X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=94c42935925979ab2b1db45f3bb05202d09c6984;hb=e894eb87d40be6e8452d19032ddffe80dad5f804;hp=2bdaf3753f457ddd717fdfc77e4cfb9501eb6367;hpb=22be3f466cd70cb03d5eae619ede8589ae69716a;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 2bdaf37..94c4293 100755 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1,640 +1,1306 @@ -package jalview.gui; - -import jalview.datamodel.*; -import jalview.analysis.*; -import jalview.schemes.*; -import javax.swing.*; -import java.awt.event.*; -import jalview.io.*; -import MCview.*; - -public class PopupMenu extends JPopupMenu -{ - 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(); - protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem(); - protected JRadioButtonMenuItem buriedColour = 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 JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); - - - 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(AlignmentPanel ap, Sequence seq) - { - /////////////////////////////////////////////////////////// - // 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); - colours.add(clustalColour); - colours.add(zappoColour); - colours.add(taylorColour); - colours.add(hydrophobicityColour); - colours.add(helixColour); - colours.add(strandColour); - colours.add(turnColour); - colours.add(buriedColour); - colours.add(abovePIDColour); - colours.add(userDefinedColour); - colours.add(PIDColour); - colours.add(BLOSUM62Colour); - - try - { jbInit(); } - catch(Exception e) - { e.printStackTrace(); } - - SequenceGroup sg = ap.av.getRubberbandGroup(); - if(sg!=null) - { - 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); - } - - - if(seq!=null) - { - residueMenu.setVisible(false); - sequenceName.setText( sequence.getName() ); - } - else - sequenceMenu.setVisible(false); - - } - private void jbInit() throws Exception - { - groupMenu.setText("Group"); - copyGroup.setText("Copy region to new Alignment"); - copyGroup.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - copyGroup_actionPerformed(e); - } - }); - moveGroup.setText("Move sequences to new Alignment"); - moveGroup.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - moveGroup_actionPerformed(e); - } - }); - deleteSequences.setText("Delete sequences"); - deleteSequences.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - deleteSequences_actionPerformed(e); - } - }); - analyze.setText("Analyze"); - analyze.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - analyze_actionPerformed(e); - } - }); - defineMenu.setText("Define"); - groupName.setText("Name"); - groupName.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - groupName_actionPerformed(e); - } - }); - groupAnnotation.setText("Annotation"); - groupAnnotation.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - 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); - this.add(sequenceMenu); - this.add(residueMenu); - groupMenu.add(defineMenu); - groupMenu.add(unGroupMenuItem); - groupMenu.addSeparator(); - groupMenu.add(copyGroup); - groupMenu.add(moveGroup); - groupMenu.add(deleteSequences); - 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.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.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - noColourmenuItem_actionPerformed(e); - } - }); - - clustalColour.setText("Clustalx colours"); - clustalColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - clustalColour_actionPerformed(e); - } - }); - zappoColour.setText("Zappo colour scheme"); - zappoColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - zappoColour_actionPerformed(e); - } - }); - taylorColour.setText("Taylor colour scheme"); - taylorColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - taylorColour_actionPerformed(e); - } - }); - hydrophobicityColour.setText("By hydrophobicity"); - hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - hydrophobicityColour_actionPerformed(e); - } - }); - helixColour.setText("Helix propensity"); - helixColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - helixColour_actionPerformed(e); - } - }); - strandColour.setText("Strand propensity"); - strandColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - strandColour_actionPerformed(e); - } - }); - turnColour.setText("Turn propensity"); - turnColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - turnColour_actionPerformed(e); - } - }); - buriedColour.setText("Buried index"); - buriedColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - buriedColour_actionPerformed(e); - } - }); - abovePIDColour.setText("Above PID threshold only"); - abovePIDColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - abovePIDColour_actionPerformed(e); - } - }); - userDefinedColour.setText("User defined colours"); - userDefinedColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - userDefinedColour_actionPerformed(e); - } - }); - PIDColour.setText("Percentage Identity"); - PIDColour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - PIDColour_actionPerformed(e); - } - }); - BLOSUM62Colour.setText("BLOSUM62 score"); - BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - BLOSUM62Colour_actionPerformed(e); - } - }); - conservationMenuItem.setText("By conservation"); - conservationMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - conservationMenuItem_actionPerformed(e); - } - }); - - - - } - - void refresh() - { - 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) - { - getGroup().cs = new ZappoColourScheme(); - refresh(); - } - - protected void taylorColour_actionPerformed(ActionEvent e) - { - getGroup().cs = new TaylorColourScheme(); - refresh(); - } - - - protected void hydrophobicityColour_actionPerformed(ActionEvent e) - { - getGroup().cs = new HydrophobicColourScheme(); - refresh(); - } - - protected void helixColour_actionPerformed(ActionEvent e) - { - getGroup().cs = new HelixColourScheme(); - refresh(); - } - - protected void strandColour_actionPerformed(ActionEvent e) - { - getGroup().cs = new StrandColourScheme(); - refresh(); - } - - protected void turnColour_actionPerformed(ActionEvent e) - { - getGroup().cs = new TurnColourScheme(); - refresh(); - } - - protected void buriedColour_actionPerformed(ActionEvent e) - { - getGroup().cs = new BuriedColourScheme(); - refresh(); - } - - - 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, ap, getGroup()); - frame.setContentPane(chooser); - Desktop.addInternalFrame(frame,"User defined colours ("+getGroup().getName()+")", 450,540 ); - frame.setResizable(false); - frame.setIconifiable(false); - frame.setMaximizable(false); - - } - - protected void PIDColour_actionPerformed(ActionEvent e) - { - - } - - protected void BLOSUM62Colour_actionPerformed(ActionEvent e) - { - getGroup().cs = new Blosum62ColourScheme(ap.av); - refresh(); - } - - - protected void noColourmenuItem_actionPerformed(ActionEvent e) - { - getGroup().cs = null; - refresh(); - } - - protected void conservationMenuItem_actionPerformed(ActionEvent e) - { - SequenceGroup sg = getGroup(); - - 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); - - - sg.cs = ccs; - - Desktop.setConservationSliderSource(ap, ccs, sg.getName()); - } - else // remove ConservationColouring - { - ConservationColourScheme ccs = (ConservationColourScheme)sg.cs; - sg.cs = ccs.cs; - } - - refresh(); - } - - protected void groupAnnotation_actionPerformed(ActionEvent e) - { - - } - - protected void groupName_actionPerformed(ActionEvent e) - { - SequenceGroup sg = getGroup(); - String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE); - if(reply==null) - return; - - sg.setName(reply); - groupName.setText(reply); - } - - protected void copyGroup_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)); - 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) - { - 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 = ap.av.getRubberbandGroup(); - for (int i=0;i < sg.sequences.size(); i++) - ap.av.getAlignment().deleteSequence(sg.getSequenceAt(i)); - - ap.av.alignment.deleteGroup(sg); - ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight()); - ap.RefreshPanels(); - - } - - protected void analyze_actionPerformed(ActionEvent e) - { - CutAndPasteTransfer cap = new CutAndPasteTransfer(false); - JInternalFrame frame = new JInternalFrame(); - cap.formatForOutput(); - frame.setContentPane(cap); - Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300); - SequenceGroup sg = getGroup(); - StringBuffer sb = new StringBuffer(); - - for(int i=0; i1) + { + menuItem = new JMenuItem("Represent Group with " + seq.getName()); + menuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + hideSequences(true); + } + }); + sequenceMenu.add(menuItem); + } + + if (ap.av.hasHiddenRows) + { + final int index = ap.av.alignment.findIndex(seq); + + if (ap.av.adjustForHiddenSeqs(index) - + ap.av.adjustForHiddenSeqs(index - 1) > 1) + { + menuItem = new JMenuItem("Reveal Sequences"); + menuItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + ap.av.showSequence(index); + if (ap.overviewPanel != null) + ap.overviewPanel.updateOverviewImage(); + } + }); + add(menuItem); + } + + menuItem = new JMenuItem("Reveal All"); + menuItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + ap.av.showAllHiddenSeqs(); + if (ap.overviewPanel != null) + ap.overviewPanel.updateOverviewImage(); + } + }); + + add(menuItem); + } + + + } + + + + SequenceGroup sg = ap.av.getSelectionGroup(); + + if (sg != null) + { + 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!=null && sg.cs.conservationApplied()) + { + conservationMenuItem.setSelected(true); + } + + showText.setSelected(sg.getDisplayText()); + showColourText.setSelected(sg.getColourText()); + showBoxes.setSelected(sg.getDisplayBoxes()); + } + else + { + groupMenu.setVisible(false); + editMenu.setVisible(false); + } + + if (!ap.av.alignment.getGroups().contains(sg)) + { + unGroupMenuItem.setVisible(false); + } + + + if (seq == null) + { + sequenceMenu.setVisible(false); + pdbMenu.setVisible(false); + } + + if(links != null && links.size()>0) + { + JMenu linkMenu = new JMenu("Link"); + JMenuItem item; + for(int i=0; i -1) + { + String id = seq.getName(); + if (id.indexOf("|") > -1) + id = id.substring(id.lastIndexOf("|") + 1); + + url = link.substring(link.indexOf("|") + 1, + link.indexOf("$SEQUENCE_ID$")) + + id + + link.substring(link.indexOf("$SEQUENCE_ID$") + 13); + } + else + url = link.substring(link.lastIndexOf("|")+1); + + + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showLink(url); + } + }); + + linkMenu.add(item); + } + if(sequence!=null) + sequenceMenu.add(linkMenu); + else + add(linkMenu); + } + } + + + /** + * DOCUMENT ME! + * + * @throws Exception DOCUMENT ME! + */ + private void jbInit() throws Exception + { + groupMenu.setText("Group"); + groupMenu.setText("Selection"); + groupName.setText("Name"); + groupName.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + groupName_actionPerformed(e); + } + }); + sequenceMenu.setText("Sequence"); + sequenceName.setText("Edit Name/Description"); + sequenceName.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sequenceName_actionPerformed(e); + } + }); + PIDColour.setFocusPainted(false); + unGroupMenuItem.setText("Remove Group"); + unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + unGroupMenuItem_actionPerformed(e); + } + }); + + outline.setText("Border colour"); + outline.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + outline_actionPerformed(e); + } + }); + nucleotideMenuItem.setText("Nucleotide"); + nucleotideMenuItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent 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); + } + }); + editMenu.setText("Edit"); + cut.setText("Cut"); + cut.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + cut_actionPerformed(e); + } + }); + upperCase.setText("To Upper Case"); + upperCase.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + upperCase_actionPerformed(e); + } + }); + copy.setText("Copy"); + copy.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + copy_actionPerformed(e); + } + }); + lowerCase.setText("To Lower Case"); + lowerCase.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + lowerCase_actionPerformed(e); + } + }); + toggle.setText("Toggle Case"); + toggle.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + toggle_actionPerformed(e); + } + }); + pdbMenu.setText("Associate Structure with Sequence"); + pdbFromFile.setText("From File"); + pdbFromFile.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + pdbFromFile_actionPerformed(e); + } + }); + enterPDB.setText("Enter PDB Id"); + enterPDB.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + enterPDB_actionPerformed(e); + } + }); + discoverPDB.setText("Discover PDB ids"); + discoverPDB.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + discoverPDB_actionPerformed(e); + } + }); + outputMenu.setText("Output to Textbox..."); + add(groupMenu); + + add(sequenceMenu); + groupMenu.add(editMenu); + groupMenu.add(outputMenu); + groupMenu.addSeparator(); + groupMenu.add(groupName); + groupMenu.add(unGroupMenuItem); + groupMenu.add(colourMenu); + groupMenu.add(showBoxes); + groupMenu.add(showText); + groupMenu.add(showColourText); + groupMenu.add(outline); + sequenceMenu.add(sequenceName); + sequenceMenu.add(pdbMenu); + 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); + + if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null) + { + java.util.Enumeration userColours = jalview.gui.UserDefinedColours. + getUserColourSchemes().keys(); + + while (userColours.hasMoreElements()) + { + JMenuItem item = new JMenuItem(userColours. + nextElement().toString()); + item.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent evt) + { + userDefinedColour_actionPerformed(evt); + } + }); + colourMenu.add(item); + } + } + + + colourMenu.addSeparator(); + colourMenu.add(abovePIDColour); + colourMenu.add(conservationMenuItem); + editMenu.add(copy); + editMenu.add(cut); + editMenu.add(upperCase); + editMenu.add(lowerCase); + editMenu.add(toggle); + pdbMenu.add(pdbFromFile); + pdbMenu.add(enterPDB); + pdbMenu.add(discoverPDB); + noColourmenuItem.setText("None"); + noColourmenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + noColourmenuItem_actionPerformed(e); + } + }); + + clustalColour.setText("Clustalx colours"); + clustalColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + clustalColour_actionPerformed(e); + } + }); + zappoColour.setText("Zappo"); + zappoColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + zappoColour_actionPerformed(e); + } + }); + taylorColour.setText("Taylor"); + taylorColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + taylorColour_actionPerformed(e); + } + }); + hydrophobicityColour.setText("Hydrophobicity"); + hydrophobicityColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + hydrophobicityColour_actionPerformed(e); + } + }); + helixColour.setText("Helix propensity"); + helixColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + helixColour_actionPerformed(e); + } + }); + strandColour.setText("Strand propensity"); + strandColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + strandColour_actionPerformed(e); + } + }); + turnColour.setText("Turn propensity"); + turnColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + turnColour_actionPerformed(e); + } + }); + buriedColour.setText("Buried Index"); + buriedColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + buriedColour_actionPerformed(e); + } + }); + abovePIDColour.setText("Above % Identity"); + abovePIDColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + abovePIDColour_actionPerformed(e); + } + }); + userDefinedColour.setText("User Defined..."); + userDefinedColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + userDefinedColour_actionPerformed(e); + } + }); + PIDColour.setText("Percentage Identity"); + PIDColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + PIDColour_actionPerformed(e); + } + }); + BLOSUM62Colour.setText("BLOSUM62"); + BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + BLOSUM62Colour_actionPerformed(e); + } + }); + conservationMenuItem.setText("Conservation"); + conservationMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + conservationMenuItem_actionPerformed(e); + } + }); + } + + /** + * DOCUMENT ME! + */ + void refresh() + { + if (ap.overviewPanel != null) + ap.overviewPanel.updateOverviewImage(); + + ap.seqPanel.repaint(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void clustalColour_actionPerformed(ActionEvent e) + { + SequenceGroup sg = getGroup(); + sg.cs = new ClustalxColourScheme(sg.getSequences(true), + ap.av.alignment.getWidth()); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void zappoColour_actionPerformed(ActionEvent e) + { + getGroup().cs = new ZappoColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void taylorColour_actionPerformed(ActionEvent e) + { + getGroup().cs = new TaylorColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void hydrophobicityColour_actionPerformed(ActionEvent e) + { + getGroup().cs = new HydrophobicColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void helixColour_actionPerformed(ActionEvent e) + { + getGroup().cs = new HelixColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void strandColour_actionPerformed(ActionEvent e) + { + getGroup().cs = new StrandColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void turnColour_actionPerformed(ActionEvent e) + { + getGroup().cs = new TurnColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void buriedColour_actionPerformed(ActionEvent e) + { + getGroup().cs = new BuriedColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void nucleotideMenuItem_actionPerformed(ActionEvent e) + { + getGroup().cs = new NucleotideColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void abovePIDColour_actionPerformed(ActionEvent e) + { + SequenceGroup sg = getGroup(); + if(sg.cs==null) + return; + + if (abovePIDColour.isSelected()) + { + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(true), 0, + ap.av.alignment.getWidth())); + + int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, + getGroup().getName()); + + sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus()); + + SliderPanel.showPIDSlider(); + } + else // remove PIDColouring + { + sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); + } + + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void userDefinedColour_actionPerformed(ActionEvent e) + { + SequenceGroup sg = getGroup(); + + if (e.getActionCommand().equals("User Defined...")) + new UserDefinedColours(ap, sg); + else + { + UserColourScheme udc = (UserColourScheme) UserDefinedColours. + getUserColourSchemes().get(e.getActionCommand()); + + sg.cs = udc; + } + } + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void PIDColour_actionPerformed(ActionEvent e) + { + SequenceGroup sg = getGroup(); + sg.cs = new PIDColourScheme(); + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, + ap.av.alignment.getWidth())); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void BLOSUM62Colour_actionPerformed(ActionEvent e) + { + SequenceGroup sg = getGroup(); + + sg.cs = new Blosum62ColourScheme(); + + sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0, + ap.av.alignment.getWidth())); + + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void noColourmenuItem_actionPerformed(ActionEvent e) + { + getGroup().cs = null; + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void conservationMenuItem_actionPerformed(ActionEvent e) + { + SequenceGroup sg = getGroup(); + if(sg.cs==null) + return; + + if (conservationMenuItem.isSelected()) + { + Conservation c = new Conservation("Group", + ResidueProperties.propHash, 3, + sg.getSequences(true), 0, + ap.av.alignment.getWidth()); + + c.calculate(); + c.verdict(false, ap.av.ConsPercGaps); + + sg.cs.setConservation(c); + + SliderPanel.setConservationSlider(ap, sg.cs, sg.getName()); + SliderPanel.showConservationSlider(); + } + else // remove ConservationColouring + { + sg.cs.setConservation(null); + } + + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void groupName_actionPerformed(ActionEvent e) + { + SequenceGroup sg = getGroup(); + String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, + "Enter new group name", "Edit group name", + JOptionPane.QUESTION_MESSAGE); + + if (reply == null) + { + return; + } + + sg.setName(reply); + groupName.setText(reply); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void analyze_actionPerformed(ActionEvent e) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + JInternalFrame frame = new JInternalFrame(); + frame.setContentPane(cap); + Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300); + + SequenceGroup sg = getGroup(); + StringBuffer sb = new StringBuffer(); + + for (int i = 0; i < sg.getSize(false); i++) + { + Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i); + sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1)); + sb.append("\n"); + } + + sb.append("Something amazing will happen soon"); + cap.setText(sb.toString()); + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + SequenceGroup getGroup() + { + SequenceGroup sg = ap.av.getSelectionGroup(); + // this method won't add a new group if it already exists + if(sg!=null) + ap.av.alignment.addGroup(sg); + + return sg; + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + void sequenceName_actionPerformed(ActionEvent e) + { + JLabel idlabel = new JLabel( " Sequence Name "); + JLabel desclabel = new JLabel("Sequence Description "); + idlabel.setFont(new Font("Courier", Font.PLAIN, 12)); + desclabel.setFont(new Font("Courier", Font.PLAIN, 12)); + JTextField id = new JTextField(sequence.getName(), 40); + JTextField description = new JTextField(sequence.getDescription(), 40); + JPanel panel = new JPanel(new BorderLayout()); + JPanel panel2 = new JPanel(new BorderLayout()); + panel2.add(idlabel, BorderLayout.WEST); + panel2.add(id, BorderLayout.CENTER); + panel.add(panel2, BorderLayout.NORTH); + panel2 = new JPanel(new BorderLayout()); + panel2.add(desclabel, BorderLayout.WEST); + panel2.add(description, BorderLayout.CENTER); + panel.add(panel2, BorderLayout.SOUTH); + + + int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop, + panel, "Edit Sequence Name/Description", + JOptionPane.OK_CANCEL_OPTION ); + + + if (reply != JOptionPane.OK_OPTION ) + { + return; + } + + String s = id.getText(); + + if (s != null) + { + if (s.indexOf(" ") > -1) + { + JOptionPane.showMessageDialog(ap, + "Spaces have been converted to \"_\"", + "No spaces allowed in Sequence Name", + JOptionPane.WARNING_MESSAGE); + } + + s = s.replace(' ', '_'); + sequence.getDatasetSequence().setName(s); + sequence.setName(s); + ap.repaint(); + } + + sequence.getDatasetSequence().setDescription(description.getText()); + sequence.setDescription(description.getText()); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + void unGroupMenuItem_actionPerformed(ActionEvent e) + { + SequenceGroup sg = ap.av.getSelectionGroup(); + ap.av.alignment.deleteGroup(sg); + ap.av.setSelectionGroup(null); + refresh(); + } + + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + 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); + } + + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void showBoxes_actionPerformed(ActionEvent e) + { + getGroup().setDisplayBoxes(showBoxes.isSelected()); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void showText_actionPerformed(ActionEvent e) + { + getGroup().setDisplayText(showText.isSelected()); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void showColourText_actionPerformed(ActionEvent e) + { + getGroup().setColourText(showColourText.isSelected()); + refresh(); + } + + public void showLink(String url) + { + try + { + jalview.util.BrowserLauncher.openURL(url); + } + catch (Exception ex) + { + JOptionPane.showInternalMessageDialog(Desktop.desktop, + "Unixers: Couldn't find default web browser." + +"\nAdd the full path to your browser in Preferences.", + "Web browser not found", JOptionPane.WARNING_MESSAGE ); + + + ex.printStackTrace(); + } + } + + void hideSequences(boolean representGroup) + { + SequenceGroup sg = ap.av.getSelectionGroup(); + if(sg==null || sg.getSize(false)<1) + { + ap.av.hideSequence(sequence); + return; + } + + int index = 0; + while(index < sg.getSize(false)) + { + if(representGroup && sg.getSequenceAt(index)!=sequence) + { + sequence.addHiddenSequence(sg.getSequenceAt(index)); + ap.av.hideSequence(sg.getSequenceAt(index)); + } + else if(!representGroup) + { + ap.av.hideSequence(sg.getSequenceAt(index)); + } + index ++; + } + + ap.av.setSelectionGroup(null); + } + + public void copy_actionPerformed(ActionEvent e) + { + ap.alignFrame.copy_actionPerformed(null); + } + + public void cut_actionPerformed(ActionEvent e) + { + ap.alignFrame.cut_actionPerformed(null); + } + + public void upperCase_actionPerformed(ActionEvent e) + { + changeCase(e.getSource()); + } + + public void lowerCase_actionPerformed(ActionEvent e) + { + changeCase(e.getSource()); + } + + public void toggle_actionPerformed(ActionEvent e) + { + changeCase(e.getSource()); + } + + void changeCase(Object source) + { + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg != null) + { + for (int g = 0; g < sg.getSize(true); g++) + { + int start = sg.getStartRes(); + int end = sg.getEndRes() + 1; + + do + { + if (ap.av.hasHiddenColumns) + { + end = ap.av.colSel.getHiddenBoundaryRight(start); + if (start == end) + end = sg.getEndRes() + 1; + if (end > sg.getEndRes()) + end = sg.getEndRes() + 1; + } + + if (source == toggle) + ( (SequenceI) sg.getSequences(true).elementAt(g)) + .toggleCase(start, end); + else + ( (SequenceI) sg.getSequences(true).elementAt(g)) + .changeCase(source == upperCase, start, end); + + if (ap.av.hasHiddenColumns) + { + start = ap.av.colSel.adjustForHiddenColumns(end); + start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1; + } + + } + while (end < sg.getEndRes()); + } + ap.repaint(); + } + } + + public void outputText_actionPerformed(ActionEvent e) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + Desktop.addInternalFrame(cap, + "Alignment output - " + e.getActionCommand(), 600, + 500); + + String [] omitHidden = null; + + if(ap.av.hasHiddenColumns) + { + System.out.println("PROMPT USER HERE"); + omitHidden = ap.av.getViewAsString(true); + } + + cap.setText(new FormatAdapter().formatSequences( + e.getActionCommand(), + ap.av.getSelectionAsNewSequence(), + omitHidden)); + } + + + public void pdbFromFile_actionPerformed(ActionEvent e) + { + jalview.io.JalviewFileChooser chooser + = new jalview.io.JalviewFileChooser(jalview.bin.Cache. + getProperty( + "LAST_DIRECTORY")); + chooser.setFileView(new jalview.io.JalviewFileView()); + chooser.setDialogTitle("Select a PDB file"); + chooser.setToolTipText("Load a PDB file"); + + int value = chooser.showOpenDialog(null); + + if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION) + { + PDBEntry entry = new PDBEntry(); + String choice = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); + try + { + MCview.PDBfile pdbfile = new MCview.PDBfile(choice, + jalview.io.AppletFormatAdapter.FILE); + + if (pdbfile.id == null) + { + String reply = JOptionPane.showInternalInputDialog( + Desktop.desktop, + "Couldn't find a PDB id in the file supplied." + + "Please enter an Id to identify this structure.", + "No PDB Id in File", JOptionPane.QUESTION_MESSAGE); + if (reply == null) + return; + + entry.setId(reply); + } + else + entry.setId(pdbfile.id); + } + catch (java.io.IOException ex) + { + ex.printStackTrace(); + } + + entry.setFile(choice); + sequence.getDatasetSequence().addPDBId(entry); + } + + } + + public void enterPDB_actionPerformed(ActionEvent e) + { + String id = JOptionPane.showInternalInputDialog(Desktop.desktop, + "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE); + + if (id != null && id.length() > 0) + { + PDBEntry entry = new PDBEntry(); + entry.setId(id); + sequence.getDatasetSequence() + .addPDBId(entry); + } + } + + public void discoverPDB_actionPerformed(ActionEvent e) + { + new jalview.io.DBRefFetcher( + ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false); + } +}