MenuItem noColourmenuItem = new MenuItem();\r
protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
\r
- AlignmentPanel ap;\r
+ final AlignmentPanel ap;\r
MenuItem unGroupMenuItem = new MenuItem();\r
MenuItem nucleotideMenuItem = new MenuItem();\r
Menu colourMenu = new Menu();\r
CheckboxMenuItem showText = new CheckboxMenuItem();\r
CheckboxMenuItem showColourText = new CheckboxMenuItem();\r
\r
- public APopupMenu(AlignmentPanel ap, Sequence seq, Vector links)\r
+ public APopupMenu(AlignmentPanel apanel, Sequence seq, Vector links)\r
{\r
///////////////////////////////////////////////////////////\r
// If this is activated from the sequence panel, the user may want to\r
// If from the IDPanel, we must display the sequence menu\r
//////////////////////////////////////////////////////////\r
\r
- this.ap = ap;\r
+ this.ap = apanel;\r
\r
try\r
{\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- jalview.bin.JalviewLite.showURL(url, target);\r
+ ap.alignFrame.showURL(url, target);\r
}\r
});\r
linkMenu.add(item);\r
}\r
}\r
ap.seqPanel.seqCanvas.repaint();\r
+ if(ap.overviewPanel!=null)\r
+ ap.overviewPanel.updateOverviewImage();\r
}\r
\r
protected void clustalColour_actionPerformed(ActionEvent e)\r
protected void abovePIDColour_itemStateChanged(ItemEvent ie)\r
{\r
SequenceGroup sg = getGroup();\r
+ if(sg.cs==null)\r
+ return;\r
+\r
if (abovePIDColour.getState())\r
{\r
sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
ap.av.alignment.getWidth()));\r
int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,\r
getGroup().getName());\r
- if (sg.cs instanceof ResidueColourScheme)\r
- {\r
- ( (ResidueColourScheme) sg.cs).setThreshold(threshold);\r
- }\r
- else if (sg.cs instanceof ScoreColourScheme)\r
- {\r
- ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
- }\r
+\r
+ sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());\r
\r
SliderPanel.showPIDSlider();\r
\r
}\r
else // remove PIDColouring\r
{\r
- ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;\r
- rcs.setThreshold(0);\r
- sg.cs = rcs;\r
+ sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());\r
}\r
\r
refresh();\r
protected void conservationMenuItem_itemStateChanged(ItemEvent ie)\r
{\r
SequenceGroup sg = getGroup();\r
+ if(sg.cs==null)\r
+ return;\r
\r
if (conservationMenuItem.getState())\r
{\r
\r
c.calculate();\r
c.verdict(false, ap.av.ConsPercGaps);\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
\r
- sg.cs = ccs;\r
+ sg.cs.setConservation(c);\r
\r
- SliderPanel.setConservationSlider(ap, ccs, sg.getName());\r
+ SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());\r
SliderPanel.showConservationSlider();\r
}\r
else // remove ConservationColouring\r
{\r
- ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;\r
- sg.cs = ccs.cs;\r
+ sg.cs.setConservation(null);\r
}\r
\r
refresh();\r
\r
protected void analyze_actionPerformed(ActionEvent e)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame.applet);\r
Frame frame = new Frame();\r
frame.add(cap);\r
jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);\r