import jalview.datamodel.*;\r
import jalview.analysis.*;\r
import jalview.schemes.*;\r
+import java.awt.*;\r
import javax.swing.*;\r
import java.awt.event.*;\r
import jalview.io.*;\r
Sequence sequence;\r
JMenuItem unGroupMenuItem = new JMenuItem();\r
JMenuItem pdbMenuItem = new JMenuItem();\r
+ JMenuItem outline = new JMenuItem();\r
\r
public PopupMenu(AlignmentPanel ap, Sequence seq)\r
{\r
catch(Exception e)\r
{ e.printStackTrace(); }\r
\r
- SequenceGroup sg = ap.av.getRubberbandGroup();\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
if(sg!=null)\r
{\r
groupName.setText(sg.getName());\r
groupName_actionPerformed(e);\r
}\r
});\r
+ groupAnnotation.setEnabled(false);\r
groupAnnotation.setText("Annotation");\r
groupAnnotation.addActionListener(new java.awt.event.ActionListener()\r
{\r
}\r
});\r
residueMenu.setText("Residue");\r
+ annotateResidue.setEnabled(false);\r
+ annotateResidue.setActionCommand("annotate residue");\r
annotateResidue.setText("annotate residue???");\r
PIDColour.setFocusPainted(false);\r
unGroupMenuItem.setText("Remove Group");\r
pdbMenuItem_actionPerformed(e);\r
}\r
});\r
+ outline.setText("Border colour");\r
+ outline.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ outline_actionPerformed(e);\r
+ }\r
+ });\r
add(groupMenu);\r
this.add(sequenceMenu);\r
this.add(residueMenu);\r
defineMenu.add(groupName);\r
defineMenu.add(groupAnnotation);\r
defineMenu.addSeparator();\r
+ defineMenu.add(outline);\r
+ defineMenu.addSeparator();\r
defineMenu.add(noColourmenuItem);\r
defineMenu.add(clustalColour);\r
defineMenu.add(zappoColour);\r
if( superG !=null)\r
superG.setSuperGroupProperties( sg );\r
\r
- ap.seqPanel.seqCanvas.paintFlag=true;\r
ap.seqPanel.repaint();\r
}\r
\r
\r
protected void abovePIDColour_actionPerformed(ActionEvent e)\r
{\r
- Desktop.setPIDSliderSource(ap, getGroup().cs, getGroup().getName());\r
+ SequenceGroup sg = getGroup();\r
+ if (abovePIDColour.isSelected())\r
+ {\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+ ap.av.alignment.getWidth()));\r
+ int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());\r
+ if (sg.cs instanceof ResidueColourScheme)\r
+ ( (ResidueColourScheme)sg. cs).setThreshold(threshold);\r
+ else if (sg.cs instanceof ScoreColourScheme)\r
+ ( (ScoreColourScheme) sg.cs).setThreshold(threshold);\r
+\r
+ SliderPanel.showPIDSlider();\r
+\r
+\r
+ }\r
+ else // remove PIDColouring\r
+ {\r
+ ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;\r
+ rcs.setThreshold(0);\r
+ sg.cs = rcs;\r
+ }\r
+\r
+ refresh();\r
+\r
}\r
\r
\r
\r
protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
{\r
- getGroup().cs = new Blosum62ColourScheme(ap.av);\r
+ SequenceGroup sg = getGroup();\r
+\r
+ sg.cs = new Blosum62ColourScheme();\r
+\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+ ap.av.alignment.getWidth()));\r
+\r
refresh();\r
}\r
\r
ap.av.alignment.getWidth());\r
\r
c.calculate();\r
- c.verdict(false, 100);\r
+ c.verdict(false, ap.av.ConsPercGaps);\r
ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
\r
\r
sg.cs = ccs;\r
\r
- Desktop.setConservationSliderSource(ap, ccs, sg.getName());\r
+ SliderPanel.setConservationSlider(ap, ccs, sg.getName());\r
+ SliderPanel.showConservationSlider();\r
}\r
else // remove ConservationColouring\r
{\r
\r
SequenceGroup getGroup()\r
{\r
- SequenceGroup sg = ap.av.getRubberbandGroup();\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
\r
// this method won't add a new group if it already exists\r
ap.av.alignment.addGroup(sg);\r
+\r
return sg;\r
}\r
\r
if(s!=null)\r
{\r
sequence.setName(s);\r
- ap.RefreshPanels();\r
+ ap.repaint();\r
}\r
\r
}\r
\r
void unGroupMenuItem_actionPerformed(ActionEvent e)\r
{\r
- SequenceGroup sg = ap.av.getRubberbandGroup();\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
ap.av.alignment.deleteGroup(sg);\r
- ap.av.setRubberbandGroup(null);\r
- ap.RefreshPanels();\r
+ ap.av.setSelectionGroup(null);\r
+ ap.repaint();\r
}\r
\r
void pdbMenuItem_actionPerformed(ActionEvent e)\r
}\r
}\r
\r
+ protected void outline_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = getGroup();\r
+ Color col = JColorChooser.showDialog(this, "Select Outline Colour", Color.BLUE);\r
+ if(col!=null)\r
+ sg.setOutlineColour(col);\r
+ }\r
+\r
}\r