X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=d85fabcc1a5978df2d537d49a44c30616c64d9a5;hb=60d2bc892983abad01d082cbff73466f093879f2;hp=4928189ba6148bae5315638a397e23ce4f975aff;hpb=00506d5a86e6f2c09529134ef8ddbf114656b681;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 4928189..d85fabc 100755 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -3,21 +3,16 @@ package jalview.gui; import jalview.datamodel.*; import jalview.analysis.*; import jalview.schemes.*; +import java.awt.*; import javax.swing.*; import java.awt.event.*; - +import jalview.io.*; +import MCview.*; public class PopupMenu extends JPopupMenu { - JMenuItem residueMenu = new JMenuItem(); JMenu groupMenu = new JMenu(); - JMenuItem copyGroup = new JMenuItem(); - JMenuItem moveGroup = new JMenuItem(); - JMenuItem deleteSequences = new JMenuItem(); - JMenuItem analyze = new JMenuItem(); - JMenu defineMenu = new JMenu(); JMenuItem groupName = new JMenuItem(); - JMenuItem groupAnnotation = new JMenuItem(); protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem(); @@ -26,22 +21,38 @@ public class PopupMenu extends JPopupMenu protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem abovePIDColour = new JRadioButtonMenuItem(); + protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem(); protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem(); protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem(); JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem(); - protected JMenuItem conservationColourIncMenuItem = new JMenuItem(); protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); - AlignViewport av; - SeqPanel seqPanel; - - public PopupMenu(AlignViewport av, SeqPanel sp) + AlignmentPanel ap; + JMenu sequenceMenu = new JMenu(); + JMenuItem sequenceName = new JMenuItem(); + Sequence sequence; + JMenuItem unGroupMenuItem = new JMenuItem(); + JMenuItem pdbMenuItem = new JMenuItem(); + JMenuItem outline = new JMenuItem(); + JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem(); + JMenu colourMenu = new JMenu(); + JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem(); + JCheckBoxMenuItem showText = new JCheckBoxMenuItem(); + JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem(); + + public PopupMenu(AlignmentPanel ap, Sequence seq) { - this.av = av; - seqPanel = sp; + /////////////////////////////////////////////////////////// + // If this is activated from the sequence panel, the user may want to + // edit or annotate a particular residue. Therefore display the residue menu + // + // If from the IDPanel, we must display the sequence menu + ////////////////////////////////////////////////////////// + + this.ap = ap; + sequence = seq; ButtonGroup colours = new ButtonGroup(); colours.add(noColourmenuItem); @@ -59,102 +70,168 @@ public class PopupMenu extends JPopupMenu colours.add(BLOSUM62Colour); try - { - jbInit(); - } + { jbInit(); } catch(Exception e) + { e.printStackTrace(); } + + SequenceGroup sg = ap.av.getSelectionGroup(); + if(sg!=null) { - e.printStackTrace(); + groupName.setText(sg.getName()); + if(sg.cs instanceof ZappoColourScheme) + zappoColour.setSelected(true); + else if(sg.cs instanceof TaylorColourScheme) + taylorColour.setSelected(true); + else if (sg.cs instanceof PIDColourScheme) + PIDColour.setSelected(true); + else if (sg.cs instanceof Blosum62ColourScheme) + BLOSUM62Colour.setSelected(true); + else if (sg.cs instanceof UserColourScheme) + userDefinedColour.setSelected(true); + else if (sg.cs instanceof HydrophobicColourScheme) + hydrophobicityColour.setSelected(true); + else if (sg.cs instanceof HelixColourScheme) + helixColour.setSelected(true); + else if (sg.cs instanceof StrandColourScheme) + strandColour.setSelected(true); + else if (sg.cs instanceof TurnColourScheme) + turnColour.setSelected(true); + else if (sg.cs instanceof BuriedColourScheme) + buriedColour.setSelected(true); + else if (sg.cs instanceof ClustalxColourScheme) + clustalColour.setSelected(true); + else + noColourmenuItem.setSelected(true); + + if (sg.cs instanceof ConservationColourScheme) + conservationMenuItem.setSelected(true); + + showText.setSelected(sg.getDisplayText()); + showColourText.setSelected(sg.getColourText()); + showBoxes.setSelected(sg.getDisplayBoxes()); } - SequenceGroup sg = av.getRubberbandGroup(); - groupName.setText( sg.getName() ); + if( !ap.av.alignment.getGroups().contains(sg)) + unGroupMenuItem.setVisible(false); + else + groupMenu.insertSeparator(3); + + if(seq==null) + sequenceMenu.setVisible(false); + } private void jbInit() throws Exception { - residueMenu.setText("Residue"); groupMenu.setText("Group"); - copyGroup.setText("Copy region to new Alignment"); - copyGroup.addActionListener(new java.awt.event.ActionListener() + groupMenu.setText("Define"); + groupName.setText("Name"); + groupName.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - copyGroup_actionPerformed(e); + groupName_actionPerformed(e); } }); - moveGroup.setText("Move sequences to new Alignment"); - moveGroup.addActionListener(new java.awt.event.ActionListener() + sequenceMenu.setText("Sequence"); + sequenceName.setText("Edit name"); + sequenceName.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - moveGroup_actionPerformed(e); + sequenceName_actionPerformed(e); } }); - deleteSequences.setText("Delete sequences"); - deleteSequences.addActionListener(new java.awt.event.ActionListener() + PIDColour.setFocusPainted(false); + unGroupMenuItem.setText("Remove Group"); + unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - deleteSequences_actionPerformed(e); + unGroupMenuItem_actionPerformed(e); } }); - analyze.setText("Analyze"); - analyze.addActionListener(new java.awt.event.ActionListener() + pdbMenuItem.setText("View PDB structure"); + pdbMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - analyze_actionPerformed(e); + pdbMenuItem_actionPerformed(e); } }); - defineMenu.setText("Define"); - groupName.setText("Name"); - groupName.addActionListener(new java.awt.event.ActionListener() + outline.setText("Border colour"); + outline.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - groupName_actionPerformed(e); + outline_actionPerformed(e); } }); - groupAnnotation.setText("Annotation"); - groupAnnotation.addActionListener(new java.awt.event.ActionListener() + nucleotideMenuItem.setText("Nucleotide"); + nucleotideMenuItem.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - groupAnnotation_actionPerformed(e); + nucleotideMenuItem_actionPerformed(e); + } + }); + colourMenu.setText("Group Colour"); + showBoxes.setText("Boxes"); + showBoxes.setState(true); + showBoxes.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showBoxes_actionPerformed(e); + } + }); + showText.setText("Text"); + showText.setState(true); + showText.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showText_actionPerformed(e); + } + }); + showColourText.setText("Colour Text"); + showColourText.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showColourText_actionPerformed(e); } }); add(groupMenu); - add(residueMenu); - groupMenu.add(defineMenu); + add(sequenceMenu); + groupMenu.add(groupName); groupMenu.addSeparator(); - groupMenu.add(copyGroup); - groupMenu.add(moveGroup); - groupMenu.add(deleteSequences); + groupMenu.add(unGroupMenuItem); + groupMenu.add(colourMenu); groupMenu.addSeparator(); - groupMenu.add(analyze); - defineMenu.add(groupName); - defineMenu.add(groupAnnotation); - defineMenu.addSeparator(); - defineMenu.add(noColourmenuItem); - defineMenu.add(clustalColour); - defineMenu.add(zappoColour); - defineMenu.add(taylorColour); - defineMenu.add(hydrophobicityColour); - defineMenu.add(helixColour); - defineMenu.add(strandColour); - defineMenu.add(turnColour); - defineMenu.add(buriedColour); - defineMenu.add(userDefinedColour); - defineMenu.addSeparator(); - defineMenu.add(conservationMenuItem); - defineMenu.add(conservationColourIncMenuItem); - defineMenu.addSeparator(); - defineMenu.add(abovePIDColour); - defineMenu.add(PIDColour); - defineMenu.add(BLOSUM62Colour); - + groupMenu.add(showBoxes); + groupMenu.add(showText); + groupMenu.add(showColourText); + groupMenu.addSeparator(); + groupMenu.add(outline); + sequenceMenu.add(sequenceName); + sequenceMenu.add(pdbMenuItem); + colourMenu.add(noColourmenuItem); + colourMenu.add(clustalColour); + colourMenu.add(BLOSUM62Colour); + colourMenu.add(PIDColour); + colourMenu.add(zappoColour); + colourMenu.add(taylorColour); + colourMenu.add(hydrophobicityColour); + colourMenu.add(helixColour); + colourMenu.add(strandColour); + colourMenu.add(turnColour); + colourMenu.add(buriedColour); + colourMenu.add(nucleotideMenuItem); + colourMenu.add(userDefinedColour); + colourMenu.addSeparator(); + colourMenu.add(abovePIDColour); + colourMenu.add(conservationMenuItem); noColourmenuItem.setText("None"); - noColourmenuItem.setSelected(true); noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -163,8 +240,6 @@ public class PopupMenu extends JPopupMenu } }); - clustalColour.setEnabled(false); - clustalColour.setSelected(false); clustalColour.setText("Clustalx colours"); clustalColour.addActionListener(new java.awt.event.ActionListener() { @@ -173,7 +248,7 @@ public class PopupMenu extends JPopupMenu clustalColour_actionPerformed(e); } }); - zappoColour.setText("Zappo colour scheme"); + zappoColour.setText("Zappo"); zappoColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -181,7 +256,7 @@ public class PopupMenu extends JPopupMenu zappoColour_actionPerformed(e); } }); - taylorColour.setText("Taylor colour scheme"); + taylorColour.setText("Taylor"); taylorColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -189,7 +264,7 @@ public class PopupMenu extends JPopupMenu taylorColour_actionPerformed(e); } }); - hydrophobicityColour.setText("By hydrophobicity"); + hydrophobicityColour.setText("Hydrophobicity"); hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -221,7 +296,7 @@ public class PopupMenu extends JPopupMenu turnColour_actionPerformed(e); } }); - buriedColour.setText("Buried index"); + buriedColour.setText("Buried Index"); buriedColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -229,8 +304,7 @@ public class PopupMenu extends JPopupMenu buriedColour_actionPerformed(e); } }); - abovePIDColour.setEnabled(false); - abovePIDColour.setText("Above PID threshold only"); + abovePIDColour.setText("Above % Identity"); abovePIDColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -238,7 +312,7 @@ public class PopupMenu extends JPopupMenu abovePIDColour_actionPerformed(e); } }); - userDefinedColour.setText("User defined colours"); + userDefinedColour.setText("User Defined"); userDefinedColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -246,8 +320,7 @@ public class PopupMenu extends JPopupMenu userDefinedColour_actionPerformed(e); } }); - PIDColour.setEnabled(false); - PIDColour.setText("By PID"); + PIDColour.setText("Percentage Identity"); PIDColour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -255,7 +328,7 @@ public class PopupMenu extends JPopupMenu PIDColour_actionPerformed(e); } }); - BLOSUM62Colour.setText("By BLOSUM62 score"); + BLOSUM62Colour.setText("BLOSUM62"); BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -263,7 +336,7 @@ public class PopupMenu extends JPopupMenu BLOSUM62Colour_actionPerformed(e); } }); - conservationMenuItem.setText("By conservation"); + conservationMenuItem.setText("Conservation"); conservationMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -272,28 +345,25 @@ public class PopupMenu extends JPopupMenu } }); - conservationColourIncMenuItem.setEnabled(false); - conservationColourIncMenuItem.setText("Conservation Colour Increment"); - conservationColourIncMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - conservationColourIncMenuItem_actionPerformed(e); - } - }); } void refresh() { - seqPanel.seqCanvas.paintFlag=true; - seqPanel.repaint(); + SequenceGroup sg = getGroup(); + SuperGroup superG = ap.av.alignment.getSuperGroup( sg ); + if( superG !=null) + superG.setSuperGroupProperties( sg ); + + ap.seqPanel.repaint(); } protected void clustalColour_actionPerformed(ActionEvent e) { - + SequenceGroup sg = getGroup(); + sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth()); + refresh(); } protected void zappoColour_actionPerformed(ActionEvent e) @@ -339,42 +409,66 @@ public class PopupMenu extends JPopupMenu refresh(); } + public void nucleotideMenuItem_actionPerformed(ActionEvent e) + { + getGroup().cs = new NucleotideColourScheme(); + refresh(); + } - protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e) - { - -} -/* -public void conservationColourIncMenuItem_actionPerformed(ActionEvent e) -{ -ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel); -JInternalFrame frame = new JInternalFrame(); -frame.setContentPane(cip); -Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90); -frame.setMaximizable(false); - - }*/ protected void abovePIDColour_actionPerformed(ActionEvent e) { + SequenceGroup sg = getGroup(); + if (abovePIDColour.isSelected()) + { + sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, + ap.av.alignment.getWidth())); + int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName()); + if (sg.cs instanceof ResidueColourScheme) + ( (ResidueColourScheme)sg. cs).setThreshold(threshold); + else if (sg.cs instanceof ScoreColourScheme) + ( (ScoreColourScheme) sg.cs).setThreshold(threshold); + + SliderPanel.showPIDSlider(); + + + } + else // remove PIDColouring + { + ResidueColourScheme rcs = (ResidueColourScheme) sg.cs; + rcs.setThreshold(0); + sg.cs = rcs; + } + + refresh(); } protected void userDefinedColour_actionPerformed(ActionEvent e) { - + new UserDefinedColours( ap, getGroup()); } protected void PIDColour_actionPerformed(ActionEvent e) { - + SequenceGroup sg = getGroup(); + sg.cs = new PIDColourScheme(); + sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, + ap.av.alignment.getWidth())); + refresh(); } protected void BLOSUM62Colour_actionPerformed(ActionEvent e) { - getGroup().cs = new Blosum62ColourScheme(av); + SequenceGroup sg = getGroup(); + + sg.cs = new Blosum62ColourScheme(); + + sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, + ap.av.alignment.getWidth())); + refresh(); } @@ -389,25 +483,34 @@ frame.setMaximizable(false); { SequenceGroup sg = getGroup(); - Alignment al = (Alignment)av.getAlignment(); - Conservation c = new Conservation("Group", al.cons, - ResidueProperties.propHash, 3, sg.sequences, sg.getStartRes(), - sg.getEndRes() ); + if(conservationMenuItem.isSelected()) + { - c.calculate(); - c.verdict(false, 100); - ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs); + Conservation c = new Conservation("Group", + ResidueProperties.propHash, 3, + sg.sequences, 0, + ap.av.alignment.getWidth()); - sg.cs = ccs; + c.calculate(); + c.verdict(false, ap.av.ConsPercGaps); + ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs); - refresh(); - } - protected void groupAnnotation_actionPerformed(ActionEvent e) - { + sg.cs = ccs; + SliderPanel.setConservationSlider(ap, ccs, sg.getName()); + SliderPanel.showConservationSlider(); + } + else // remove ConservationColouring + { + ConservationColourScheme ccs = (ConservationColourScheme)sg.cs; + sg.cs = ccs.cs; + } + + refresh(); } + protected void groupName_actionPerformed(ActionEvent e) { SequenceGroup sg = getGroup(); @@ -418,80 +521,12 @@ frame.setMaximizable(false); sg.setName(reply); groupName.setText(reply); } - /* public void deleteSelectedMenuItem_actionPerformed(ActionEvent e) - { - addHistoryItem("delete selection"); - - for (int i=0;i < viewport.getSelection().size(); i++) - viewport.getAlignment().deleteSequence(viewport.getSelection().sequenceAt(i)); - - viewport.getSelection().clear(); - viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getHeight()); - alignPanel.RefreshPanels(); - } - public void moveSelectedMenuItem_actionPerformed(ActionEvent e) - { - copySelectedMenuItem_actionPerformed(null); - deleteSelectedMenuItem_actionPerformed(null); - alignPanel.repaint(); - } - - public void copySelectedMenuItem_actionPerformed(ActionEvent e) - { - if(viewport.getSelection().size()==0) - return; - - SequenceI[] s = new Sequence[viewport.getSelection().size()]; - for (int i=0; i < viewport.getSelection().size(); i++) { - s[i] = new Sequence(viewport.getSelection().sequenceAt(i)); - } - AlignFrame af = new AlignFrame(new Alignment(s)); - int newHeight = s.length * af.viewport.getCharHeight() + 200; - if(newHeight>500) - newHeight=500; - Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight); - } -*/ - protected void copyGroup_actionPerformed(ActionEvent e) - { - SequenceGroup sg = av.getRubberbandGroup(); - - SequenceI[] s = new Sequence[sg.sequences.size()]; - for (int i=0; i < sg.sequences.size(); i++) - { - s[i] = new Sequence( sg.getSequenceAt(i)); - s[i].setSequence( s[i].getSequence(sg.getStartRes(), sg.getEndRes()+1) ); - } - AlignFrame af = new AlignFrame(new Alignment(s)); - int newHeight = s.length * af.viewport.getCharHeight() + 200; - if (newHeight > 500) - newHeight = 500; - Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight); - } - - protected void moveGroup_actionPerformed(ActionEvent e) - { - - } - - protected void deleteSequences_actionPerformed(ActionEvent e) - { - SequenceGroup sg = av.getRubberbandGroup(); - for (int i=0;i < sg.sequences.size(); i++) - av.getAlignment().deleteSequence(sg.getSequenceAt(i)); - - av.alignment.deleteGroup(sg); - av.resetSeqLimits(seqPanel.seqCanvas.getHeight()); - seqPanel.parent.RefreshPanels(); - - } protected void analyze_actionPerformed(ActionEvent e) { - CutAndPasteTransfer cap = new CutAndPasteTransfer(false); + CutAndPasteTransfer cap = new CutAndPasteTransfer(); JInternalFrame frame = new JInternalFrame(); - cap.formatForOutput(); frame.setContentPane(cap); Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300); SequenceGroup sg = getGroup(); @@ -511,10 +546,90 @@ frame.setMaximizable(false); SequenceGroup getGroup() { - SequenceGroup sg = av.getRubberbandGroup(); + SequenceGroup sg = ap.av.getSelectionGroup(); // this method won't add a new group if it already exists - av.alignment.addGroup(sg); + ap.av.alignment.addGroup(sg); + return sg; } + + void sequenceName_actionPerformed(ActionEvent e) + { + String id = sequence.getName(); + String s = (String)JOptionPane.showInternalInputDialog( + ap, + "Edit sequence name", + "Edit sequence name ("+sequence.getName()+")", + JOptionPane.PLAIN_MESSAGE, + null, + null, + id); + + if(s!=null) + { + sequence.setName(s); + ap.repaint(); + } + + } + + void unGroupMenuItem_actionPerformed(ActionEvent e) + { + SequenceGroup sg = ap.av.getSelectionGroup(); + ap.av.alignment.deleteGroup(sg); + ap.av.setSelectionGroup(null); + ap.repaint(); + } + + void pdbMenuItem_actionPerformed(ActionEvent e) + { + if(sequence.getPDBId()==null) + return; + + try + { + EBIFetchClient ebi = new EBIFetchClient(); + String[] result = ebi.fetchData("pdb:" + sequence.getPDBId(), null, null); + + PDBfile pdb = new PDBfile(result); + + rotCanvas rc = new rotCanvas(pdb, sequence, ap.av); + JInternalFrame frame = new JInternalFrame(); + frame.setContentPane(rc); + Desktop.addInternalFrame(frame,sequence.getName()+" "+ sequence.getPDBId(), 400, 400); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + + protected void outline_actionPerformed(ActionEvent e) + { + SequenceGroup sg = getGroup(); + Color col = JColorChooser.showDialog(this, "Select Outline Colour", Color.BLUE); + if(col!=null) + sg.setOutlineColour(col); + ap.repaint(); + } + + public void showBoxes_actionPerformed(ActionEvent e) + { + getGroup().setDisplayBoxes(showBoxes.isSelected()); + refresh(); + } + + public void showText_actionPerformed(ActionEvent e) + { + getGroup().setDisplayText(showText.isSelected()); + refresh(); + } + + public void showColourText_actionPerformed(ActionEvent e) + { + getGroup().setColourText(showColourText.isSelected()); + refresh(); + } + }