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
+ JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();\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
+ nucleotideMenuItem.setText("Nucleotide");\r
+ nucleotideMenuItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ nucleotideMenuItem_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(BLOSUM62Colour);\r
+ defineMenu.add(PIDColour);\r
+\r
defineMenu.add(zappoColour);\r
defineMenu.add(taylorColour);\r
defineMenu.add(hydrophobicityColour);\r
defineMenu.add(strandColour);\r
defineMenu.add(turnColour);\r
defineMenu.add(buriedColour);\r
+ defineMenu.add(nucleotideMenuItem);\r
+\r
defineMenu.add(userDefinedColour);\r
- defineMenu.add(PIDColour);\r
- defineMenu.add(BLOSUM62Colour);\r
+\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
clustalColour_actionPerformed(e);\r
}\r
});\r
- zappoColour.setText("Zappo colour scheme");\r
+ zappoColour.setText("Zappo");\r
zappoColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
zappoColour_actionPerformed(e);\r
}\r
});\r
- taylorColour.setText("Taylor colour scheme");\r
+ taylorColour.setText("Taylor");\r
taylorColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
taylorColour_actionPerformed(e);\r
}\r
});\r
- hydrophobicityColour.setText("By hydrophobicity");\r
+ hydrophobicityColour.setText("Hydrophobicity");\r
hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
turnColour_actionPerformed(e);\r
}\r
});\r
- buriedColour.setText("Buried index");\r
+ buriedColour.setText("Buried Index");\r
buriedColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
buriedColour_actionPerformed(e);\r
}\r
});\r
- abovePIDColour.setText("Above PID threshold only");\r
+ abovePIDColour.setText("Above % Identity");\r
abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
abovePIDColour_actionPerformed(e);\r
}\r
});\r
- userDefinedColour.setText("User defined colours");\r
+ userDefinedColour.setText("User Defined");\r
userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
PIDColour_actionPerformed(e);\r
}\r
});\r
- BLOSUM62Colour.setText("BLOSUM62 score");\r
+ BLOSUM62Colour.setText("BLOSUM62");\r
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
BLOSUM62Colour_actionPerformed(e);\r
}\r
});\r
- conservationMenuItem.setText("By conservation");\r
+ conservationMenuItem.setText("Conservation");\r
conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
if( superG !=null)\r
superG.setSuperGroupProperties( sg );\r
\r
- ap.seqPanel.seqCanvas.paintFlag=true;\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
refresh();\r
}\r
\r
+ public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ getGroup().cs = new NucleotideColourScheme();\r
+ refresh();\r
+ }\r
\r
-/*\r
-public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)\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
\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
+ 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
protected void userDefinedColour_actionPerformed(ActionEvent e)\r
{\r
- JInternalFrame frame = new JInternalFrame();\r
- UserDefinedColours chooser = new UserDefinedColours( frame, ap, getGroup());\r
- frame.setContentPane(chooser);\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
+ UserDefinedColours chooser = new UserDefinedColours( ap, getGroup());\r
}\r
\r
protected void PIDColour_actionPerformed(ActionEvent e)\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
{\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
+ c.calculate();\r
+ c.verdict(false, ap.av.ConsPercGaps);\r
+ ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
\r
- sg.cs = ccs;\r
+\r
+ sg.cs = ccs;\r
+\r
+ SliderPanel.setConservationSlider(ap, ccs, sg.getName());\r
+ SliderPanel.showConservationSlider();\r
+ }\r
+ else // remove ConservationColouring\r
+ {\r
+ ConservationColourScheme ccs = (ConservationColourScheme)sg.cs;\r
+ sg.cs = ccs.cs;\r
+ }\r
\r
refresh();\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
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.getSelectionGroup();\r
+ ap.av.alignment.deleteGroup(sg);\r
+ ap.av.setSelectionGroup(null);\r
+ ap.repaint();\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
+ System.out.println("Got "+ sequence.getPDBId() );\r
+ PDBfile pdb = new PDBfile(result);\r
+\r
+ rotCanvas rc = new rotCanvas(pdb, sequence, ap.av);\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