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
- JMenuItem residueMenu = new JMenuItem();\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
protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();\r
- protected JRadioButtonMenuItem abovePIDColour = new JRadioButtonMenuItem();\r
+ protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();\r
protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();\r
JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();\r
- protected JMenuItem conservationColourIncMenuItem = new JMenuItem();\r
protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();\r
\r
\r
- AlignViewport av;\r
- SeqPanel seqPanel;\r
+ AlignmentPanel ap;\r
+ JMenu sequenceMenu = new JMenu();\r
+ JMenuItem sequenceName = new JMenuItem();\r
+ JMenu residueMenu = new JMenu();\r
+ JMenuItem annotateResidue = new JMenuItem();\r
+\r
+ Sequence sequence;\r
+ JMenuItem unGroupMenuItem = new JMenuItem();\r
+ JMenuItem pdbMenuItem = new JMenuItem();\r
+ JMenuItem outline = new JMenuItem();\r
\r
- public PopupMenu(AlignViewport av, SeqPanel sp)\r
+ public PopupMenu(AlignmentPanel ap, Sequence seq)\r
{\r
- this.av = av;\r
- seqPanel = sp;\r
+ ///////////////////////////////////////////////////////////\r
+ // If this is activated from the sequence panel, the user may want to\r
+ // edit or annotate a particular residue. Therefore display the residue menu\r
+ //\r
+ // If from the IDPanel, we must display the sequence menu\r
+ //////////////////////////////////////////////////////////\r
+\r
+ this.ap = ap;\r
+ sequence = seq;\r
\r
ButtonGroup colours = new ButtonGroup();\r
colours.add(noColourmenuItem);\r
colours.add(BLOSUM62Colour);\r
\r
try\r
- {\r
- jbInit();\r
- }\r
+ { jbInit(); }\r
catch(Exception e)\r
+ { e.printStackTrace(); }\r
+\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ if(sg!=null)\r
{\r
- e.printStackTrace();\r
+ groupName.setText(sg.getName());\r
+ if(sg.cs instanceof ZappoColourScheme)\r
+ zappoColour.setSelected(true);\r
+ else if(sg.cs instanceof TaylorColourScheme)\r
+ taylorColour.setSelected(true);\r
+ else if (sg.cs instanceof PIDColourScheme)\r
+ PIDColour.setSelected(true);\r
+ else if (sg.cs instanceof Blosum62ColourScheme)\r
+ BLOSUM62Colour.setSelected(true);\r
+ else if (sg.cs instanceof UserColourScheme)\r
+ userDefinedColour.setSelected(true);\r
+ else if (sg.cs instanceof HydrophobicColourScheme)\r
+ hydrophobicityColour.setSelected(true);\r
+ else if (sg.cs instanceof HelixColourScheme)\r
+ helixColour.setSelected(true);\r
+ else if (sg.cs instanceof StrandColourScheme)\r
+ strandColour.setSelected(true);\r
+ else if (sg.cs instanceof TurnColourScheme)\r
+ turnColour.setSelected(true);\r
+ else if (sg.cs instanceof BuriedColourScheme)\r
+ buriedColour.setSelected(true);\r
+ else if (sg.cs instanceof ClustalxColourScheme)\r
+ clustalColour.setSelected(true);\r
+ else\r
+ noColourmenuItem.setSelected(true);\r
+\r
+ if (sg.cs instanceof ConservationColourScheme)\r
+ conservationMenuItem.setSelected(true);\r
}\r
\r
- SequenceGroup sg = av.getRubberbandGroup();\r
- groupName.setText( sg.getName() );\r
+\r
+ if(seq!=null)\r
+ residueMenu.setVisible(false);\r
+ else\r
+ sequenceMenu.setVisible(false);\r
+\r
}\r
private void jbInit() throws Exception\r
{\r
- residueMenu.setText("Residue");\r
groupMenu.setText("Group");\r
- copyGroup.setText("Copy region to new Alignment");\r
- copyGroup.addActionListener(new java.awt.event.ActionListener()\r
+ analyze.setText("Analyze");\r
+ analyze.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- copyGroup_actionPerformed(e);\r
+ analyze_actionPerformed(e);\r
}\r
});\r
- moveGroup.setText("Move sequences to new Alignment");\r
- moveGroup.addActionListener(new java.awt.event.ActionListener()\r
+ defineMenu.setText("Define");\r
+ groupName.setText("Name");\r
+ groupName.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- moveGroup_actionPerformed(e);\r
+ groupName_actionPerformed(e);\r
}\r
});\r
- deleteSequences.setText("Delete sequences");\r
- deleteSequences.addActionListener(new java.awt.event.ActionListener()\r
+ groupAnnotation.setEnabled(false);\r
+ groupAnnotation.setText("Annotation");\r
+ groupAnnotation.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- deleteSequences_actionPerformed(e);\r
+ groupAnnotation_actionPerformed(e);\r
}\r
});\r
- analyze.setText("Analyze");\r
- analyze.addActionListener(new java.awt.event.ActionListener()\r
+ sequenceMenu.setText("Sequence");\r
+ sequenceName.setText("Edit name");\r
+ sequenceName.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- analyze_actionPerformed(e);\r
+ sequenceName_actionPerformed(e);\r
}\r
});\r
- defineMenu.setText("Define");\r
- groupName.setText("Name");\r
- groupName.addActionListener(new java.awt.event.ActionListener()\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
- groupName_actionPerformed(e);\r
+ unGroupMenuItem_actionPerformed(e);\r
}\r
});\r
- groupAnnotation.setText("Annotation");\r
- groupAnnotation.addActionListener(new java.awt.event.ActionListener()\r
+ pdbMenuItem.setText("View PDB structure");\r
+ pdbMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- groupAnnotation_actionPerformed(e);\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
- add(residueMenu);\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(turnColour);\r
defineMenu.add(buriedColour);\r
defineMenu.add(userDefinedColour);\r
- defineMenu.addSeparator();\r
- defineMenu.add(conservationMenuItem);\r
- defineMenu.add(conservationColourIncMenuItem);\r
- defineMenu.addSeparator();\r
- defineMenu.add(abovePIDColour);\r
defineMenu.add(PIDColour);\r
defineMenu.add(BLOSUM62Colour);\r
+ defineMenu.addSeparator();\r
+ defineMenu.add(abovePIDColour);\r
+ defineMenu.add(conservationMenuItem);\r
+\r
+ sequenceMenu.add(sequenceName);\r
+ sequenceMenu.add(pdbMenuItem);\r
+ residueMenu.add(annotateResidue);\r
\r
noColourmenuItem.setText("None");\r
- noColourmenuItem.setSelected(true);\r
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
}\r
});\r
\r
- clustalColour.setEnabled(false);\r
- clustalColour.setSelected(false);\r
clustalColour.setText("Clustalx colours");\r
clustalColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
buriedColour_actionPerformed(e);\r
}\r
});\r
- abovePIDColour.setEnabled(false);\r
abovePIDColour.setText("Above PID threshold only");\r
abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
userDefinedColour_actionPerformed(e);\r
}\r
});\r
- PIDColour.setEnabled(false);\r
- PIDColour.setText("By PID");\r
+ PIDColour.setText("Percentage Identity");\r
PIDColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
PIDColour_actionPerformed(e);\r
}\r
});\r
- BLOSUM62Colour.setText("By BLOSUM62 score");\r
+ BLOSUM62Colour.setText("BLOSUM62 score");\r
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
}\r
});\r
\r
- conservationColourIncMenuItem.setEnabled(false);\r
- conservationColourIncMenuItem.setText("Conservation Colour Increment");\r
- conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- conservationColourIncMenuItem_actionPerformed(e);\r
- }\r
- });\r
\r
\r
}\r
\r
void refresh()\r
{\r
- seqPanel.seqCanvas.paintFlag=true;\r
- seqPanel.repaint();\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
-\r
+ SequenceGroup sg = getGroup();\r
+ sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());\r
+ refresh();\r
}\r
\r
protected void zappoColour_actionPerformed(ActionEvent e)\r
}\r
\r
\r
- protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
- {\r
+ protected void abovePIDColour_actionPerformed(ActionEvent e)\r
+ {\r
+ if(abovePIDColour.isSelected())\r
+{\r
\r
+ Desktop.setPIDSliderSource(ap, getGroup().cs, getGroup().getName());\r
+ refresh();\r
}\r
-/*\r
-public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\r
+else // remove PIDColouring\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
+ 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
\r
}\r
\r
protected void userDefinedColour_actionPerformed(ActionEvent e)\r
{\r
JInternalFrame frame = new JInternalFrame();\r
- UserDefinedColours chooser = new UserDefinedColours( frame, seqPanel.parent, getGroup());\r
+ UserDefinedColours chooser = new UserDefinedColours( frame, ap, getGroup());\r
frame.setContentPane(chooser);\r
- Desktop.addInternalFrame(frame,"User defined colours", 450,540 );\r
+ Desktop.addInternalFrame(frame,"User defined colours ("+getGroup().getName()+")", 450,540 );\r
frame.setResizable(false);\r
frame.setIconifiable(false);\r
frame.setMaximizable(false);\r
\r
protected void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
{\r
- getGroup().cs = new Blosum62ColourScheme(av);\r
+ getGroup().cs = new Blosum62ColourScheme(ap.av);\r
refresh();\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
+ if(conservationMenuItem.isSelected())\r
+ {\r
+\r
+ Conservation c = new Conservation("Group",\r
+ ResidueProperties.propHash, 3,\r
+ sg.sequences, 0,\r
+ ap.av.alignment.getWidth());\r
+\r
+ c.calculate();\r
+ c.verdict(false, 100);\r
+ ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
\r
- c.calculate();\r
- c.verdict(false, 100);\r
- ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
\r
- sg.cs = ccs;\r
+ sg.cs = ccs;\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
refresh();\r
}\r
sg.setName(reply);\r
groupName.setText(reply);\r
}\r
- /* public void deleteSelectedMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem("delete selection");\r
-\r
- for (int i=0;i < viewport.getSelection().size(); i++)\r
- viewport.getAlignment().deleteSequence(viewport.getSelection().sequenceAt(i));\r
-\r
- viewport.getSelection().clear();\r
- viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight());\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
- public void moveSelectedMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- copySelectedMenuItem_actionPerformed(null);\r
- deleteSelectedMenuItem_actionPerformed(null);\r
- alignPanel.repaint();\r
- }\r
-\r
- public void copySelectedMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if(viewport.getSelection().size()==0)\r
- return;\r
-\r
- SequenceI[] s = new Sequence[viewport.getSelection().size()];\r
- for (int i=0; i < viewport.getSelection().size(); i++) {\r
- s[i] = new Sequence(viewport.getSelection().sequenceAt(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
- protected void copyGroup_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = 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
-\r
- }\r
-\r
- protected void deleteSequences_actionPerformed(ActionEvent e)\r
- {\r
- SequenceGroup sg = av.getRubberbandGroup();\r
- for (int i=0;i < sg.sequences.size(); i++)\r
- av.getAlignment().deleteSequence(sg.getSequenceAt(i));\r
\r
- av.alignment.deleteGroup(sg);\r
- av.resetSeqLimits(seqPanel.seqCanvas.getHeight());\r
- seqPanel.parent.RefreshPanels();\r
-\r
- }\r
\r
protected void analyze_actionPerformed(ActionEvent e)\r
{\r
\r
SequenceGroup getGroup()\r
{\r
- SequenceGroup sg = av.getRubberbandGroup();\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
\r
// this method won't add a new group if it already exists\r
- av.alignment.addGroup(sg);\r
+ ap.av.alignment.addGroup(sg);\r
+\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 ("+sequence.getName()+")",\r
+ JOptionPane.PLAIN_MESSAGE,\r
+ null,\r
+ null,\r
+ id);\r
+\r
+ if(s!=null)\r
+ {\r
+ sequence.setName(s);\r
+ ap.RefreshPanels();\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