-
- 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();
- }
- }
-
- 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);
- }
- }
-
- /**
- * returns the visible column regions of the alignment
- *
- * @param selectedRegionOnly
- * true to just return the contigs intersecting with the
- * selected area
- * @return
- */
- public int[] getViewAsVisibleContigs(boolean selectedRegionOnly)
- {
- int[] viscontigs = null;
- int start = 0, end = 0;
- if (selectedRegionOnly && selectionGroup != null)
- {
- start = selectionGroup.getStartRes();
- end = selectionGroup.getEndRes() + 1;
- }
- else
- {
- end = alignment.getWidth();
- }
- viscontigs = colSel.getVisibleContigs(start, end);
- return viscontigs;
- }
-
- /**
- * get hash of undo and redo list for the alignment
- *
- * @return long[] { historyList.hashCode, redoList.hashCode };
- */
- public long[] getUndoRedoHash()
- {
- if (historyList == null || redoList == null)
- return new long[]
- { -1, -1 };
- return new long[]
- { historyList.hashCode(), this.redoList.hashCode() };
- }
-
- /**
- * test if a particular set of hashcodes are different to the hashcodes for
- * the undo and redo list.
- *
- * @param undoredo
- * the stored set of hashcodes as returned by getUndoRedoHash
- * @return true if the hashcodes differ (ie the alignment has been edited) or
- * the stored hashcode array differs in size
- */
- public boolean isUndoRedoHashModified(long[] undoredo)
- {
- if (undoredo == null)
- {
- return true;
- }
- long[] cstate = getUndoRedoHash();
- if (cstate.length != undoredo.length)
- {
- return true;
- }
-
- for (int i = 0; i < cstate.length; i++)
- {
- if (cstate[i] != undoredo[i])
- {
- return true;
- }
- }
- return false;
- }
-
- public boolean getCentreColumnLabels()
- {
- return centreColumnLabels;
- }
-
- public void setCentreColumnLabels(boolean centrecolumnlabels)
- {
- centreColumnLabels = centrecolumnlabels;
- }
-
- public void updateSequenceIdColours()
- {
- Vector groups = alignment.getGroups();
- if (sequenceColours == null)
- {
- sequenceColours = new Hashtable();
- }
- 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++)
- {
- sequenceColours.put(sqs.elementAt(s), sg.idColour);
- }
- }
- }
- }
-
- /**
- * enable or disable the display of Database Cross References in the sequence ID tooltip
- */
- public void setShowDbRefs(boolean show)
- {
- showdbrefs=show;
- }
-
- /**
- *
- * @return true if Database References are to be displayed on tooltips.
- */
- public boolean isShowDbRefs()
- {
- return showdbrefs;
- }
-
- /**
- *
- * @return true if Non-positional features are to be displayed on tooltips.
- */
- public boolean isShowNpFeats()
- {
- return shownpfeats;
- }
- /**
- * enable or disable the display of Non-Positional sequence features in the sequence ID tooltip
- * @param show
- */
- public void setShowNpFeats(boolean show)
- {
- shownpfeats=show;
- }
- /**
- *
- * @return true if view has hidden rows
- */
- public boolean hasHiddenRows()
- {
- return hasHiddenRows;
- }
- /**
- *
- * @return true if view has hidden columns
- */
- public boolean hasHiddenColumns()
- {
- return hasHiddenColumns;
- }
- /**
- * when set, view will scroll to show the highlighted position
- */
- public boolean followHighlight=true;
- /**
- * @return true if view should scroll to show the highlighted region of a sequence
- * @return
- */
- public boolean getFollowHighlight() {
- return followHighlight;
- }
- public boolean followSelection=true;
- /**
- * @return true if view selection should always follow the selections broadcast by other selection sources
- */
- public boolean getFollowSelection() {
- return followSelection;
- }
- private long sgrouphash=-1,colselhash=-1;
-
- boolean showSeqFeaturesHeight;
- /**
- * checks current SelectionGroup against record of last hash value, and updates record.
- * @return true if SelectionGroup changed since last call
- */
- boolean isSelectionGroupChanged() {
- int hc=(selectionGroup==null) ? -1 : selectionGroup.hashCode();
- if (hc!=sgrouphash)
- {
- sgrouphash = hc;
- return true;
- }
- return false;
- }
- /**
- * checks current colsel against record of last hash value, and updates record.
- * @return true if colsel changed since last call
- */
- boolean isColSelChanged() {
- int hc=(colSel==null) ? -1 : colSel.hashCode();
- if (hc!=colselhash)
- {
- colselhash = hc;
- return true;
- }
- return false;
- }
- public void sendSelection()
- {
- jalview.structure.StructureSelectionManager.getStructureSelectionManager().sendSelection(new SequenceGroup(getSelectionGroup()), new ColumnSelection(getColumnSelection()), this);
- }
- public void setShowSequenceFeaturesHeight(boolean selected)
- {
- showSeqFeaturesHeight = selected;
- }
- public boolean getShowSequenceFeaturesHeight()
- {
- return showSeqFeaturesHeight;
- }
- boolean showUnconserved=false;
- public boolean getShowUnconserved()
- {
- return showUnconserved;
- }
- public void setShowUnconserved(boolean showunconserved)
- {
- showUnconserved=showunconserved;
- }
- /**
- * return the alignPanel containing the given viewport. Use this to get the
- * components currently handling the given viewport.
- * @param av
- * @return null or an alignPanel guaranteed to have non-null alignFrame reference
- */
- public AlignmentPanel getAlignPanel()
- {
- AlignmentPanel[] aps = PaintRefresher.getAssociatedPanels(this.getSequenceSetId());
- AlignmentPanel ap=null;
- for (int p=0;aps!=null && p<aps.length; p++)
- {
- if (aps[p].av == this)
- {
- return aps[p];
- }
- }
- return null;
- }
- public boolean getSortByTree()
- {
- return sortByTree;
- }
- public void setSortByTree(boolean sort) {
- sortByTree = sort;
- }
- /**
- * should conservation rows be shown for groups
- */
- boolean showGroupConservation = false;
- /**
- * should consensus rows be shown for groups
- */
- boolean showGroupConsensus = false;
- /**
- * should consensus profile be rendered by default
- */
- 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 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 the includeAllConsensusSymbols
- */
- public boolean isIncludeAllConsensusSymbols()
- {
- return includeAllConsensusSymbols;
- }
- /**
- * @param includeAllConsensusSymbols the includeAllConsensusSymbols to set
- */
- public void setIncludeAllConsensusSymbols(boolean includeAllConsensusSymbols)
- {
- this.includeAllConsensusSymbols = includeAllConsensusSymbols;
- }
-
- /**
- *
- * @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);
- }
- }