X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=2bdaf3753f457ddd717fdfc77e4cfb9501eb6367;hb=22be3f466cd70cb03d5eae619ede8589ae69716a;hp=458a6bed4315767e275700518d6b8e1a3650e82c;hpb=f44e5d441ae27d834b3a5096060ac8b5df5c5c9c;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 458a6be..2bdaf37 100755 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -5,11 +5,11 @@ import jalview.analysis.*; import jalview.schemes.*; 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(); @@ -26,22 +26,35 @@ 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; + AlignmentPanel ap; + JMenu sequenceMenu = new JMenu(); + JMenuItem sequenceName = new JMenuItem(); + JMenu residueMenu = new JMenu(); + JMenuItem annotateResidue = new JMenuItem(); + + Sequence sequence; + JMenuItem unGroupMenuItem = new JMenuItem(); + JMenuItem pdbMenuItem = new JMenuItem(); - public PopupMenu(AlignViewport av, SeqPanel sp) + 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); @@ -59,20 +72,55 @@ public class PopupMenu extends JPopupMenu colours.add(BLOSUM62Colour); try + { jbInit(); } + catch(Exception e) + { e.printStackTrace(); } + + SequenceGroup sg = ap.av.getRubberbandGroup(); + if(sg!=null) { - jbInit(); + 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); } - catch(Exception e) + + + if(seq!=null) { - e.printStackTrace(); + residueMenu.setVisible(false); + sequenceName.setText( sequence.getName() ); } + else + sequenceMenu.setVisible(false); - SequenceGroup sg = av.getRubberbandGroup(); - groupName.setText( sg.getName() ); } 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() @@ -123,9 +171,39 @@ public class PopupMenu extends JPopupMenu groupAnnotation_actionPerformed(e); } }); + sequenceMenu.setText("Sequence"); + sequenceName.setText("sequenceName"); + sequenceName.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sequenceName_actionPerformed(e); + } + }); + residueMenu.setText("Residue"); + annotateResidue.setText("annotate residue???"); + PIDColour.setFocusPainted(false); + unGroupMenuItem.setText("Remove Group"); + unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + unGroupMenuItem_actionPerformed(e); + } + }); + pdbMenuItem.setText("View PDB structure"); + pdbMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + pdbMenuItem_actionPerformed(e); + } + }); add(groupMenu); - add(residueMenu); + this.add(sequenceMenu); + this.add(residueMenu); groupMenu.add(defineMenu); + groupMenu.add(unGroupMenuItem); groupMenu.addSeparator(); groupMenu.add(copyGroup); groupMenu.add(moveGroup); @@ -145,16 +223,17 @@ public class PopupMenu extends JPopupMenu 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); + defineMenu.addSeparator(); + defineMenu.add(abovePIDColour); + defineMenu.add(conservationMenuItem); + + sequenceMenu.add(sequenceName); + sequenceMenu.add(pdbMenuItem); + residueMenu.add(annotateResidue); noColourmenuItem.setText("None"); - noColourmenuItem.setSelected(true); noColourmenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -163,8 +242,6 @@ public class PopupMenu extends JPopupMenu } }); - clustalColour.setEnabled(false); - clustalColour.setSelected(false); clustalColour.setText("Clustalx colours"); clustalColour.addActionListener(new java.awt.event.ActionListener() { @@ -229,7 +306,6 @@ public class PopupMenu extends JPopupMenu buriedColour_actionPerformed(e); } }); - abovePIDColour.setEnabled(false); abovePIDColour.setText("Above PID threshold only"); abovePIDColour.addActionListener(new java.awt.event.ActionListener() { @@ -246,8 +322,7 @@ 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 +330,7 @@ public class PopupMenu extends JPopupMenu PIDColour_actionPerformed(e); } }); - BLOSUM62Colour.setText("By BLOSUM62 score"); + BLOSUM62Colour.setText("BLOSUM62 score"); BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) @@ -272,28 +347,26 @@ 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.seqCanvas.paintFlag=true; + 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) @@ -340,34 +413,18 @@ public class PopupMenu extends JPopupMenu } - 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) { - + Desktop.setPIDSliderSource(ap, getGroup().cs, getGroup().getName()); } protected void userDefinedColour_actionPerformed(ActionEvent e) { JInternalFrame frame = new JInternalFrame(); - UserDefinedColours chooser = new UserDefinedColours( frame, seqPanel.parent, getGroup()); + UserDefinedColours chooser = new UserDefinedColours( frame, ap, getGroup()); frame.setContentPane(chooser); - Desktop.addInternalFrame(frame,"User defined colours", 450,540 ); + Desktop.addInternalFrame(frame,"User defined colours ("+getGroup().getName()+")", 450,540 ); frame.setResizable(false); frame.setIconifiable(false); frame.setMaximizable(false); @@ -381,7 +438,7 @@ frame.setMaximizable(false); protected void BLOSUM62Colour_actionPerformed(ActionEvent e) { - getGroup().cs = new Blosum62ColourScheme(av); + getGroup().cs = new Blosum62ColourScheme(ap.av); refresh(); } @@ -396,15 +453,28 @@ frame.setMaximizable(false); { SequenceGroup sg = getGroup(); - Conservation c = new Conservation("Group", - ResidueProperties.propHash, 3, sg.sequences, sg.getStartRes(), - sg.getEndRes() ); + if(conservationMenuItem.isSelected()) + { + + Conservation c = new Conservation("Group", + ResidueProperties.propHash, 3, + sg.sequences, 0, + ap.av.alignment.getWidth()); + + c.calculate(); + c.verdict(false, 100); + ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs); - c.calculate(); - c.verdict(false, 100); - ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs); - sg.cs = ccs; + sg.cs = ccs; + + Desktop.setConservationSliderSource(ap, ccs, sg.getName()); + } + else // remove ConservationColouring + { + ConservationColourScheme ccs = (ConservationColourScheme)sg.cs; + sg.cs = ccs.cs; + } refresh(); } @@ -424,44 +494,10 @@ 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(); + SequenceGroup sg = ap.av.getRubberbandGroup(); SequenceI[] s = new Sequence[sg.sequences.size()]; for (int i=0; i < sg.sequences.size(); i++) @@ -474,22 +510,43 @@ frame.setMaximizable(false); if (newHeight > 500) newHeight = 500; Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight); - } + } protected void moveGroup_actionPerformed(ActionEvent e) { + SequenceGroup sg = ap.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)); + + 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); + + + for (int i=0; i < sg.sequences.size(); i++) + ap.av.alignment.deleteSequence(sg.getSequenceAt(i)); + + + ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight()); + ap.RefreshPanels(); + } protected void deleteSequences_actionPerformed(ActionEvent e) { - SequenceGroup sg = av.getRubberbandGroup(); + SequenceGroup sg = ap.av.getRubberbandGroup(); for (int i=0;i < sg.sequences.size(); i++) - av.getAlignment().deleteSequence(sg.getSequenceAt(i)); + ap.av.getAlignment().deleteSequence(sg.getSequenceAt(i)); - av.alignment.deleteGroup(sg); - av.resetSeqLimits(seqPanel.seqCanvas.getHeight()); - seqPanel.parent.RefreshPanels(); + ap.av.alignment.deleteGroup(sg); + ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight()); + ap.RefreshPanels(); } @@ -517,10 +574,67 @@ frame.setMaximizable(false); SequenceGroup getGroup() { - SequenceGroup sg = av.getRubberbandGroup(); + SequenceGroup sg = ap.av.getRubberbandGroup(); // 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", + JOptionPane.PLAIN_MESSAGE, + null, + null, + id); + + if(s!=null) + { + sequence.setName(s); + ap.RefreshPanels(); + } + + } + + void unGroupMenuItem_actionPerformed(ActionEvent e) + { + SequenceGroup sg = ap.av.getRubberbandGroup(); + ap.av.alignment.deleteGroup(sg); + ap.av.setRubberbandGroup(null); + ap.RefreshPanels(); + } + + 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); + sequence.setPDBfile(pdb); + + ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).isVisible = true; + ( (PDBChain) pdb.chains.elementAt(sequence.maxchain)).sequence = sequence; + // ( (PDBChain)pdb.chains.elementAt(sequence.maxchain)).colourBySequence(); + + rotCanvas rc = new rotCanvas(pdb); + JInternalFrame frame = new JInternalFrame(); + frame.setContentPane(rc); + Desktop.addInternalFrame(frame,sequence.getName()+" "+ sequence.getPDBId(), 400, 400); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + }