+ }
+ break;
+
+ case KeyEvent.VK_U:
+ if (evt.isControlDown())
+ {
+ this.deleteGroups_actionPerformed();
+ }
+ break;
+
+ case KeyEvent.VK_T:
+ if (evt.isControlDown())
+ {
+ newView(null);
+ }
+ break;
+
+ }
+ alignPanel.paintAlignment(true);
+ }
+
+ public void keyReleased(KeyEvent evt)
+ {
+ }
+
+ public void keyTyped(KeyEvent evt)
+ {
+ }
+
+ public void itemStateChanged(ItemEvent evt)
+ {
+ if (evt.getSource() == displayNonconservedMenuItem)
+ {
+ displayNonconservedMenuItem_actionPerformed();
+ }
+ else if (evt.getSource() == colourTextMenuItem)
+ {
+ colourTextMenuItem_actionPerformed();
+ }
+ else if (evt.getSource() == wrapMenuItem)
+ {
+ wrapMenuItem_actionPerformed();
+ }
+ else if (evt.getSource() == scaleAbove)
+ {
+ viewport.setScaleAboveWrapped(scaleAbove.getState());
+ }
+ else if (evt.getSource() == scaleLeft)
+ {
+ viewport.setScaleLeftWrapped(scaleLeft.getState());
+ }
+ else if (evt.getSource() == scaleRight)
+ {
+ viewport.setScaleRightWrapped(scaleRight.getState());
+ }
+ else if (evt.getSource() == seqLimits)
+ {
+ seqLimits_itemStateChanged();
+ }
+ else if (evt.getSource() == viewBoxesMenuItem)
+ {
+ viewport.setShowBoxes(viewBoxesMenuItem.getState());
+ }
+ else if (evt.getSource() == viewTextMenuItem)
+ {
+ viewport.setShowText(viewTextMenuItem.getState());
+ }
+ else if (evt.getSource() == renderGapsMenuItem)
+ {
+ viewport.setRenderGaps(renderGapsMenuItem.getState());
+ }
+ else if (evt.getSource() == annotationPanelMenuItem)
+ {
+ viewport.setShowAnnotation(annotationPanelMenuItem.getState());
+ alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
+ }
+ else if (evt.getSource() == sequenceFeatures)
+ {
+ viewport.showSequenceFeatures(sequenceFeatures.getState());
+ alignPanel.seqPanel.seqCanvas.repaint();
+ }
+ else if (evt.getSource() == conservationMenuItem)
+ {
+ conservationMenuItem_actionPerformed();
+ }
+ else if (evt.getSource() == abovePIDThreshold)
+ {
+ abovePIDThreshold_actionPerformed();
+ }
+ else if (evt.getSource() == applyToAllGroups)
+ {
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
+ }
+ else if (evt.getSource() == autoCalculate)
+ {
+ viewport.autocalculateConsensus = autoCalculate.getState();
+ }
+ else if (evt.getSource() == this.centreColumnLabelFlag)
+ {
+ centreColumnLabelFlag_stateChanged();
+ } else if (evt.getSource() == this.followMouseOverFlag)
+ {
+ mouseOverFlag_stateChanged();
+ }
+
+ alignPanel.paintAlignment(true);
+ }
+
+ private void mouseOverFlag_stateChanged()
+ {
+ viewport.followHighlight = followMouseOverFlag.getState();
+ // TODO: could kick the scrollTo mechanism to reset view for current searchresults.
+ }
+
+ private void centreColumnLabelFlag_stateChanged()
+ {
+ viewport.centreColumnLabels = centreColumnLabelFlag.getState();
+ this.alignPanel.annotationPanel.repaint();
+ }
+
+ public void actionPerformed(ActionEvent evt)
+ {
+ Object source = evt.getSource();
+
+ if (source == inputText)
+ {
+ inputText_actionPerformed();
+ }
+ else if (source == loadTree)
+ {
+ loadTree_actionPerformed();
+ }
+ else if (source == loadApplication)
+ {
+ launchFullApplication();
+ }
+ else if (source == loadAnnotations)
+ {
+ loadAnnotations();
+ }
+ else if (source == outputAnnotations)
+ {
+ outputAnnotations(true);
+ }
+ else if (source == outputFeatures)
+ {
+ outputFeatures(true, "Jalview");
+ }
+ else if (source == closeMenuItem)
+ {
+ closeMenuItem_actionPerformed();
+ }
+ else if (source == copy)
+ {
+ copy_actionPerformed();
+ }
+ else if (source == undoMenuItem)
+ {
+ undoMenuItem_actionPerformed();
+ }
+ else if (source == redoMenuItem)
+ {
+ redoMenuItem_actionPerformed();
+ }
+ else if (source == inputText)
+ {
+ inputText_actionPerformed();
+ }
+ else if (source == closeMenuItem)
+ {
+ closeMenuItem_actionPerformed();
+ }
+ else if (source == undoMenuItem)
+ {
+ undoMenuItem_actionPerformed();
+ }
+ else if (source == redoMenuItem)
+ {
+ redoMenuItem_actionPerformed();
+ }
+ else if (source == copy)
+ {
+ copy_actionPerformed();
+ }
+ else if (source == pasteNew)
+ {
+ pasteNew_actionPerformed();
+ }
+ else if (source == pasteThis)
+ {
+ pasteThis_actionPerformed();
+ }
+ else if (source == cut)
+ {
+ cut_actionPerformed();
+ }
+ else if (source == delete)
+ {
+ delete_actionPerformed();
+ }
+ else if (source == deleteGroups)
+ {
+ deleteGroups_actionPerformed();
+ }
+ else if (source == selectAllSequenceMenuItem)
+ {
+ selectAllSequenceMenuItem_actionPerformed();
+ }
+ else if (source == deselectAllSequenceMenuItem)
+ {
+ deselectAllSequenceMenuItem_actionPerformed();
+ }
+ else if (source == invertSequenceMenuItem)
+ {
+ invertSequenceMenuItem_actionPerformed();
+ }
+ else if (source == invertColSel)
+ {
+ viewport.invertColumnSelection();
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == remove2LeftMenuItem)
+ {
+ trimAlignment(true);
+ }
+ else if (source == remove2RightMenuItem)
+ {
+ trimAlignment(false);
+ }
+ else if (source == removeGappedColumnMenuItem)
+ {
+ removeGappedColumnMenuItem_actionPerformed();
+ }
+ else if (source == removeAllGapsMenuItem)
+ {
+ removeAllGapsMenuItem_actionPerformed();
+ }
+ else if (source == findMenuItem)
+ {
+ findMenuItem_actionPerformed();
+ }
+ else if (source == font)
+ {
+ new FontChooser(alignPanel);
+ }
+ else if (source == newView)
+ {
+ newView(null);
+ }
+ else if (source == showColumns)
+ {
+ viewport.showAllHiddenColumns();
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == showSeqs)
+ {
+ viewport.showAllHiddenSeqs();
+ }
+ else if (source == hideColumns)
+ {
+ viewport.hideSelectedColumns();
+ alignPanel.paintAlignment(true);
+ }
+ else if (source == hideSequences
+ && viewport.getSelectionGroup() != null)
+ {
+ viewport.hideAllSelectedSeqs();
+ }
+ else if (source == featureSettings)
+ {
+ new FeatureSettings(alignPanel);
+ }
+ else if (source == alProperties)
+ {
+ StringBuffer contents = new StringBuffer();