\r
import java.awt.*;\r
import java.awt.event.*;\r
+import java.util.Vector;\r
\r
import jalview.analysis.*;\r
import jalview.datamodel.*;\r
MenuItem noColourmenuItem = new MenuItem();\r
protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
\r
- AlignmentPanel ap;\r
- Menu sequenceMenu = new Menu();\r
- MenuItem sequenceName = new MenuItem();\r
- Sequence sequence;\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)\r
+ public APopupMenu(AlignmentPanel apanel, final 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
- sequence = seq;\r
+ this.ap = apanel;\r
\r
try\r
{\r
groupMenu.remove(unGroupMenuItem);\r
}\r
\r
- if (seq == null)\r
+ if (seq != null && links!=null)\r
{\r
- remove(sequenceMenu);\r
+ Menu linkMenu = new Menu("Link");\r
+ MenuItem item;\r
+ String link;\r
+ for(int i=0; i<links.size(); i++)\r
+ {\r
+ link = links.elementAt(i).toString();\r
+ final String target = link.substring(0, link.indexOf("|"));\r
+ item = new MenuItem(target);\r
+ String id = seq.getName();\r
+ if(id.indexOf("|")>-1)\r
+ id = id.substring(id.lastIndexOf("|")+1);\r
+\r
+ final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))\r
+ + id +\r
+ link.substring(link.indexOf("$SEQUENCE_ID$") + 13);\r
+\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ ap.alignFrame.showURL(url, target);\r
+ }\r
+ });\r
+ linkMenu.add(item);\r
+ }\r
+ add(linkMenu);\r
+\r
+ item = new MenuItem("Show PDB Structure");\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ addPDB(seq);\r
+ }\r
+ });\r
+\r
+ add(item);\r
+\r
+\r
}\r
+ }\r
\r
+ void addPDB(Sequence seq)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame.applet);\r
+ cap.setText("Paste your PDB file here.");\r
+ cap.setPDBImport(seq, ap.seqPanel.seqCanvas);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);\r
}\r
\r
private void jbInit()\r
groupMenu.setLabel("Group");\r
groupMenu.setLabel("Define");\r
\r
- sequenceMenu.setLabel("Sequence");\r
- sequenceName.setLabel("Edit name");\r
unGroupMenuItem.setLabel("Remove Group");\r
unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
});\r
\r
add(groupMenu);\r
- this.add(sequenceMenu);\r
groupMenu.add(unGroupMenuItem);\r
groupMenu.add(colourMenu);\r
groupMenu.addSeparator();\r
groupMenu.add(showBoxes);\r
groupMenu.add(showText);\r
groupMenu.add(showColourText);\r
- sequenceMenu.add(sequenceName);\r
colourMenu.add(noColourmenuItem);\r
colourMenu.add(clustalColour);\r
colourMenu.add(BLOSUM62Colour);\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
\r
- protected void analyze_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);\r
- SequenceGroup sg = getGroup();\r
- StringBuffer sb = new StringBuffer();\r
-\r
- for (int i = 0; i < sg.sequences.size(); i++)\r
- {\r
- Sequence tmp = (Sequence) sg.sequences.elementAt(i);\r
- sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));\r
- sb.append("\n");\r
- }\r
-\r
- sb.append("Something amazing will happen soon");\r
- cap.setText(sb.toString());\r
-\r
- }\r
\r
SequenceGroup getGroup()\r
{\r
git://source.jalview.org / jalview.git / blobdiff