+ cs.setConservationApplied(recalc = getConservationSelected());
+ if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
+ || cs instanceof Blosum62ColourScheme)
+ {
+ recalc = true;
+ cs.setThreshold(viewStyle.getThreshold(),
+ ignoreGapsInConsensusCalculation);
+ }
+ else
+ {
+ cs.setThreshold(0, ignoreGapsInConsensusCalculation);
+ }
+ if (recalc)
+ {
+ cs.setConsensus(hconsensus);
+ cs.setConservation(hconservation);
+ }
+ cs.alignmentChanged(alignment, hiddenRepSequences);
+ }
+ if (getColourAppliesToAllGroups())
+ {
+ for (SequenceGroup sg : getAlignment().getGroups())
+ {
+ if (cs == null)
+ {
+ sg.cs = null;
+ continue;
+ }
+ sg.cs = cs.applyTo(sg, getHiddenRepSequences());
+ sg.setConsPercGaps(ConsPercGaps);
+ if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
+ || cs instanceof Blosum62ColourScheme)
+ {
+ sg.cs.setThreshold(viewStyle.getThreshold(),
+ isIgnoreGapsConsensus());
+ recalc = true;
+ }
+ else
+ {
+ sg.cs.setThreshold(0, isIgnoreGapsConsensus());
+ }
+
+ if (getConservationSelected())
+ {
+ sg.cs.setConservationApplied(true);
+ recalc = true;
+ }
+ else
+ {
+ sg.cs.setConservation(null);
+ // sg.cs.setThreshold(0, getIgnoreGapsConsensus());
+ }
+ if (recalc)
+ {
+ sg.recalcConservation();
+ }
+ else
+ {
+ sg.cs.alignmentChanged(sg, hiddenRepSequences);
+ }
+ }
+ }
+ }
+
+ @Override
+ public ColourSchemeI getGlobalColourScheme()
+ {
+ return globalColourScheme;
+ }
+
+ protected AlignmentAnnotation consensus;
+
+ protected AlignmentAnnotation complementConsensus;
+
+ protected AlignmentAnnotation strucConsensus;
+
+ protected AlignmentAnnotation conservation;
+
+ protected AlignmentAnnotation quality;
+
+ protected AlignmentAnnotation[] groupConsensus;
+
+ protected AlignmentAnnotation[] groupConservation;
+
+ /**
+ * results of alignment consensus analysis for visible portion of view
+ */
+ protected Hashtable[] hconsensus = null;
+
+ /**
+ * results of cDNA complement consensus visible portion of view
+ */
+ protected Hashtable[] hcomplementConsensus = null;
+
+ /**
+ * results of secondary structure base pair consensus for visible portion of
+ * view
+ */
+ protected Hashtable[] hStrucConsensus = null;
+
+ protected Conservation hconservation = null;
+
+ @Override
+ public void setConservation(Conservation cons)
+ {
+ hconservation = cons;
+ }
+
+ /**
+ * percentage gaps allowed in a column before all amino acid properties should
+ * be considered unconserved
+ */
+ int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
+
+ @Override
+ public int getConsPercGaps()
+ {
+ return ConsPercGaps;
+ }
+
+ @Override
+ public void setSequenceConsensusHash(Hashtable[] hconsensus)
+ {
+ this.hconsensus = hconsensus;
+ }
+
+ @Override
+ public void setComplementConsensusHash(Hashtable[] hconsensus)
+ {
+ this.hcomplementConsensus = hconsensus;
+ }
+
+ @Override
+ public Hashtable[] getSequenceConsensusHash()
+ {
+ return hconsensus;
+ }
+
+ @Override
+ public Hashtable[] getComplementConsensusHash()
+ {
+ return hcomplementConsensus;
+ }
+
+ @Override
+ public Hashtable[] getRnaStructureConsensusHash()
+ {
+ return hStrucConsensus;
+ }
+
+ @Override
+ public void setRnaStructureConsensusHash(Hashtable[] hStrucConsensus)
+ {
+ this.hStrucConsensus = hStrucConsensus;
+
+ }
+
+ @Override
+ public AlignmentAnnotation getAlignmentQualityAnnot()
+ {
+ return quality;
+ }
+
+ @Override
+ public AlignmentAnnotation getAlignmentConservationAnnotation()
+ {
+ return conservation;
+ }
+
+ @Override
+ public AlignmentAnnotation getAlignmentConsensusAnnotation()
+ {
+ return consensus;
+ }
+
+ @Override
+ public AlignmentAnnotation getComplementConsensusAnnotation()
+ {
+ return complementConsensus;
+ }
+
+ @Override
+ public AlignmentAnnotation getAlignmentStrucConsensusAnnotation()
+ {
+ return strucConsensus;
+ }
+
+ protected AlignCalcManagerI calculator = new AlignCalcManager();
+
+ /**
+ * trigger update of conservation annotation
+ */
+ public void updateConservation(final AlignmentViewPanel ap)
+ {
+ // see note in mantis : issue number 8585
+ if (alignment.isNucleotide() || conservation == null
+ || !autoCalculateConsensus)
+ {
+ return;
+ }
+ if (calculator
+ .getRegisteredWorkersOfClass(jalview.workers.ConservationThread.class) == null)
+ {
+ calculator.registerWorker(new jalview.workers.ConservationThread(
+ this, ap));
+ }
+ }
+
+ /**
+ * trigger update of consensus annotation
+ */
+ public void updateConsensus(final AlignmentViewPanel ap)
+ {
+ // see note in mantis : issue number 8585
+ if (consensus == null || !autoCalculateConsensus)
+ {
+ return;
+ }
+ if (calculator.getRegisteredWorkersOfClass(ConsensusThread.class) == null)
+ {
+ calculator.registerWorker(new ConsensusThread(this, ap));
+ }
+
+ /*
+ * A separate thread to compute cDNA consensus for a protein alignment
+ */
+ final AlignmentI al = this.getAlignment();
+ if (!al.isNucleotide() && al.getCodonFrames() != null
+ && !al.getCodonFrames().isEmpty())
+ {
+ if (calculator
+ .getRegisteredWorkersOfClass(ComplementConsensusThread.class) == null)
+ {
+ calculator.registerWorker(new ComplementConsensusThread(this, ap));
+ }
+ }
+ }
+
+ // --------START Structure Conservation
+ public void updateStrucConsensus(final AlignmentViewPanel ap)
+ {
+ if (autoCalculateStrucConsensus && strucConsensus == null
+ && alignment.isNucleotide() && alignment.hasRNAStructure())
+ {
+ // secondary structure has been added - so init the consensus line
+ initRNAStructure();
+ }
+
+ // see note in mantis : issue number 8585
+ if (strucConsensus == null || !autoCalculateStrucConsensus)
+ {
+ return;
+ }
+ if (calculator.getRegisteredWorkersOfClass(StrucConsensusThread.class) == null)
+ {
+ calculator.registerWorker(new StrucConsensusThread(this, ap));
+ }
+ }
+
+ public boolean isCalcInProgress()
+ {
+ return calculator.isWorking();
+ }
+
+ @Override
+ public boolean isCalculationInProgress(
+ AlignmentAnnotation alignmentAnnotation)
+ {
+ if (!alignmentAnnotation.autoCalculated)
+ {
+ return false;
+ }
+ if (calculator.workingInvolvedWith(alignmentAnnotation))
+ {
+ // System.err.println("grey out ("+alignmentAnnotation.label+")");
+ return true;
+ }
+ return false;
+ }
+
+ @Override
+ public boolean isClosed()
+ {
+ // TODO: check that this isClosed is only true after panel is closed, not
+ // before it is fully constructed.
+ return alignment == null;
+ }
+
+ @Override
+ public AlignCalcManagerI getCalcManager()
+ {
+ return calculator;
+ }
+
+ /**
+ * should conservation rows be shown for groups
+ */
+ protected boolean showGroupConservation = false;
+
+ /**
+ * should consensus rows be shown for groups
+ */
+ protected boolean showGroupConsensus = false;
+
+ /**
+ * should consensus profile be rendered by default
+ */
+ protected boolean showSequenceLogo = false;
+
+ /**
+ * should consensus profile be rendered normalised to row height
+ */
+ protected boolean normaliseSequenceLogo = false;
+
+ /**
+ * should consensus histograms be rendered by default
+ */
+ protected boolean showConsensusHistogram = true;
+
+ /**
+ * @return the showConsensusProfile
+ */
+ @Override
+ public boolean isShowSequenceLogo()
+ {
+ return showSequenceLogo;
+ }
+
+ /**
+ * @param showSequenceLogo
+ * the new value
+ */
+ public void setShowSequenceLogo(boolean showSequenceLogo)
+ {
+ if (showSequenceLogo != this.showSequenceLogo)
+ {
+ // TODO: decouple settings setting from calculation when refactoring
+ // annotation update method from alignframe to viewport
+ this.showSequenceLogo = showSequenceLogo;
+ calculator.updateAnnotationFor(ConsensusThread.class);
+ calculator.updateAnnotationFor(ComplementConsensusThread.class);
+ calculator.updateAnnotationFor(StrucConsensusThread.class);
+ }
+ this.showSequenceLogo = showSequenceLogo;
+ }
+
+ /**
+ * @param showConsensusHistogram
+ * the showConsensusHistogram to set
+ */
+ public void setShowConsensusHistogram(boolean showConsensusHistogram)
+ {
+ this.showConsensusHistogram = showConsensusHistogram;
+ }
+
+ /**
+ * @return the showGroupConservation
+ */
+ public boolean isShowGroupConservation()
+ {
+ return showGroupConservation;
+ }
+
+ /**
+ * @param showGroupConservation
+ * the showGroupConservation to set
+ */
+ public void setShowGroupConservation(boolean showGroupConservation)
+ {
+ this.showGroupConservation = showGroupConservation;
+ }
+
+ /**
+ * @return the showGroupConsensus
+ */
+ public boolean isShowGroupConsensus()
+ {
+ return showGroupConsensus;
+ }
+
+ /**
+ * @param showGroupConsensus
+ * the showGroupConsensus to set
+ */
+ public void setShowGroupConsensus(boolean showGroupConsensus)
+ {
+ this.showGroupConsensus = showGroupConsensus;
+ }
+
+ /**
+ *
+ * @return flag to indicate if the consensus histogram should be rendered by
+ * default
+ */
+ @Override
+ public boolean isShowConsensusHistogram()
+ {
+ return this.showConsensusHistogram;
+ }
+
+ /**
+ * when set, updateAlignment will always ensure sequences are of equal length
+ */
+ private boolean padGaps = false;
+
+ /**
+ * when set, alignment should be reordered according to a newly opened tree
+ */
+ public boolean sortByTree = false;
+
+ /**
+ *
+ *
+ * @return null or the currently selected sequence region
+ */
+ @Override
+ public SequenceGroup getSelectionGroup()
+ {
+ return selectionGroup;
+ }
+
+ /**
+ * Set the selection group for this window.
+ *
+ * @param sg
+ * - group holding references to sequences in this alignment view
+ *
+ */
+ @Override
+ public void setSelectionGroup(SequenceGroup sg)
+ {
+ selectionGroup = sg;
+ }
+
+ public void setHiddenColumns(ColumnSelection colsel)
+ {
+ this.colSel = colsel;
+ }
+
+ @Override
+ public ColumnSelection getColumnSelection()
+ {
+ return colSel;
+ }
+
+ @Override
+ public void setColumnSelection(ColumnSelection colSel)
+ {
+ this.colSel = colSel;
+ if (colSel != null)
+ {
+ updateHiddenColumns();
+ }
+ }
+
+ /**
+ *
+ * @return
+ */
+ @Override
+ public Map<SequenceI, SequenceCollectionI> getHiddenRepSequences()
+ {
+ return hiddenRepSequences;
+ }
+
+ @Override
+ public void setHiddenRepSequences(
+ Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ {
+ this.hiddenRepSequences = hiddenRepSequences;
+ }
+
+ @Override
+ public boolean hasHiddenColumns()
+ {
+ return colSel != null && colSel.hasHiddenColumns();
+ }
+
+ public void updateHiddenColumns()
+ {
+ // this method doesn't really do anything now. But - it could, since a
+ // column Selection could be in the process of modification
+ // hasHiddenColumns = colSel.hasHiddenColumns();
+ }
+
+ @Override
+ public boolean hasHiddenRows()
+ {
+ return alignment.getHiddenSequences().getSize() > 0;
+ }
+
+ protected SequenceGroup selectionGroup;
+
+ public void setSequenceSetId(String newid)
+ {
+ if (sequenceSetID != null)
+ {
+ System.err
+ .println("Warning - overwriting a sequenceSetId for a viewport!");
+ }
+ sequenceSetID = new String(newid);
+ }
+
+ @Override
+ public String getSequenceSetId()
+ {
+ if (sequenceSetID == null)
+ {
+ sequenceSetID = alignment.hashCode() + "";
+ }
+
+ return sequenceSetID;
+ }
+
+ /**
+ * unique viewId for synchronizing state (e.g. with stored Jalview Project)
+ *
+ */
+ protected String viewId = null;
+
+ @Override
+ public String getViewId()
+ {
+ if (viewId == null)
+ {
+ viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
+ }