- 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 showUnconserved 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;
- }