--- /dev/null
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.workers;
+
+import jalview.analysis.AAFrequency;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.ProfilesI;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.ResidueShaderI;
+
+public class SecondaryStructureConsensusThread extends AlignCalcWorker
+{
+ public SecondaryStructureConsensusThread(AlignViewportI alignViewport,
+ AlignmentViewPanel alignPanel)
+ {
+ super(alignViewport, alignPanel);
+ }
+
+ @Override
+ public void run()
+ {
+ if (calcMan.isPending(this))
+ {
+ return;
+ }
+ calcMan.notifyStart(this);
+ // long started = System.currentTimeMillis();
+ try
+ {
+ AlignmentAnnotation ssConsensus = getSSConsensusAnnotation();
+ AlignmentAnnotation gap = getGapAnnotation();
+ if ((ssConsensus == null && gap == null) || calcMan.isPending(this))
+ {
+ calcMan.workerComplete(this);
+ return;
+ }
+ while (!calcMan.notifyWorking(this))
+ {
+ try
+ {
+ if (ap != null)
+ {
+ ap.paintAlignment(false, false);
+ }
+ Thread.sleep(200);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ if (alignViewport.isClosed())
+ {
+ abortAndDestroy();
+ return;
+ }
+ AlignmentI alignment = alignViewport.getAlignment();
+
+ int aWidth = -1;
+
+ if (alignment == null || (aWidth = alignment.getWidth()) < 0)
+ {
+ calcMan.workerComplete(this);
+ return;
+ }
+
+ eraseSSConsensus(aWidth);
+ computeSSConsensus(alignment);
+ updateResultAnnotation(true);
+
+ if (ap != null)
+ {
+ ap.paintAlignment(true, true);
+ }
+ } catch (OutOfMemoryError error)
+ {
+ 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);
+ }
+ }
+
+ /**
+ * Clear out any existing consensus annotations
+ *
+ * @param aWidth
+ * the width (number of columns) of the annotated alignment
+ */
+ protected void eraseSSConsensus(int aWidth)
+ {
+ AlignmentAnnotation ssConsensus = getSSConsensusAnnotation();
+ if (ssConsensus != null)
+ {
+ ssConsensus.annotations = new Annotation[aWidth];
+ }
+ AlignmentAnnotation gap = getGapAnnotation();
+ if (gap != null)
+ {
+ gap.annotations = new Annotation[aWidth];
+ }
+ }
+
+ /**
+ * @param alignment
+ */
+ protected void computeSSConsensus(AlignmentI alignment)
+ {
+
+ SequenceI[] aseqs = getSequences();
+ int width = alignment.getWidth();
+ ProfilesI hSSConsensus = AAFrequency.calculateSS(aseqs, width, 0, width,
+ true);
+
+ alignViewport.setSequenceSSConsensusHash(hSSConsensus);
+ setColourSchemeConsensus(hSSConsensus);
+ }
+
+ /**
+ * @return
+ */
+ protected SequenceI[] getSequences()
+ {
+ return alignViewport.getAlignment().getSequencesArray();
+ }
+
+ /**
+ * @param hconsensus
+ */
+ protected void setColourSchemeConsensus(ProfilesI hSSconsensus)
+ {
+ ResidueShaderI cs = alignViewport.getResidueShading();
+ if (cs != null)
+ {
+ cs.setSsConsensus(hSSconsensus);
+ }
+ }
+
+ /**
+ * Get the Consensus annotation for the alignment
+ *
+ * @return
+ */
+ protected AlignmentAnnotation getSSConsensusAnnotation()
+ {
+ return alignViewport.getAlignmentSecondaryStructureConsensusAnnotation();
+ }
+
+ /**
+ * 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.
+ */
+ @Override
+ public void updateAnnotation()
+ {
+ updateResultAnnotation(false);
+ }
+
+ public void updateResultAnnotation(boolean immediate)
+ {
+ AlignmentAnnotation ssConsensus = getSSConsensusAnnotation();
+ ProfilesI hSSConsensus = (ProfilesI) getViewportSSConsensus();
+ if (immediate || !calcMan.isWorking(this) && ssConsensus != null
+ && hSSConsensus != null)
+ {
+ deriveSSConsensus(ssConsensus, hSSConsensus);
+ AlignmentAnnotation gap = getGapAnnotation();
+ if (gap != null)
+ {
+ deriveGap(gap, hSSConsensus);
+ }
+ }
+ }
+
+ /**
+ * 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 deriveSSConsensus(AlignmentAnnotation ssConsensusAnnotation,
+ ProfilesI hSSConsensus)
+ {
+
+ long nseq = getSequences().length;
+ AAFrequency.completeSSConsensus(ssConsensusAnnotation, hSSConsensus,
+ hSSConsensus.getStartColumn(), hSSConsensus.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 getViewportSSConsensus()
+ {
+ // TODO convert ComplementConsensusThread to use Profile
+ return alignViewport.getSequenceSSConsensusHash();
+ }
+}
git://source.jalview.org / jalview.git / blobdiff