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
import jalview.io.*;\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
- JMenuItem groupAnnotation = new JMenuItem();\r
protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();\r
protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();\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
+ JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();\r
+ JMenu colourMenu = new JMenu();\r
+ JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();\r
+ JCheckBoxMenuItem showText = new JCheckBoxMenuItem();\r
+ JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();\r
\r
public PopupMenu(AlignmentPanel ap, Sequence seq)\r
{\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
+ showText.setSelected(sg.getDisplayText());\r
+ showColourText.setSelected(sg.getColourText());\r
+ showBoxes.setSelected(sg.getDisplayBoxes());\r
}\r
\r
+ if( !ap.av.alignment.getGroups().contains(sg))\r
+ unGroupMenuItem.setVisible(false);\r
\r
- if(seq!=null)\r
- residueMenu.setVisible(false);\r
- else\r
- sequenceMenu.setVisible(false);\r
+ if(seq==null)\r
+ sequenceMenu.setVisible(false);\r
\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
+ groupMenu.setText("Define");\r
+ groupName.setText("Name");\r
+ groupName.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- copyGroup_actionPerformed(e);\r
+ groupName_actionPerformed(e);\r
}\r
});\r
- moveGroup.setText("Move sequences to new Alignment");\r
- moveGroup.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
- moveGroup_actionPerformed(e);\r
+ sequenceName_actionPerformed(e);\r
}\r
});\r
- deleteSequences.setText("Delete sequences");\r
- deleteSequences.addActionListener(new java.awt.event.ActionListener()\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
- deleteSequences_actionPerformed(e);\r
+ unGroupMenuItem_actionPerformed(e);\r
}\r
});\r
- analyze.setText("Analyze");\r
- analyze.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
- analyze_actionPerformed(e);\r
+ pdbMenuItem_actionPerformed(e);\r
}\r
});\r
- defineMenu.setText("Define");\r
- groupName.setText("Name");\r
- groupName.addActionListener(new java.awt.event.ActionListener()\r
+ outline.setText("Border colour");\r
+ outline.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- groupName_actionPerformed(e);\r
+ outline_actionPerformed(e);\r
}\r
});\r
- groupAnnotation.setText("Annotation");\r
- groupAnnotation.addActionListener(new java.awt.event.ActionListener()\r
+ nucleotideMenuItem.setText("Nucleotide");\r
+ nucleotideMenuItem.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- groupAnnotation_actionPerformed(e);\r
+ nucleotideMenuItem_actionPerformed(e);\r
}\r
});\r
- sequenceMenu.setText("Sequence");\r
- sequenceName.setText("Edit name");\r
- sequenceName.addActionListener(new java.awt.event.ActionListener()\r
+ colourMenu.setText("Group Colour");\r
+ showBoxes.setText("Boxes");\r
+ showBoxes.setState(true);\r
+ showBoxes.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- sequenceName_actionPerformed(e);\r
+ showBoxes_actionPerformed(e);\r
}\r
});\r
- residueMenu.setText("Residue");\r
- annotateResidue.setText("annotate residue???");\r
- PIDColour.setFocusPainted(false);\r
- unGroupMenuItem.setText("Remove Group");\r
- unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ showText.setText("Text");\r
+ showText.setState(true);\r
+ showText.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- unGroupMenuItem_actionPerformed(e);\r
+ showText_actionPerformed(e);\r
}\r
});\r
- pdbMenuItem.setText("View PDB structure");\r
- pdbMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ showColourText.setText("Colour Text");\r
+ showColourText.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- pdbMenuItem_actionPerformed(e);\r
+ showColourText_actionPerformed(e);\r
}\r
});\r
add(groupMenu);\r
- this.add(sequenceMenu);\r
- this.add(residueMenu);\r
- groupMenu.add(defineMenu);\r
+ add(sequenceMenu);\r
+ groupMenu.add(groupName);\r
+ groupMenu.addSeparator();\r
groupMenu.add(unGroupMenuItem);\r
groupMenu.addSeparator();\r
- groupMenu.add(copyGroup);\r
- groupMenu.add(moveGroup);\r
- groupMenu.add(deleteSequences);\r
+ groupMenu.add(colourMenu);\r
groupMenu.addSeparator();\r
- groupMenu.add(analyze);\r
- defineMenu.add(groupName);\r
- defineMenu.add(groupAnnotation);\r
- defineMenu.addSeparator();\r
- defineMenu.add(noColourmenuItem);\r
- defineMenu.add(clustalColour);\r
- defineMenu.add(zappoColour);\r
- defineMenu.add(taylorColour);\r
- defineMenu.add(hydrophobicityColour);\r
- defineMenu.add(helixColour);\r
- defineMenu.add(strandColour);\r
- defineMenu.add(turnColour);\r
- defineMenu.add(buriedColour);\r
- defineMenu.add(userDefinedColour);\r
- defineMenu.add(PIDColour);\r
- defineMenu.add(BLOSUM62Colour);\r
- defineMenu.addSeparator();\r
- defineMenu.add(abovePIDColour);\r
- defineMenu.add(conservationMenuItem);\r
-\r
+ groupMenu.add(showBoxes);\r
+ groupMenu.add(showText);\r
+ groupMenu.add(showColourText);\r
+ groupMenu.addSeparator();\r
+ groupMenu.add(outline);\r
sequenceMenu.add(sequenceName);\r
sequenceMenu.add(pdbMenuItem);\r
- residueMenu.add(annotateResidue);\r
-\r
+ colourMenu.add(noColourmenuItem);\r
+ colourMenu.add(clustalColour);\r
+ colourMenu.add(BLOSUM62Colour);\r
+ colourMenu.add(PIDColour);\r
+ colourMenu.add(zappoColour);\r
+ colourMenu.add(taylorColour);\r
+ colourMenu.add(hydrophobicityColour);\r
+ colourMenu.add(helixColour);\r
+ colourMenu.add(strandColour);\r
+ colourMenu.add(turnColour);\r
+ colourMenu.add(buriedColour);\r
+ colourMenu.add(nucleotideMenuItem);\r
+ colourMenu.add(userDefinedColour);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(abovePIDColour);\r
+ colourMenu.add(conservationMenuItem);\r
noColourmenuItem.setText("None");\r
noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\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
refresh();\r
}\r
\r
+ public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ getGroup().cs = new NucleotideColourScheme();\r
+ refresh();\r
+ }\r
+\r
+\r
\r
protected void abovePIDColour_actionPerformed(ActionEvent e)\r
{\r
- Desktop.setPIDSliderSource(ap, getGroup().cs, getGroup().getName());\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
+ new UserDefinedColours( ap, getGroup());\r
}\r
\r
protected void PIDColour_actionPerformed(ActionEvent e)\r
{\r
-\r
+ SequenceGroup sg = getGroup();\r
+ sg.cs = new PIDColourScheme();\r
+ sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,\r
+ ap.av.alignment.getWidth()));\r
+ refresh();\r
}\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
ap.av.alignment.getWidth());\r
\r
c.calculate();\r
- c.verdict(false, 100);\r
+ c.verdict(false, ap.av.ConsPercGaps);\r
ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);\r
\r
\r
sg.cs = ccs;\r
\r
- Desktop.setConservationSliderSource(ap, ccs, sg.getName());\r
+ SliderPanel.setConservationSlider(ap, ccs, sg.getName());\r
+ SliderPanel.showConservationSlider();\r
}\r
else // remove ConservationColouring\r
{\r
refresh();\r
}\r
\r
- protected void groupAnnotation_actionPerformed(ActionEvent e)\r
- {\r
-\r
- }\r
\r
protected void groupName_actionPerformed(ActionEvent e)\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.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
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.getRubberbandGroup();\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
ap.av.alignment.deleteGroup(sg);\r
- ap.av.setRubberbandGroup(null);\r
- ap.RefreshPanels();\r
+ ap.av.setSelectionGroup(null);\r
+ ap.repaint();\r
}\r
\r
void pdbMenuItem_actionPerformed(ActionEvent e)\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
+ 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
}\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
+ ap.repaint();\r
+ }\r
+\r
+ public void showBoxes_actionPerformed(ActionEvent e)\r
+ {\r
+ getGroup().setDisplayBoxes(showBoxes.isSelected());\r
+ refresh();\r
+ }\r
+\r
+ public void showText_actionPerformed(ActionEvent e)\r
+ {\r
+ getGroup().setDisplayText(showText.isSelected());\r
+ refresh();\r
+ }\r
+\r
+ public void showColourText_actionPerformed(ActionEvent e)\r
+ {\r
+ getGroup().setColourText(showColourText.isSelected());\r
+ refresh();\r
+ }\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff