignment
+ *
+ * @return
+ */
+ protected AlignmentAnnotation getGapAnnotation()
+ {
+ return alignViewport.getAlignmentGapAnnotation();
+ }
+
+ /**
* update the consensus annotation from the sequence profile data using
* current visualization settings.
*/
public void updateResultAnnotation(boolean immediate)
{
- AlignmentAnnotation consensus = alignViewport
- .getAlignmentConsensusAnnotation();
- Hashtable[] hconsensus = alignViewport.getSequenceConsensusHash();
+ AlignmentAnnotation consensus = getConsensusAnnotation();
+ ProfilesI hconsensus = (ProfilesI) getViewportConsensus();
if (immediate || !calcMan.isWorking(this) && consensus != null
&& hconsensus != null)
{
- AAFrequency.completeConsensus(consensus, hconsensus, 0,
- hconsensus.length, alignViewport.getIgnoreGapsConsensus(),
- alignViewport.isShowSequenceLogo());
+ deriveConsensus(consensus, hconsensus);
+ AlignmentAnnotation gap = getGapAnnotation();
+ if (gap != null)
+ {
+ deriveGap(gap, hconsensus);
+ }
}
}
+
+ /**
+ * Convert the computed consensus data into the desired annotation for
+ * display.
+ *
+ * @param consensusAnnotation
+ * the annotation to be populated
+ * @param hconsensus
+ * the computed consensus data
+ */
+ protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
+ ProfilesI hconsensus)
+ {
+
+ long nseq = getSequences().length;
+ AAFrequency.completeConsensus(consensusAnnotation, hconsensus,
+ hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
+ alignViewport.isIgnoreGapsConsensus(),
+ alignViewport.isShowSequenceLogo(), nseq);
+ }
+
+ /**
+ * Convert the computed consensus data into a gap annotation row for display.
+ *
+ * @param gapAnnotation
+ * the annotation to be populated
+ * @param hconsensus
+ * the computed consensus data
+ */
+ protected void deriveGap(AlignmentAnnotation gapAnnotation,
+ ProfilesI hconsensus)
+ {
+ long nseq = getSequences().length;
+ AAFrequency.completeGapAnnot(gapAnnotation, hconsensus,
+ hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
+ nseq);
+ }
+
+ /**
+ * Get the consensus data stored on the viewport.
+ *
+ * @return
+ */
+ protected Object getViewportConsensus()
+ {
+ // TODO convert ComplementConsensusThread to use Profile
+ return alignViewport.getSequenceConsensusHash();
+ }
}
git://source.jalview.org / jalview.git / blobdiff