-/*\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme( null );\r
- changeColour();\r
- }\r
-\r
-\r
- public void clustalColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme(new ClustalxColourScheme( ));\r
- conservationMenuItem.setSelected(false);\r
- abovePIDThreshold.setSelected(false);\r
- changeColour();\r
- }\r
-\r
- public void zappoColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme(new ZappoColourScheme() );\r
- changeColour();\r
- }\r
-\r
- public void taylorColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme(new TaylorColourScheme() );\r
- changeColour();\r
- }\r
-\r
-\r
- public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme( new HydrophobicColourScheme() );\r
- changeColour();\r
- }\r
-\r
- public void helixColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme( new HelixColourScheme() );\r
- changeColour();\r
- }\r
-\r
-\r
- public void strandColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme(new StrandColourScheme() );\r
- changeColour();\r
- }\r
-\r
-\r
- public void turnColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme(new TurnColourScheme() );\r
- changeColour();\r
- }\r
-\r
-\r
- public void buriedColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme( new BuriedColourScheme() );\r
- changeColour();\r
- }\r
-\r
- void changeColour()\r
- {\r
- if(abovePIDThreshold.isSelected())\r
- abovePIDThreshold_actionPerformed(null);\r
- else if(conservationMenuItem.isSelected())\r
- conservationMenuItem_actionPerformed(null);\r
-\r
- alignPanel.seqPanel.seqCanvas.paintFlag = true;\r
- alignPanel.repaint();\r
- }\r
-\r
- void addConservationOrPIDColour()\r
- {\r
- int x=0, y=0, threshold = 70;\r
-\r
- if(sliderFrame!=null)\r
- try\r
- {\r
- x = sliderFrame.getX();\r
- y = sliderFrame.getY();\r
- SliderPanel sp = (SliderPanel) sliderFrame.getContentPane();\r
- threshold = sp.getValue();\r
- sliderFrame.setClosed(true);\r
- }\r
- catch (Exception ex)\r
- { ex.printStackTrace(); }\r
-\r
- ColourSchemeI oldCs = viewport.getGlobalColourScheme();\r
-\r
- ConservationColourScheme ccs = null;\r
- if (oldCs instanceof ConservationColourScheme)\r
- ccs = (ConservationColourScheme) oldCs;\r
-\r
- if(conservationMenuItem.isSelected())\r
- {\r
- Alignment al = (Alignment)viewport.alignment;\r
- Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3, al.getSequences(), 0,\r
- al.getWidth() );\r
-\r
- c.calculate();\r
- c.verdict(false, 100);\r
-\r
- if(ccs!=null)\r
- ccs = new ConservationColourScheme(c, ccs.cs);\r
- else\r
- ccs = new ConservationColourScheme(c, oldCs);\r
-\r
- viewport.setGlobalColourScheme( ccs );\r
-\r
- }\r
- else if(oldCs instanceof ConservationColourScheme)\r
- {\r
- oldCs = ccs.cs;\r
- viewport.setGlobalColourScheme( oldCs );\r
- }\r
-\r
-\r
- if( conservationMenuItem.isSelected() || abovePIDThreshold.isSelected() )\r
- {\r
- sliderFrame = new JInternalFrame();\r
- sliderFrame.setMaximizable(false);\r
- sliderFrame.setResizable(false);\r
-\r
- SliderPanel sp = null;\r
- if (conservationMenuItem.isSelected())\r
- {\r
- if(threshold > 50)\r
- threshold = 30;\r
- sp = new SliderPanel(alignPanel, threshold, true,ccs);\r
- Desktop.addInternalFrame(sliderFrame, "Conservation Colour Increment (Global colour)", 400, 90);\r
- threshold = 0;\r
- }\r
- else if (abovePIDThreshold.isSelected())\r
- {\r
- sp = new SliderPanel(alignPanel, threshold, false, oldCs);\r
- sp.cs = oldCs;\r
- Desktop.addInternalFrame(sliderFrame, "Percentage Identity Threshold (Global colour)", 400, 90);\r
- }\r
-\r
- sliderFrame.setContentPane(sp);\r
- if(x!=0 && y!=0)\r
- sliderFrame.setLocation(x,y);\r
-\r
- }\r
- else\r
- threshold = 0;\r
-\r
-\r
- if (oldCs instanceof ResidueColourScheme)\r
- {\r
- ResidueColourScheme rcs = (ResidueColourScheme) oldCs;\r
- rcs.setThreshold(threshold);\r
- }\r
- else if (oldCs instanceof ScoreColourScheme)\r
- {\r
- ScoreColourScheme scs = (ScoreColourScheme) oldCs;\r
- scs.setThreshold(threshold);\r
- }\r
-\r
- alignPanel.seqPanel.seqCanvas.paintFlag = true;\r
- alignPanel.repaint();\r
-\r
- }\r
-\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if(abovePIDThreshold.isSelected())\r
- abovePIDThreshold.setSelected(false);\r
-\r
- viewport.setConservationSelected(conservationMenuItem.isSelected());\r
-\r
- addConservationOrPIDColour();\r
- }\r
-\r
- JInternalFrame sliderFrame;\r
- public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
- {\r
- if(conservationMenuItem.isSelected())\r
- conservationMenuItem.setSelected(false);\r
-\r
- addConservationOrPIDColour();\r
- }\r
-\r
-\r
-\r
- public void userDefinedColour_actionPerformed(ActionEvent e)\r
- {\r
- JInternalFrame frame = new JInternalFrame();\r
- UserDefinedColours chooser = new UserDefinedColours( frame, alignPanel, null);\r
- frame.setContentPane(chooser);\r
- Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
- frame.setResizable(false);\r
- frame.setIconifiable(false);\r
- frame.setMaximizable(false);\r
- }\r
-\r
- public void PIDColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme( new PIDColourScheme() );\r
- alignPanel.setColourScheme( );\r
- }\r
-\r
-\r
- public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme( new Blosum62ColourScheme(viewport) );\r
- alignPanel.setColourScheme();\r
- }\r
-*/\r
-//////////////////////////////////////\r
- protected void groupAnnotation_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
-\r
- protected void groupName_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = getGroup();\r
- String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);\r
- if(reply==null)\r
- return;\r
-\r
- sg.setName(reply);\r
- groupName.setText(reply);\r
- }\r
-\r
- protected void copyGroup_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = ap.av.getRubberbandGroup();\r
-\r
- SequenceI[] s = new Sequence[sg.sequences.size()];\r
- for (int i=0; i < sg.sequences.size(); i++)\r
- {\r
- s[i] = new Sequence( sg.getSequenceAt(i));\r
- s[i].setSequence( s[i].getSequence(sg.getStartRes(), sg.getEndRes()+1) );\r
- }\r
- AlignFrame af = new AlignFrame(new Alignment(s));\r
- int newHeight = s.length * af.viewport.getCharHeight() + 200;\r
- if (newHeight > 500)\r
- newHeight = 500;\r
- Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);\r
- }\r
-\r
- protected void moveGroup_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = ap.av.getRubberbandGroup();\r
-\r
- SequenceI[] s = new Sequence[sg.sequences.size()];\r
-\r
- for (int i=0; i < sg.sequences.size(); i++)\r
- s[i] = new Sequence( sg.getSequenceAt(i));\r
-\r
- AlignFrame af = new AlignFrame(new Alignment(s));\r
- int newHeight = s.length * af.viewport.getCharHeight() + 200;\r
- if(newHeight>500)\r
- newHeight=500;\r
- Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);\r
-\r
-\r
- for (int i=0; i < sg.sequences.size(); i++)\r
- ap.av.alignment.deleteSequence(sg.getSequenceAt(i));\r
-\r
-\r
- ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());\r
- ap.RefreshPanels();\r
-\r
-\r
- }\r
-\r
- protected void deleteSequences_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = ap.av.getRubberbandGroup();\r
- for (int i=0;i < sg.sequences.size(); i++)\r
- ap.av.getAlignment().deleteSequence(sg.getSequenceAt(i));\r
-\r
- ap.av.alignment.deleteGroup(sg);\r
- ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());\r
- ap.seqPanel.parent.RefreshPanels();\r
-\r
- }\r
-\r
- protected void analyze_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false);\r
- JInternalFrame frame = new JInternalFrame();\r
- cap.formatForOutput();\r
- frame.setContentPane(cap);\r
- Desktop.addInternalFrame(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.get(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
- SequenceGroup sg = ap.av.getRubberbandGroup();\r
-\r
- // this method won't add a new group if it already exists\r
- ap.av.alignment.addGroup(sg);\r
- return sg;\r
- }\r
-\r
- void sequenceName_actionPerformed(ActionEvent e)\r
- {\r
- String id = sequence.getName();\r
- String s = (String)JOptionPane.showInternalInputDialog(\r
- ap,\r
- "Edit sequence name",\r
- "Edit sequence name",\r
- JOptionPane.PLAIN_MESSAGE,\r
- null,\r
- null,\r
- id);\r