X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=398294b7cd9874d59c3d78a31c2adb7de99d81ca;hb=e7ed63f1ea56432246a6ed1553f0fe56d26f56ea;hp=458a6bed4315767e275700518d6b8e1a3650e82c;hpb=f44e5d441ae27d834b3a5096060ac8b5df5c5c9c;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 458a6be..398294b 100755 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -3,17 +3,15 @@ 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(); @@ -26,22 +24,36 @@ 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(); + JMenuItem outline = 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); @@ -59,82 +71,129 @@ 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); } - SequenceGroup sg = av.getRubberbandGroup(); - groupName.setText( sg.getName() ); + + if(seq!=null) + residueMenu.setVisible(false); + else + 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() + analyze.setText("Analyze"); + analyze.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - copyGroup_actionPerformed(e); + analyze_actionPerformed(e); } }); - moveGroup.setText("Move sequences to new Alignment"); - moveGroup.addActionListener(new java.awt.event.ActionListener() + defineMenu.setText("Define"); + groupName.setText("Name"); + groupName.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - moveGroup_actionPerformed(e); + groupName_actionPerformed(e); } }); - deleteSequences.setText("Delete sequences"); - deleteSequences.addActionListener(new java.awt.event.ActionListener() + groupAnnotation.setEnabled(false); + groupAnnotation.setText("Annotation"); + groupAnnotation.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - deleteSequences_actionPerformed(e); + groupAnnotation_actionPerformed(e); } }); - analyze.setText("Analyze"); - analyze.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) { - analyze_actionPerformed(e); + sequenceName_actionPerformed(e); } }); - defineMenu.setText("Define"); - groupName.setText("Name"); - groupName.addActionListener(new java.awt.event.ActionListener() + residueMenu.setText("Residue"); + annotateResidue.setEnabled(false); + annotateResidue.setActionCommand("annotate residue"); + annotateResidue.setText("annotate residue???"); + PIDColour.setFocusPainted(false); + unGroupMenuItem.setText("Remove Group"); + unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - groupName_actionPerformed(e); + unGroupMenuItem_actionPerformed(e); } }); - groupAnnotation.setText("Annotation"); - groupAnnotation.addActionListener(new java.awt.event.ActionListener() + pdbMenuItem.setText("View PDB structure"); + pdbMenuItem.addActionListener(new java.awt.event.ActionListener() { public void actionPerformed(ActionEvent e) { - groupAnnotation_actionPerformed(e); + pdbMenuItem_actionPerformed(e); + } + }); + outline.setText("Border colour"); + outline.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + outline_actionPerformed(e); } }); add(groupMenu); - add(residueMenu); + this.add(sequenceMenu); + this.add(residueMenu); groupMenu.add(defineMenu); - groupMenu.addSeparator(); - groupMenu.add(copyGroup); - groupMenu.add(moveGroup); - groupMenu.add(deleteSequences); + groupMenu.add(unGroupMenuItem); groupMenu.addSeparator(); groupMenu.add(analyze); defineMenu.add(groupName); defineMenu.add(groupAnnotation); defineMenu.addSeparator(); + defineMenu.add(outline); + defineMenu.addSeparator(); defineMenu.add(noColourmenuItem); defineMenu.add(clustalColour); defineMenu.add(zappoColour); @@ -145,16 +204,17 @@ 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 +223,6 @@ public class PopupMenu extends JPopupMenu } }); - clustalColour.setEnabled(false); - clustalColour.setSelected(false); clustalColour.setText("Clustalx colours"); clustalColour.addActionListener(new java.awt.event.ActionListener() { @@ -229,7 +287,6 @@ 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 +303,7 @@ 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 +311,7 @@ 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 +328,25 @@ 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) @@ -340,24 +393,31 @@ public class PopupMenu extends JPopupMenu } - protected void conservationColourIncMenuItem_actionPerformed(ActionEvent e) - { + 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); -} -/* -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); + SliderPanel.showPIDSlider(); - }*/ + } + else // remove PIDColouring + { + ResidueColourScheme rcs = (ResidueColourScheme) sg.cs; + rcs.setThreshold(0); + sg.cs = rcs; + } - protected void abovePIDColour_actionPerformed(ActionEvent e) - { + refresh(); } @@ -365,9 +425,9 @@ frame.setMaximizable(false); 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 +441,13 @@ frame.setMaximizable(false); 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(); } @@ -396,15 +462,29 @@ 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, ap.av.ConsPercGaps); + ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs); - sg.cs = ccs; + + sg.cs = ccs; + + SliderPanel.setConservationSlider(ap, ccs, sg.getName()); + SliderPanel.showConservationSlider(); + } + else // remove ConservationColouring + { + ConservationColourScheme ccs = (ConservationColourScheme)sg.cs; + sg.cs = ccs.cs; + } refresh(); } @@ -424,74 +504,7 @@ 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) { @@ -517,10 +530,76 @@ 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); + 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(); + } + } + + 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); + } + }