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
-\r
+import jalview.io.*;\r
+import MCview.*;\r
\r
public class PopupMenu extends JPopupMenu\r
{\r
JMenu groupMenu = new JMenu();\r
- JMenuItem copyGroup = new JMenuItem();\r
- JMenuItem moveGroup = new JMenuItem();\r
- JMenuItem deleteSequences = new JMenuItem();\r
JMenuItem analyze = new JMenuItem();\r
JMenu defineMenu = new JMenu();\r
JMenuItem groupName = new JMenuItem();\r
JMenu residueMenu = new JMenu();\r
JMenuItem annotateResidue = new JMenuItem();\r
\r
- SequenceI sequence;\r
+ Sequence sequence;\r
+ JMenuItem unGroupMenuItem = new JMenuItem();\r
+ JMenuItem pdbMenuItem = new JMenuItem();\r
+ JMenuItem outline = new JMenuItem();\r
\r
- public PopupMenu(AlignmentPanel ap, SequenceI seq)\r
+ public PopupMenu(AlignmentPanel ap, Sequence seq)\r
{\r
///////////////////////////////////////////////////////////\r
// If this is activated from the sequence panel, the user may want to\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
\r
if (sg.cs instanceof ConservationColourScheme)\r
conservationMenuItem.setSelected(true);\r
-\r
}\r
\r
+\r
if(seq!=null)\r
- {\r
residueMenu.setVisible(false);\r
- sequenceName.setText( sequence.getName() );\r
- }\r
else\r
sequenceMenu.setVisible(false);\r
\r
private void jbInit() throws Exception\r
{\r
groupMenu.setText("Group");\r
- copyGroup.setText("Copy region to new Alignment");\r
- copyGroup.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- copyGroup_actionPerformed(e);\r
- }\r
- });\r
- moveGroup.setText("Move sequences to new Alignment");\r
- moveGroup.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- moveGroup_actionPerformed(e);\r
- }\r
- });\r
- deleteSequences.setText("Delete sequences");\r
- deleteSequences.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- deleteSequences_actionPerformed(e);\r
- }\r
- });\r
analyze.setText("Analyze");\r
analyze.addActionListener(new java.awt.event.ActionListener()\r
{\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
sequenceMenu.setText("Sequence");\r
- sequenceName.setText("sequenceName");\r
+ sequenceName.setText("Edit name");\r
sequenceName.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\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
+ unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ unGroupMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ pdbMenuItem.setText("View PDB structure");\r
+ pdbMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\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
groupMenu.add(defineMenu);\r
- groupMenu.addSeparator();\r
- groupMenu.add(copyGroup);\r
- groupMenu.add(moveGroup);\r
- groupMenu.add(deleteSequences);\r
+ groupMenu.add(unGroupMenuItem);\r
groupMenu.addSeparator();\r
groupMenu.add(analyze);\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
defineMenu.add(conservationMenuItem);\r
\r
sequenceMenu.add(sequenceName);\r
+ sequenceMenu.add(pdbMenuItem);\r
residueMenu.add(annotateResidue);\r
\r
noColourmenuItem.setText("None");\r
\r
void refresh()\r
{\r
- ap.seqPanel.seqCanvas.paintFlag=true;\r
+ SequenceGroup sg = getGroup();\r
+ SuperGroup superG = ap.av.alignment.getSuperGroup( sg );\r
+ if( superG !=null)\r
+ superG.setSuperGroupProperties( sg );\r
+\r
ap.seqPanel.repaint();\r
}\r
\r
protected void clustalColour_actionPerformed(ActionEvent e)\r
{\r
- getGroup().cs = new ClustalxColourScheme();\r
+ SequenceGroup sg = getGroup();\r
+ sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());\r
refresh();\r
}\r
\r
}\r
\r
\r
-/*\r
-public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
+ protected void abovePIDColour_actionPerformed(ActionEvent e)\r
+ {\r
+ if(abovePIDColour.isSelected())\r
{\r
-ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);\r
-JInternalFrame frame = new JInternalFrame();\r
-frame.setContentPane(cip);\r
-Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);\r
-frame.setMaximizable(false);\r
\r
- }*/\r
+ Desktop.setPIDSliderSource(ap, getGroup().cs, getGroup().getName());\r
+ refresh();\r
+}\r
+else // remove PIDColouring\r
+{\r
+ ColourSchemeI cs = getGroup().cs;\r
+ ResidueColourScheme rcs = (ResidueColourScheme)cs;\r
+ rcs.setThreshold(0);\r
+ getGroup().cs = rcs;\r
+ refresh();\r
+}\r
\r
\r
- protected void abovePIDColour_actionPerformed(ActionEvent e)\r
- {\r
- SliderPanel sp = new SliderPanel(ap, 70, false, getGroup().cs );\r
- JInternalFrame frame = new JInternalFrame();\r
- frame.setContentPane(sp);\r
- Desktop.addInternalFrame(frame, "Percentage Identity Threshold ("+getGroup().getName()+")" , 400,90);\r
- frame.setMaximizable(false);\r
\r
}\r
\r
{\r
SequenceGroup sg = getGroup();\r
\r
- Conservation c = new Conservation("Group",\r
- ResidueProperties.propHash, 3, sg.sequences, sg.getStartRes(),\r
- sg.getEndRes() );\r
-\r
- c.calculate();\r
- c.verdict(false, 100);\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
-\r
- sg.cs = ccs;\r
-\r
- refresh();\r
- }\r
-\r
-/*\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
+ if(conservationMenuItem.isSelected())\r
+ {\r
\r
- JInternalFrame sliderFrame;\r
- public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
- {\r
- if(conservationMenuItem.isSelected())\r
- conservationMenuItem.setSelected(false);\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3,\r
+ sg.sequences, 0,\r
+ ap.av.alignment.getWidth());\r
\r
- addConservationOrPIDColour();\r
- }\r
+ c.calculate();\r
+ c.verdict(false, 100);\r
+ ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
\r
\r
+ sg.cs = ccs;\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
+ Desktop.setConservationSliderSource(ap, ccs, sg.getName());\r
+ }\r
+ else // remove ConservationColouring\r
+ {\r
+ ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
+ sg.cs = ccs.cs;\r
+ }\r
\r
- public void PIDColour_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setGlobalColourScheme( new PIDColourScheme() );\r
- alignPanel.setColourScheme( );\r
+ refresh();\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
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
\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
String s = (String)JOptionPane.showInternalInputDialog(\r
ap,\r
"Edit sequence name",\r
- "Edit sequence name",\r
+ "Edit sequence name ("+sequence.getName()+")",\r
JOptionPane.PLAIN_MESSAGE,\r
null,\r
null,\r
}\r
\r
}\r
+\r
+ void unGroupMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ ap.av.alignment.deleteGroup(sg);\r
+ ap.av.setSelectionGroup(null);\r
+ ap.RefreshPanels();\r
+ }\r
+\r
+ void pdbMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ if(sequence.getPDBId()==null)\r
+ return;\r
+\r
+ try\r
+ {\r
+ EBIFetchClient ebi = new EBIFetchClient();\r
+ String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, null);\r
+\r
+ PDBfile pdb = new PDBfile(result);\r
+ sequence.setPDBfile(pdb);\r
+\r
+ ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).isVisible = true;\r
+ ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).sequence = sequence;\r
+ // ( (PDBChain)pdb.chains.elementAt(sequence.maxchain)).colourBySequence();\r
+\r
+ rotCanvas rc = new rotCanvas(pdb);\r
+ JInternalFrame frame = new JInternalFrame();\r
+ frame.setContentPane(rc);\r
+ Desktop.addInternalFrame(frame,sequence.getName()+" "+ sequence.getPDBId(), 400, 400);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\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
git://source.jalview.org / jalview.git / blobdiff