- for (i = 0; i < iSize; i++)
- {
- if (hasHiddenColumns)
- {
- StringBuffer visibleSeq = new StringBuffer();
- Vector regions = colSel.getHiddenColumns();
-
- int blockStart = start, blockEnd = end;
- int[] region;
- int hideStart, hideEnd;
-
- for (int j = 0; j < regions.size(); j++)
- {
- region = (int[]) regions.elementAt(j);
- hideStart = region[0];
- hideEnd = region[1];
-
- if (hideStart < start)
- {
- continue;
- }
-
- blockStart = Math.min(blockStart, hideEnd + 1);
- blockEnd = Math.min(blockEnd, hideStart);
-
- if (blockStart > blockEnd)
- {
- break;
- }
-
- visibleSeq.append(seqs[i].getSequence(blockStart, blockEnd));
-
- blockStart = hideEnd + 1;
- blockEnd = end;
- }
-
- if (end > blockStart)
- {
- visibleSeq.append(seqs[i].getSequence(blockStart, end));
- }
-
- selection[i] = visibleSeq.toString();
- }
- else
- {
- selection[i] = seqs[i].getSequenceAsString(start, end);
- }
- }
-
- return selection;
- }
-
- public boolean getShowHiddenMarkers()
- {
- return showHiddenMarkers;
- }
-
- public void setShowHiddenMarkers(boolean show)
- {
- showHiddenMarkers = show;
- }
-
- 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;
- }
- /**
- * unique viewId for synchronizing state (e.g. with stored Jalview Project)
- *
- */
- private String viewId = null;
-
- public String getViewId()
- {
- if (viewId == null)
- {
- viewId = this.getSequenceSetId() + "." + this.hashCode() + "";
- }
- return viewId;
- }
-
- 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())
- {
- cs.setConservation(Conservation.calculateConservation("All",
- ResidueProperties.propHash, 3, alignment.getSequences(), 0,
- alignment.getWidth(), false, getConsPercGaps(), false));
- }
- }
-
- 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 = true;
-
- 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;
-
- /**
- * 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(applet).sendSelection(
- new SequenceGroup(getSelectionGroup()),
- new ColumnSelection(getColumnSelection()), this);
- }
-
-
-
-
- /**
- * 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;
- }
-
- /**
- * 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 profile be rendered normalised to row height
- */
- public boolean normaliseSequenceLogo = 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)
- {
- if (showSequenceLogo != this.showSequenceLogo)
- {
- // TODO: decouple settings setting from calculation when refactoring
- // annotation update method from alignframe to viewport
- this.showSequenceLogo = showSequenceLogo;
- if (consensusThread != null)
- {
- consensusThread.updateAnnotation();
- }
- }
- 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
- */
- 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);
- }
- }
- }
-
- @Override
- public boolean hasHiddenColumns()
- {
- return hasHiddenColumns;
- }
-
- public boolean isNormaliseSequenceLogo()
- {
- return normaliseSequenceLogo;
- }
-
- public void setNormaliseSequenceLogo(boolean state)
- {
- normaliseSequenceLogo = state;
- }
-
- public boolean isCalcInProgress()
- {
- // TODO generalise to iterate over all calculators associated with av
- return updatingConsensus || updatingConservation || updatingStrucConsensus;
- }
-
- public boolean isCalculationInProgress(
- AlignmentAnnotation alignmentAnnotation)
- {
- if (!alignmentAnnotation.autoCalculated)
- return false;
- if ((updatingConsensus && consensus==alignmentAnnotation)
- || (updatingConservation && (conservation==alignmentAnnotation || quality==alignmentAnnotation))
- // || (updatingStrucConsensus && strucConsensus==alignmentAnnotation)
- )
- {
- return true;
- }
- return false;
- }
-
- /**
- *
- * @return true if alignment characters should be displayed
- */
- public boolean isValidCharWidth()
- {
- return validCharWidth;
- }
-
- @Override
- public Hashtable[] getSequenceConsensusHash()
- {
- return hconsensus;
- }
-
- @Override
- public Hashtable[] getRnaStructureConsensusHash()
- {
- return null; // TODO: JAL-891 port to jvlite : refactor and introduce hStrucConsensus;
- }
-
- @Override
- public AlignmentAnnotation getAlignmentQualityAnnot()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public AlignmentAnnotation getAlignmentConservationAnnotation()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- public boolean isClosed()
- {
- System.err.println("Alignment is "+alignment==null ? "closed" : "open");
- return alignment==null;
- }
-
- @Override
- public AlignCalcManagerI getCalcManager()
- {
- // TODO Auto-generated method stub
- return null;
- }