+ public Color getSequenceColour(SequenceI seq)
+ {
+ if (sequenceColours == null || !sequenceColours.containsKey(seq))
+ {
+ return Color.white;
+ }
+ else
+ {
+ return (Color) sequenceColours.get(seq);
+ }
+ }
+
+ public void setSequenceColour(SequenceI seq, Color col)
+ {
+ if (sequenceColours == null)
+ {
+ sequenceColours = new Hashtable();
+ }
+
+ if (col == null)
+ {
+ sequenceColours.remove(seq);
+ }
+ else
+ {
+ sequenceColours.put(seq, col);
+ }
+ }
+
+ public String getSequenceSetId()
+ {
+ if (sequenceSetID == null)
+ {
+ sequenceSetID = alignment.hashCode() + "";
+ }
+
+ return sequenceSetID;
+ }
+
+ public void alignmentChanged(AlignmentPanel ap)
+ {
+ alignment.padGaps();
+
+ if (hconsensus != null && autocalculateConsensus)
+ {
+ updateConsensus(ap);
+ updateConservation(ap);
+ }
+
+ // Reset endRes of groups if beyond alignment width
+ int alWidth = alignment.getWidth();
+ Vector groups = alignment.getGroups();
+ if (groups != null)
+ {
+ for (int i = 0; i < groups.size(); i++)
+ {
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(i);
+ if (sg.getEndRes() > alWidth)
+ {
+ sg.setEndRes(alWidth - 1);
+ }
+ }
+ }
+
+ if (selectionGroup != null && selectionGroup.getEndRes() > alWidth)
+ {
+ selectionGroup.setEndRes(alWidth - 1);
+ }
+
+ resetAllColourSchemes();
+
+ // AW alignment.adjustSequenceAnnotations();
+ }
+
+ void resetAllColourSchemes()
+ {
+ ColourSchemeI cs = globalColourScheme;
+ if (cs != null)
+ {
+ if (cs instanceof ClustalxColourScheme)
+ {
+ ((ClustalxColourScheme) cs).resetClustalX(alignment.getSequences(),
+ alignment.getWidth());
+ }
+
+ cs.setConsensus(hconsensus);
+ if (cs.conservationApplied())
+ {
+ Alignment al = (Alignment) alignment;
+ Conservation c = new Conservation("All",
+ ResidueProperties.propHash, 3, al.getSequences(), 0, al
+ .getWidth() - 1);
+ c.calculate();
+ c.verdict(false, ConsPercGaps);
+
+ cs.setConservation(c);
+ }
+ }
+
+ int s, sSize = alignment.getGroups().size();
+ for (s = 0; s < sSize; s++)
+ {
+ SequenceGroup sg = (SequenceGroup) alignment.getGroups().elementAt(s);
+ if (sg.cs != null && sg.cs instanceof ClustalxColourScheme)
+ {
+ ((ClustalxColourScheme) sg.cs).resetClustalX(sg
+ .getSequences(hiddenRepSequences), sg.getWidth());
+ }
+ sg.recalcConservation();
+ }
+ }
+
+ boolean centreColumnLabels;
+
+ public boolean getCentreColumnLabels()
+ {
+ return centreColumnLabels;
+ }
+
+ public void updateSequenceIdColours()
+ {
+ Vector groups = alignment.getGroups();
+ for (int ig = 0, igSize = groups.size(); ig < igSize; ig++)
+ {
+ SequenceGroup sg = (SequenceGroup) groups.elementAt(ig);
+ if (sg.idColour != null)
+ {
+ Vector sqs = sg.getSequences(hiddenRepSequences);
+ for (int s = 0, sSize = sqs.size(); s < sSize; s++)
+ {
+ this.setSequenceColour((SequenceI) sqs.elementAt(s), sg.idColour);
+ }
+ }
+ }
+ }
+
+ public boolean followHighlight = false;
+
+ public boolean getFollowHighlight()
+ {
+ return followHighlight;
+ }
+
+ /**
+ * show non-conserved residues only
+ */
+ public boolean showUnconserved = false;
+
+ /**
+ * when set, alignment should be reordered according to a newly opened tree
+ */
+ public boolean sortByTree = false;
+
+ /**
+ * @return the showUnconserved
+ */
+ public boolean getShowunconserved()
+ {
+ return showUnconserved;
+ }
+
+ /**
+ * @param showNonconserved
+ * the showUnconserved to set
+ */
+ public void setShowunconserved(boolean displayNonconserved)
+ {
+ this.showUnconserved = displayNonconserved;
+ }
+
+ /**
+ * consensus annotation includes all percentage for all symbols in column
+ * DISABLED FOR 2.5 RELEASE (bug #60064 logo rendering is not AWT 1.1
+ * compatible)
+ */
+ private boolean includeAllConsensusSymbols = false;
+
+ /**
+ * should conservation rows be shown for groups DISABLED FOR 2.5 RELEASE (bug
+ * 62446)
+ */
+ boolean showGroupConservation = false;
+
+ /**
+ * should consensus rows be shown for groups DISABLED FOR 2.5 RELEASE (bug
+ * 62446)
+ */
+ boolean showGroupConsensus = false;
+
+ /**
+ * should consensus profile be rendered by default DISABLED FOR 2.5 RELEASE
+ * (bug #60064 logo rendering is not AWT 1.1 compatible)
+ */
+ public boolean showSequenceLogo = false;
+
+ /**
+ * should consensus histograms be rendered by default
+ */
+ public boolean showConsensusHistogram = true;
+
+ /**
+ * @return the showConsensusProfile
+ */
+ public boolean isShowSequenceLogo()
+ {
+ return showSequenceLogo;
+ }
+
+ /**
+ * @param showSequenceLogo
+ * the new value public void setShowSequenceLogo(boolean
+ * showSequenceLogo) { this.showSequenceLogo = showSequenceLogo; }
+ */
+ /**
+ * @param showGroupConsensus
+ * the showGroupConsensus to set
+ */
+ public void setShowGroupConsensus(boolean showGroupConsensus)
+ {
+ this.showGroupConsensus = showGroupConsensus;
+ }
+
+ /**
+ * @return the includeAllConsensusSymbols
+ */
+ public boolean isIncludeAllConsensusSymbols()
+ {
+ return false;
+ }
+
+ /**
+ *
+ * @return flag to indicate if the consensus histogram should be rendered by
+ * default
+ */
+ public boolean isShowConsensusHistogram()
+ {
+ return this.showConsensusHistogram;
+ }
+
+ /**
+ * synthesize a column selection if none exists so it covers the given
+ * selection group. if wholewidth is false, no column selection is made if the
+ * selection group covers the whole alignment width.
+ *
+ * @param sg
+ * @param wholewidth
+ */
+ public void expandColSelection(SequenceGroup sg, boolean wholewidth)
+ {
+ int sgs, sge;
+ if (sg != null
+ && (sgs = sg.getStartRes()) >= 0
+ && sg.getStartRes() <= (sge = sg.getEndRes())
+ && (colSel == null || colSel.getSelected() == null || colSel
+ .getSelected().size() == 0))
+ {
+ if (!wholewidth && alignment.getWidth() == (1 + sge - sgs))
+ {
+ // do nothing
+ return;
+ }
+ if (colSel == null)
+ {
+ colSel = new ColumnSelection();
+ }
+ for (int cspos = sg.getStartRes(); cspos <= sg.getEndRes(); cspos++)
+ {
+ colSel.addElement(cspos);
+ }
+ }
+ }