alignPanel);
viewport.updateConservation(alignPanel);
viewport.updateConsensus(alignPanel);
+ viewport.initInformationWorker(alignPanel);
displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
followMouseOverFlag.setState(viewport.isFollowHighlight());
createAlignFrameWindow(embedded);
validate();
alignPanel.adjustAnnotationHeight();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
}
public AlignViewport getAlignViewport()
{
viewport.featureSettings.refreshTable();
}
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
statusBar.setText(MessageManager
.getString("label.successfully_added_features_alignment"));
}
break;
}
- alignPanel.paintAlignment(true);
+ // TODO: repaint flags set only if the keystroke warrants it
+ alignPanel.paintAlignment(true, true);
}
/**
{
applyAutoAnnotationSettings_actionPerformed();
}
- alignPanel.paintAlignment(true);
+ // TODO: repaint flags set only if warranted
+ alignPanel.paintAlignment(true, true);
}
/**
else if (source == invertColSel)
{
viewport.invertColumnSelection();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
viewport.sendSelection();
}
else if (source == remove2LeftMenuItem)
else if (source == showColumns)
{
viewport.showAllHiddenColumns();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
else if (source == showSeqs)
{
viewport.showAllHiddenSeqs();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
// uncomment if we want to slave sequence selections in split frame
// viewport.sendSelection();
}
else if (source == hideColumns)
{
viewport.hideSelectedColumns();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
else if (source == hideSequences
&& viewport.getSelectionGroup() != null)
{
viewport.hideAllSelectedSeqs();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
// uncomment if we want to slave sequence selections in split frame
// viewport.sendSelection();
}
else if (source == hideAllButSelection)
{
toggleHiddenRegions(false, false);
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
else if (source == hideAllSelection)
viewport.expandColSelection(sg, false);
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
else if (source == showAllHidden)
{
viewport.showAllHiddenColumns();
viewport.showAllHiddenSeqs();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
viewport.sendSelection();
}
else if (source == showGroupConsensus)
FeaturesFile formatter = new FeaturesFile();
if (format.equalsIgnoreCase("Jalview"))
{
- features = formatter.printJalviewFormat(viewport.getAlignment()
- .getSequencesArray(), getDisplayedFeatureCols(),
- getDisplayedFeatureGroups(), true);
+ features = formatter.printJalviewFormat(
+ viewport.getAlignment().getSequencesArray(),
+ getDisplayedFeatureCols(), null, getDisplayedFeatureGroups(),
+ true);
}
else
{
}
viewport.getAlignment().moveSelectedSequencesByOne(sg,
up ? null : viewport.getHiddenRepSequences(), up);
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
/*
* Also move cDNA/protein complement sequences
viewport, complement);
complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
up ? null : complement.getHiddenRepSequences(), up);
- getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
+ getSplitFrame().getComplement(this).alignPanel.paintAlignment(true,
+ false);
}
}
static StringBuffer copiedSequences;
- static Vector<int[]> copiedHiddenColumns;
+ static HiddenColumns copiedHiddenColumns;
protected void copy_actionPerformed()
{
if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
{
- copiedHiddenColumns = new Vector<>(viewport.getAlignment()
- .getHiddenColumns().getHiddenColumnsCopy());
int hiddenOffset = viewport.getSelectionGroup().getStartRes();
- for (int[] region : copiedHiddenColumns)
- {
- region[0] = region[0] - hiddenOffset;
- region[1] = region[1] - hiddenOffset;
- }
+ int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
+
+ // create new HiddenColumns object with copy of hidden regions
+ // between startRes and endRes, offset by startRes
+ copiedHiddenColumns = new HiddenColumns(
+ viewport.getAlignment().getHiddenColumns(), hiddenOffset,
+ hiddenCutoff, hiddenOffset);
}
else
{
{
try
{
-
if (copiedSequences == null)
{
return;
}
- StringTokenizer st = new StringTokenizer(copiedSequences.toString());
+ StringTokenizer st = new StringTokenizer(copiedSequences.toString(),
+ "\t");
Vector seqs = new Vector();
while (st.hasMoreElements())
{
}
AlignFrame af = new AlignFrame(new Alignment(newSeqs),
viewport.applet, newtitle, false);
- if (copiedHiddenColumns != null)
- {
- for (int i = 0; i < copiedHiddenColumns.size(); i++)
- {
- int[] region = copiedHiddenColumns.elementAt(i);
- af.viewport.hideColumns(region[0], region[1]);
- }
- }
+ af.viewport.setHiddenColumns(copiedHiddenColumns);
jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
frameHeight);
{
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
}
}
// JAL-2034 - should delegate to
// alignPanel to decide if overview needs
// updating.
- alignPanel.paintAlignment(false);
+ alignPanel.paintAlignment(false, false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
// JAL-2034 - should delegate to
// alignPanel to decide if overview needs
// updating.
- alignPanel.paintAlignment(false);
+ alignPanel.paintAlignment(false, false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
public void invertColSel_actionPerformed()
{
viewport.invertColumnSelection();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
{
viewport.setShowJVSuffix(seqLimits.getState());
alignPanel.fontChanged();
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
protected void colourTextMenuItem_actionPerformed()
{
viewport.setColourText(colourTextMenuItem.getState());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
protected void displayNonconservedMenuItem_actionPerformed()
{
viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
protected void wrapMenuItem_actionPerformed()
scaleAbove.setEnabled(wrapMenuItem.getState());
scaleLeft.setEnabled(wrapMenuItem.getState());
scaleRight.setEnabled(wrapMenuItem.getState());
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
public void overviewMenuItem_actionPerformed()
{
viewport.setGlobalColourScheme(cs);
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, true);
}
protected void modifyPID_actionPerformed()
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
public void sortIDMenuItem_actionPerformed()
AlignmentSorter.sortByID(viewport.getAlignment());
addHistoryItem(
new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
public void sortLengthMenuItem_actionPerformed()
AlignmentSorter.sortByLength(viewport.getAlignment());
addHistoryItem(new OrderCommand("Length Sort", oldOrder,
viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
public void sortGroupMenuItem_actionPerformed()
AlignmentSorter.sortByGroup(viewport.getAlignment());
addHistoryItem(new OrderCommand("Group Sort", oldOrder,
viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
current.insertCharAt(Width - 1, viewport.getGapCharacter());
}
}
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
if ((viewport.getSelectionGroup() != null
current.insertCharAt(Width - 1, viewport.getGapCharacter());
}
}
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(false, false);
}
addHistoryItem(new OrderCommand(MessageManager
.formatMessage("label.order_by_params", new String[]
{ title }), oldOrder, viewport.getAlignment()));
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
}
/**
addHistoryItem(new OrderCommand(undoname, oldOrder,
viewport.getAlignment()));
}
- alignPanel.paintAlignment(true);
+ alignPanel.paintAlignment(true, false);
return true;
}
{
// register the association(s) and quit, don't create any windows.
if (StructureSelectionManager.getStructureSelectionManager(applet)
- .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
+ .setMapping(seqs, chains, pdb.getFile(), protocol, null) == null)
{
System.err.println("Failed to map " + pdb.getFile() + " ("
+ protocol + ") to any sequences");