viewport.sendSelection();
}
else if (source == showSeqs)
{
viewport.showAllHiddenSeqs();
viewport.sendSelection();
}
else if (source == showSeqs)
{
viewport.showAllHiddenSeqs();
// uncomment if we want to slave sequence selections in split frame
// viewport.sendSelection();
}
else if (source == hideColumns)
{
viewport.hideSelectedColumns();
// uncomment if we want to slave sequence selections in split frame
// viewport.sendSelection();
}
else if (source == hideColumns)
{
viewport.hideSelectedColumns();
viewport.sendSelection();
}
else if (source == hideSequences
&& viewport.getSelectionGroup() != null)
{
viewport.hideAllSelectedSeqs();
viewport.sendSelection();
}
else if (source == hideSequences
&& viewport.getSelectionGroup() != null)
{
viewport.hideAllSelectedSeqs();
// uncomment if we want to slave sequence selections in split frame
// viewport.sendSelection();
}
else if (source == hideAllButSelection)
{
toggleHiddenRegions(false, false);
// uncomment if we want to slave sequence selections in split frame
// viewport.sendSelection();
}
else if (source == hideAllButSelection)
{
toggleHiddenRegions(false, false);
viewport.expandColSelection(sg, false);
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
viewport.expandColSelection(sg, false);
viewport.hideAllSelectedSeqs();
viewport.hideSelectedColumns();
viewport.sendSelection();
}
else if (source == showAllHidden)
{
viewport.showAllHiddenColumns();
viewport.showAllHiddenSeqs();
viewport.sendSelection();
}
else if (source == showAllHidden)
{
viewport.showAllHiddenColumns();
viewport.showAllHiddenSeqs();
+ private List<String> getDisplayedFeatureGroups()
+ {
+ if (alignPanel.getFeatureRenderer() != null
+ && viewport.getFeaturesDisplayed() != null)
+ {
+ return alignPanel.getFeatureRenderer().getDisplayedFeatureGroups();
+
+ }
+ return null;
+ }
+
public String outputFeatures(boolean displayTextbox, String format)
{
String features;
FeaturesFile formatter = new FeaturesFile();
if (format.equalsIgnoreCase("Jalview"))
{
public String outputFeatures(boolean displayTextbox, String format)
{
String features;
FeaturesFile formatter = new FeaturesFile();
if (format.equalsIgnoreCase("Jalview"))
{
- features = formatter.printJalviewFormat(
- viewport.getAlignment().getSequencesArray(),
- getDisplayedFeatureCols());
+ features = formatter.printJalviewFormat(viewport.getAlignment()
+ .getSequencesArray(), getDisplayedFeatureCols(),
+ getDisplayedFeatureGroups(), true);
- features = formatter.printGffFormat(
- viewport.getAlignment().getSequencesArray(),
- getDisplayedFeatureCols());
+ features = formatter.printGffFormat(viewport.getAlignment()
+ .getSequencesArray(), getDisplayedFeatureCols(),
+ getDisplayedFeatureGroups(), true);
}
viewport.getAlignment().moveSelectedSequencesByOne(sg,
up ? null : viewport.getHiddenRepSequences(), up);
}
viewport.getAlignment().moveSelectedSequencesByOne(sg,
up ? null : viewport.getHiddenRepSequences(), up);
viewport, complement);
complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
up ? null : complement.getHiddenRepSequences(), up);
viewport, complement);
complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
up ? null : complement.getHiddenRepSequences(), up);
{
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
{
PaintRefresher.Refresh(this, viewport.getSequenceSetId());
alignPanel.updateAnnotation();
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
viewport.sendSelection();
}
PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
newaf.alignPanel.av.getSequenceSetId());
PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
newaf.alignPanel.av.getSequenceSetId());
}
protected void colourTextMenuItem_actionPerformed()
{
viewport.setColourText(colourTextMenuItem.getState());
}
protected void colourTextMenuItem_actionPerformed()
{
viewport.setColourText(colourTextMenuItem.getState());
}
protected void displayNonconservedMenuItem_actionPerformed()
{
viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
}
protected void displayNonconservedMenuItem_actionPerformed()
{
viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
scaleAbove.setEnabled(wrapMenuItem.getState());
scaleLeft.setEnabled(wrapMenuItem.getState());
scaleRight.setEnabled(wrapMenuItem.getState());
scaleAbove.setEnabled(wrapMenuItem.getState());
scaleLeft.setEnabled(wrapMenuItem.getState());
scaleRight.setEnabled(wrapMenuItem.getState());
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
viewport.getAlignment()));
addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
viewport.getAlignment()));
AlignmentSorter.sortByID(viewport.getAlignment());
addHistoryItem(
new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
AlignmentSorter.sortByID(viewport.getAlignment());
addHistoryItem(
new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
AlignmentSorter.sortByLength(viewport.getAlignment());
addHistoryItem(new OrderCommand("Length Sort", oldOrder,
viewport.getAlignment()));
AlignmentSorter.sortByLength(viewport.getAlignment());
addHistoryItem(new OrderCommand("Length Sort", oldOrder,
viewport.getAlignment()));
AlignmentSorter.sortByGroup(viewport.getAlignment());
addHistoryItem(new OrderCommand("Group Sort", oldOrder,
viewport.getAlignment()));
AlignmentSorter.sortByGroup(viewport.getAlignment());
addHistoryItem(new OrderCommand("Group Sort", oldOrder,
viewport.getAlignment()));
addHistoryItem(new OrderCommand(MessageManager
.formatMessage("label.order_by_params", new String[]
{ title }), oldOrder, viewport.getAlignment()));
addHistoryItem(new OrderCommand(MessageManager
.formatMessage("label.order_by_params", new String[]
{ title }), oldOrder, viewport.getAlignment()));
addHistoryItem(new OrderCommand(undoname, oldOrder,
viewport.getAlignment()));
}
addHistoryItem(new OrderCommand(undoname, oldOrder,
viewport.getAlignment()));
}
{
// register the association(s) and quit, don't create any windows.
if (StructureSelectionManager.getStructureSelectionManager(applet)
{
// 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)