+ protected void initAutoAnnotation()
+ {
+ // TODO: add menu option action that nulls or creates consensus object
+ // depending on if the user wants to see the annotation or not in a
+ // specific alignment
+
+ if (hconsensus == null && !isDataset)
+ {
+ if (!alignment.isNucleotide())
+ {
+ initConservation();
+ initQuality();
+ }
+ else
+ {
+ initRNAStructure();
+ }
+ initConsensus();
+ }
+ }
+
+ private void initConsensus()
+ {
+
+ consensus = new AlignmentAnnotation("Consensus", "PID",
+ new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+ consensus.hasText = true;
+ consensus.autoCalculated = true;
+
+ if (showConsensus)
+ {
+ alignment.addAnnotation(consensus);
+ }
+ }
+
+ private void initConservation()
+ {
+ if (showConservation)
+ {
+ if (conservation == null)
+ {
+ conservation = new AlignmentAnnotation("Conservation",
+ "Conservation of total alignment less than "
+ + getConsPercGaps() + "% gaps", new Annotation[1],
+ 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
+ conservation.hasText = true;
+ conservation.autoCalculated = true;
+ alignment.addAnnotation(conservation);
+ }
+ }
+ }
+
+ private void initQuality()
+ {
+ if (showQuality)
+ {
+ if (quality == null)
+ {
+ quality = new AlignmentAnnotation("Quality",
+ "Alignment Quality based on Blosum62 scores",
+ new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
+ quality.hasText = true;
+ quality.autoCalculated = true;
+ alignment.addAnnotation(quality);
+ }
+ }
+ }
+
+ private void initRNAStructure()
+ {
+ if (alignment.hasRNAStructure() && strucConsensus == null)
+ {
+ strucConsensus = new AlignmentAnnotation("StrucConsensus", "PID",
+ new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH);
+ strucConsensus.hasText = true;
+ strucConsensus.autoCalculated = true;
+
+ if (showConsensus)
+ {
+ alignment.addAnnotation(strucConsensus);
+ }
+ }
+ }
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see jalview.api.AlignViewportI#calcPanelHeight()
+ */
+ public int calcPanelHeight()
+ {
+ // setHeight of panels
+ AlignmentAnnotation[] aa = getAlignment().getAlignmentAnnotation();
+ int height = 0;
+ int charHeight = getCharHeight();
+ if (aa != null)
+ {
+ BitSet graphgrp = new BitSet();
+ for (int i = 0; i < aa.length; i++)
+ {
+ if (aa[i] == null)
+ {
+ System.err.println("Null annotation row: ignoring.");
+ continue;
+ }
+ if (!aa[i].visible)
+ {
+ continue;
+ }
+ if (aa[i].graphGroup > -1)
+ {
+ if (graphgrp.get(aa[i].graphGroup))
+ {
+ continue;
+ }
+ else
+ {
+ graphgrp.set(aa[i].graphGroup);
+ }
+ }
+ aa[i].height = 0;
+
+ if (aa[i].hasText)
+ {
+ aa[i].height += charHeight;
+ }
+
+ if (aa[i].hasIcons)
+ {
+ aa[i].height += 16;
+ }
+
+ if (aa[i].graph > 0)
+ {
+ aa[i].height += aa[i].graphHeight;
+ }
+
+ if (aa[i].height == 0)
+ {
+ aa[i].height = 20;
+ }
+
+ height += aa[i].height;
+ }
+ }
+ if (height == 0)
+ {
+ // set minimum
+ height = 20;
+ }
+ return height;
+ }
+
+ @Override
+ public void updateGroupAnnotationSettings(boolean applyGlobalSettings,
+ boolean preserveNewGroupSettings)
+ {
+ boolean updateCalcs = false;
+ boolean conv = isShowGroupConservation();
+ boolean cons = isShowGroupConsensus();
+ boolean showprf = isShowSequenceLogo();
+ boolean showConsHist = isShowConsensusHistogram();
+ boolean normLogo = isNormaliseSequenceLogo();
+
+ /**
+ * TODO reorder the annotation rows according to group/sequence ordering on
+ * alignment
+ */
+ boolean sortg = true;
+
+ // remove old automatic annotation
+ // add any new annotation
+
+ // intersect alignment annotation with alignment groups
+
+ AlignmentAnnotation[] aan = alignment.getAlignmentAnnotation();
+ List<SequenceGroup> oldrfs = new ArrayList<SequenceGroup>();
+ if (aan != null)
+ {
+ for (int an = 0; an < aan.length; an++)
+ {
+ if (aan[an].autoCalculated && aan[an].groupRef != null)
+ {
+ oldrfs.add(aan[an].groupRef);
+ alignment.deleteAnnotation(aan[an], false);
+ }
+ }
+ }
+ if (alignment.getGroups() != null)
+ {
+ for (SequenceGroup sg : alignment.getGroups())
+ {
+ updateCalcs = false;
+ if (applyGlobalSettings
+ || (!preserveNewGroupSettings && !oldrfs.contains(sg)))
+ {
+ // set defaults for this group's conservation/consensus
+ sg.setshowSequenceLogo(showprf);
+ sg.setShowConsensusHistogram(showConsHist);
+ sg.setNormaliseSequenceLogo(normLogo);
+ }
+ if (conv)
+ {
+ updateCalcs = true;
+ alignment.addAnnotation(sg.getConservationRow(), 0);
+ }
+ if (cons)
+ {
+ updateCalcs = true;
+ alignment.addAnnotation(sg.getConsensus(), 0);
+ }
+ // refresh the annotation rows
+ if (updateCalcs)
+ {
+ sg.recalcConservation();
+ }
+ }
+ }
+ oldrfs.clear();
+ }
+
+ @Override
+ public Color getSequenceColour(SequenceI seq)
+ {
+ Color sqc = Color.white;
+ if (sequenceColours != null)
+ {
+ sqc = (Color) sequenceColours.get(seq);
+ if (sqc == null)
+ {
+ sqc = Color.white;
+ }
+ }
+ return sqc;
+ }
+
+ @Override
+ public void setSequenceColour(SequenceI seq, Color col)
+ {
+ if (sequenceColours == null)
+ {
+ sequenceColours = new Hashtable();
+ }
+
+ if (col == null)
+ {
+ sequenceColours.remove(seq);
+ }
+ else
+ {
+ sequenceColours.put(seq, col);
+ }
+ }
+
+ @Override
+ public void updateSequenceIdColours()
+ {
+ if (sequenceColours == null)
+ {
+ sequenceColours = new Hashtable();
+ }
+ for (SequenceGroup sg : alignment.getGroups())
+ {
+ if (sg.idColour != null)
+ {
+ for (SequenceI s : sg.getSequences(getHiddenRepSequences()))
+ {
+ sequenceColours.put(s, sg.idColour);
+ }
+ }
+ }
+ }
+
+ @Override
+ public void clearSequenceColours()
+ {
+ sequenceColours = null;
+ };