X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=bd55d50c91c566e28ab9763fdb3839d6cfc008e7;hb=a3a196ed2104760ffeeebbca65fc03c361d29b17;hp=d85fabcc1a5978df2d537d49a44c30616c64d9a5;hpb=b618755c67d798ace34ebd6d0f384e913e8574c9;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index d85fabc..bd55d50 100755 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -1,635 +1,1624 @@ -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 -{ - JMenu groupMenu = new JMenu(); - JMenuItem groupName = 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(); - 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) - { - /////////////////////////////////////////////////////////// - // 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.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 instanceof ConservationColourScheme) - conservationMenuItem.setSelected(true); - - showText.setSelected(sg.getDisplayText()); - showColourText.setSelected(sg.getColourText()); - showBoxes.setSelected(sg.getDisplayBoxes()); - } - - 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 - { - groupMenu.setText("Group"); - groupMenu.setText("Define"); - 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"); - 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); - } - }); - pdbMenuItem.setText("View PDB structure"); - pdbMenuItem.addActionListener(new java.awt.event.ActionListener() - { - public void actionPerformed(ActionEvent e) - { - pdbMenuItem_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); - } - }); - add(groupMenu); - add(sequenceMenu); - groupMenu.add(groupName); - groupMenu.addSeparator(); - groupMenu.add(unGroupMenuItem); - groupMenu.add(colourMenu); - groupMenu.addSeparator(); - 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.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); - } - }); - - - - } - - void refresh() - { - 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) - { - 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(); - } - - public void nucleotideMenuItem_actionPerformed(ActionEvent e) - { - getGroup().cs = new NucleotideColourScheme(); - refresh(); - } - - - - 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) - { - SequenceGroup sg = getGroup(); - - sg.cs = new Blosum62ColourScheme(); - - sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, - ap.av.alignment.getWidth())); - - 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, ap.av.ConsPercGaps); - ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs); - - - 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(); - 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 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 0) + { + java.util.Enumeration e = seq.getDatasetSequence().getPDBId() + .elements(); + + while (e.hasMoreElements()) + { + final PDBEntry pdb = (PDBEntry) e.nextElement(); + + menuItem = new JMenuItem(); + menuItem.setText(pdb.getId()); + menuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + Vector seqs = new Vector(); + for (int i = 0; i < ap.av.alignment.getHeight(); i++) + { + Vector pdbs = ap.av.alignment.getSequenceAt(i) + .getDatasetSequence().getPDBId(); + if (pdbs == null) + continue; + + for (int p = 0; p < pdbs.size(); p++) + { + PDBEntry p1 = (PDBEntry) pdbs.elementAt(p); + if (p1.getId().equals(pdb.getId())) + { + if (!seqs.contains(ap.av.alignment.getSequenceAt(i))) + seqs.addElement(ap.av.alignment.getSequenceAt(i)); + + continue; + } + } + } + + SequenceI[] seqs2 = new SequenceI[seqs.size()]; + seqs.toArray(seqs2); + + new AppJmol(pdb, seqs2, null, ap); + // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE); + } + }); + viewStructureMenu.add(menuItem); + + /* + * menuItem = new JMenuItem(); menuItem.setText(pdb.getId()); + * menuItem.addActionListener(new java.awt.event.ActionListener() { + * public void actionPerformed(ActionEvent e) { + * colourByStructure(pdb.getId()); } }); + * colStructureMenu.add(menuItem); + */ + } + } + else + { + structureMenu.remove(viewStructureMenu); + // structureMenu.remove(colStructureMenu); + } + + menuItem = new JMenuItem("Hide Sequences"); + menuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + hideSequences(false); + } + }); + add(menuItem); + + if (ap.av.getSelectionGroup() != null + && ap.av.getSelectionGroup().getSize() > 1) + { + 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); + structureMenu.setVisible(false); + } + + if (links != null && links.size() > 0) + { + JMenu linkMenu = new JMenu("Link"); + + for (int i = 0; i < links.size(); i++) + { + String link = links.elementAt(i).toString(); + UrlLink urlLink = null; + try + { + urlLink = new UrlLink(link); + } catch (Exception foo) + { + jalview.bin.Cache.log.error("Exception for URLLink '" + link + + "'", foo); + continue; + } + ; + if (!urlLink.isValid()) + { + jalview.bin.Cache.log.error(urlLink.getInvalidMessage()); + continue; + } + final String label = urlLink.getLabel(); + if (urlLink.isDynamic()) + { + + // collect matching db-refs + DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq + .getDBRef(), new String[] + { urlLink.getTarget() }); + // collect id string too + String id = seq.getName(); + if (dbr != null) + { + for (int r = 0; r < dbr.length; r++) + { + if (id != null && dbr[r].getAccessionId().equals(id)) + { + // suppress duplicate link creation for the bare sequence ID + // string with this link + id = null; + } + // create Bare ID link for this RUL + String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), + true); + if (urls != null) + { + for (int u = 0; u < urls.length; u += 2) + { + addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]); + } + } + } + } + if (id != null) + { + // create Bare ID link for this RUL + String[] urls = urlLink.makeUrls(id, true); + if (urls != null) + { + for (int u = 0; u < urls.length; u += 2) + { + addshowLink(linkMenu, label, urls[u + 1]); + } + } + } + } + else + { + // Add a non-dynamic link + addshowLink(linkMenu, label, urlLink.getUrl_prefix()); + } + } + if (sequence != null) + { + sequenceMenu.add(linkMenu); + } + else + { + add(linkMenu); + } + } + } + + /** + * add a show URL menu item to the given linkMenu + * + * @param linkMenu + * @param label - + * menu label string + * @param url - + * url to open + */ + private void addshowLink(JMenu linkMenu, String label, final String url) + { + JMenuItem item = new JMenuItem(label); + item.setToolTipText("open URL: " + url); + item.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + new Thread(new Runnable() + { + + public void run() + { + showLink(url); + } + + }).start(); + } + }); + + linkMenu.add(item); + } + + /** + * 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(); + } + }); + sequenceMenu.setText("Sequence"); + sequenceName.setText("Edit Name/Description"); + sequenceName.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sequenceName_actionPerformed(); + } + }); + PIDColour.setFocusPainted(false); + unGroupMenuItem.setText("Remove Group"); + unGroupMenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + unGroupMenuItem_actionPerformed(); + } + }); + + outline.setText("Border colour"); + outline.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + outline_actionPerformed(); + } + }); + nucleotideMenuItem.setText("Nucleotide"); + nucleotideMenuItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + nucleotideMenuItem_actionPerformed(); + } + }); + colourMenu.setText("Group Colour"); + showBoxes.setText("Boxes"); + showBoxes.setState(true); + showBoxes.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showBoxes_actionPerformed(); + } + }); + showText.setText("Text"); + showText.setState(true); + showText.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showText_actionPerformed(); + } + }); + showColourText.setText("Colour Text"); + showColourText.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + showColourText_actionPerformed(); + } + }); + editMenu.setText("Edit"); + cut.setText("Cut"); + cut.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + cut_actionPerformed(); + } + }); + upperCase.setText("To Upper Case"); + upperCase.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + changeCase(e); + } + }); + copy.setText("Copy"); + copy.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + copy_actionPerformed(); + } + }); + lowerCase.setText("To Lower Case"); + lowerCase.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + changeCase(e); + } + }); + toggle.setText("Toggle Case"); + toggle.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + changeCase(e); + } + }); + pdbMenu.setText("Associate Structure with Sequence"); + pdbFromFile.setText("From File"); + pdbFromFile.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + pdbFromFile_actionPerformed(); + } + }); + enterPDB.setText("Enter PDB Id"); + enterPDB.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + enterPDB_actionPerformed(); + } + }); + discoverPDB.setText("Discover PDB ids"); + discoverPDB.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + discoverPDB_actionPerformed(); + } + }); + outputMenu.setText("Output to Textbox..."); + sequenceFeature.setText("Create Sequence Feature"); + sequenceFeature.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + sequenceFeature_actionPerformed(); + } + }); + textColour.setText("Text Colour"); + textColour.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + textColour_actionPerformed(); + } + }); + jMenu1.setText("Group"); + structureMenu.setText("Structure"); + viewStructureMenu.setText("View Structure"); + // colStructureMenu.setText("Colour By Structure"); + editSequence.setText("Edit Sequence..."); + editSequence.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent actionEvent) + { + editSequence_actionPerformed(actionEvent); + } + }); + /* + * annotationMenuItem.setText("By Annotation"); + * annotationMenuItem.addActionListener(new ActionListener() { public void + * actionPerformed(ActionEvent actionEvent) { + * annotationMenuItem_actionPerformed(actionEvent); } }); + */ + + add(groupMenu); + + add(sequenceMenu); + this.add(structureMenu); + groupMenu.add(editMenu); + groupMenu.add(outputMenu); + groupMenu.add(sequenceFeature); + groupMenu.add(jMenu1); + sequenceMenu.add(sequenceName); + colourMenu.add(textColour); + 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); + // colourMenu.add(annotationMenuItem); + editMenu.add(copy); + editMenu.add(cut); + editMenu.add(editSequence); + editMenu.add(upperCase); + editMenu.add(lowerCase); + editMenu.add(toggle); + pdbMenu.add(pdbFromFile); + pdbMenu.add(enterPDB); + pdbMenu.add(discoverPDB); + jMenu1.add(groupName); + jMenu1.add(unGroupMenuItem); + jMenu1.add(colourMenu); + jMenu1.add(showBoxes); + jMenu1.add(showText); + jMenu1.add(showColourText); + jMenu1.add(outline); + structureMenu.add(pdbMenu); + structureMenu.add(viewStructureMenu); + // structureMenu.add(colStructureMenu); + noColourmenuItem.setText("None"); + noColourmenuItem.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + noColourmenuItem_actionPerformed(); + } + }); + + clustalColour.setText("Clustalx colours"); + clustalColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + clustalColour_actionPerformed(); + } + }); + zappoColour.setText("Zappo"); + zappoColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + zappoColour_actionPerformed(); + } + }); + taylorColour.setText("Taylor"); + taylorColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + taylorColour_actionPerformed(); + } + }); + hydrophobicityColour.setText("Hydrophobicity"); + hydrophobicityColour + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + hydrophobicityColour_actionPerformed(); + } + }); + helixColour.setText("Helix propensity"); + helixColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + helixColour_actionPerformed(); + } + }); + strandColour.setText("Strand propensity"); + strandColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + strandColour_actionPerformed(); + } + }); + turnColour.setText("Turn propensity"); + turnColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + turnColour_actionPerformed(); + } + }); + buriedColour.setText("Buried Index"); + buriedColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + buriedColour_actionPerformed(); + } + }); + abovePIDColour.setText("Above % Identity"); + abovePIDColour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + abovePIDColour_actionPerformed(); + } + }); + 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(); + } + }); + BLOSUM62Colour.setText("BLOSUM62"); + BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + BLOSUM62Colour_actionPerformed(); + } + }); + conservationMenuItem.setText("Conservation"); + conservationMenuItem + .addActionListener(new java.awt.event.ActionListener() + { + public void actionPerformed(ActionEvent e) + { + conservationMenuItem_actionPerformed(); + } + }); + } + + /** + * DOCUMENT ME! + */ + void refresh() + { + ap.paintAlignment(true); + + PaintRefresher.Refresh(this, ap.av.getSequenceSetId()); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void clustalColour_actionPerformed() + { + SequenceGroup sg = getGroup(); + sg.cs = new ClustalxColourScheme(sg + .getSequences(ap.av.hiddenRepSequences), ap.av.alignment + .getWidth()); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void zappoColour_actionPerformed() + { + getGroup().cs = new ZappoColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void taylorColour_actionPerformed() + { + getGroup().cs = new TaylorColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void hydrophobicityColour_actionPerformed() + { + getGroup().cs = new HydrophobicColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void helixColour_actionPerformed() + { + getGroup().cs = new HelixColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void strandColour_actionPerformed() + { + getGroup().cs = new StrandColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void turnColour_actionPerformed() + { + getGroup().cs = new TurnColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void buriedColour_actionPerformed() + { + getGroup().cs = new BuriedColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void nucleotideMenuItem_actionPerformed() + { + getGroup().cs = new NucleotideColourScheme(); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void abovePIDColour_actionPerformed() + { + SequenceGroup sg = getGroup(); + if (sg.cs == null) + { + return; + } + + if (abovePIDColour.isSelected()) + { + sg.cs.setConsensus(AAFrequency.calculate(sg + .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg + .getEndRes() + 1)); + + 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; + } + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void PIDColour_actionPerformed() + { + SequenceGroup sg = getGroup(); + sg.cs = new PIDColourScheme(); + sg.cs.setConsensus(AAFrequency.calculate(sg + .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg + .getEndRes() + 1)); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void BLOSUM62Colour_actionPerformed() + { + SequenceGroup sg = getGroup(); + + sg.cs = new Blosum62ColourScheme(); + + sg.cs.setConsensus(AAFrequency.calculate(sg + .getSequences(ap.av.hiddenRepSequences), sg.getStartRes(), sg + .getEndRes() + 1)); + + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void noColourmenuItem_actionPerformed() + { + getGroup().cs = null; + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void conservationMenuItem_actionPerformed() + { + SequenceGroup sg = getGroup(); + if (sg.cs == null) + { + return; + } + + if (conservationMenuItem.isSelected()) + { + Conservation c = new Conservation("Group", + ResidueProperties.propHash, 3, sg + .getSequences(ap.av.hiddenRepSequences), sg + .getStartRes(), sg.getEndRes() + 1); + + 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(); + } + + public void annotationMenuItem_actionPerformed(ActionEvent actionEvent) + { + SequenceGroup sg = getGroup(); + if (sg == null) + { + return; + } + + AnnotationColourGradient acg = new AnnotationColourGradient(sequence + .getAnnotation()[0], null, + AnnotationColourGradient.NO_THRESHOLD); + + acg.predefinedColours = true; + sg.cs = acg; + + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + protected void groupName_actionPerformed() + { + + SequenceGroup sg = getGroup(); + EditNameDialog dialog = new EditNameDialog(sg.getName(), sg + .getDescription(), " Group Name ", "Group Description ", + "Edit Group Name/Description"); + + if (!dialog.accept) + { + return; + } + + sg.setName(dialog.getName()); + sg.setDescription(dialog.getDescription()); + } + + /** + * 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() + { + EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence + .getDescription(), " Sequence Name ", + "Sequence Description ", "Edit Sequence Name/Description"); + + if (!dialog.accept) + { + return; + } + + if (dialog.getName() != null) + { + if (dialog.getName().indexOf(" ") > -1) + { + JOptionPane.showMessageDialog(ap, + "Spaces have been converted to \"_\"", + "No spaces allowed in Sequence Name", + JOptionPane.WARNING_MESSAGE); + } + + sequence.setName(dialog.getName().replace(' ', '_')); + ap.paintAlignment(false); + } + + sequence.setDescription(dialog.getDescription()); + + ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() + .getSequences()); + + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + void unGroupMenuItem_actionPerformed() + { + 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() + { + 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() + { + getGroup().setDisplayBoxes(showBoxes.isSelected()); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void showText_actionPerformed() + { + getGroup().setDisplayText(showText.isSelected()); + refresh(); + } + + /** + * DOCUMENT ME! + * + * @param e + * DOCUMENT ME! + */ + public void showColourText_actionPerformed() + { + 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() < 1) + { + ap.av.hideSequence(new SequenceI[] + { sequence }); + return; + } + + ap.av.setSelectionGroup(null); + + if (representGroup) + { + ap.av.hideRepSequences(sequence, sg); + + return; + } + + int gsize = sg.getSize(); + SequenceI[] hseqs; + + hseqs = new SequenceI[gsize]; + + int index = 0; + for (int i = 0; i < gsize; i++) + { + hseqs[index++] = sg.getSequenceAt(i); + } + + ap.av.hideSequence(hseqs); + } + + public void copy_actionPerformed() + { + ap.alignFrame.copy_actionPerformed(null); + } + + public void cut_actionPerformed() + { + ap.alignFrame.cut_actionPerformed(null); + } + + void changeCase(ActionEvent e) + { + Object source = e.getSource(); + SequenceGroup sg = ap.av.getSelectionGroup(); + + if (sg != null) + { + int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(), + sg.getEndRes() + 1); + + String description; + int caseChange; + + if (source == toggle) + { + description = "Toggle Case"; + caseChange = ChangeCaseCommand.TOGGLE_CASE; + } + else if (source == upperCase) + { + description = "To Upper Case"; + caseChange = ChangeCaseCommand.TO_UPPER; + } + else + { + description = "To Lower Case"; + caseChange = ChangeCaseCommand.TO_LOWER; + } + + ChangeCaseCommand caseCommand = new ChangeCaseCommand(description, sg + .getSequencesAsArray(ap.av.hiddenRepSequences), startEnd, + caseChange); + + ap.alignFrame.addHistoryItem(caseCommand); + + ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() + .getSequences()); + + } + } + + public void outputText_actionPerformed(ActionEvent e) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + cap.setForInput(null); + Desktop.addInternalFrame(cap, "Alignment output - " + + e.getActionCommand(), 600, 500); + + String[] omitHidden = null; + + System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens + // or we simply trust the user wants + // wysiwig behaviour + SequenceGroup sg = ap.av.getSelectionGroup(); + ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection()); + omitHidden = ap.av.getViewAsString(true); + Alignment oal = new Alignment(ap.av.getSequenceSelection()); + AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation(); + for (int i = 0; i < nala.length; i++) + { + AlignmentAnnotation na = nala[i]; + oal.addAnnotation(na); + } + cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), + oal, omitHidden, csel, sg)); + oal = null; + } + + public void pdbFromFile_actionPerformed() + { + 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() + { + 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.toUpperCase()); + sequence.getDatasetSequence().addPDBId(entry); + } + } + + public void discoverPDB_actionPerformed() + { + + final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[] + { sequence } + : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment)); + Thread discpdb = new Thread(new Runnable() + { + public void run() + { + + new jalview.ws.DBRefFetcher(sequences, ap.alignFrame) + .fetchDBRefs(false); + } + + }); + discpdb.start(); + } + + public void sequenceFeature_actionPerformed() + { + SequenceGroup sg = ap.av.getSelectionGroup(); + if (sg == null) + { + return; + } + int rsize=0,gSize = sg.getSize(); + SequenceI[] rseqs,seqs = new SequenceI[gSize]; + SequenceFeature[] tfeatures,features = new SequenceFeature[gSize]; + + for (int i = 0; i < gSize; i++) + { + int start = sg.getSequenceAt(i).findPosition(sg.getStartRes()); + int end = sg.findEndRes(sg.getSequenceAt(i)); + if (start<=end) + { + seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence(); + features[rsize] = new SequenceFeature(null, null, null, start, end, + "Jalview"); + rsize++; + } + } + rseqs = new SequenceI[rsize]; + tfeatures = new SequenceFeature[rsize]; + System.arraycopy(seqs,0,rseqs, 0, rsize); + System.arraycopy(features, 0, tfeatures, 0, rsize); + features = tfeatures; + seqs = rseqs; + if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs, + features, true, ap)) + { + ap.alignFrame.showSeqFeatures.setSelected(true); + ap.av.setShowSequenceFeatures(true); + ap.highlightSearchResults(null); + } + } + + public void textColour_actionPerformed() + { + SequenceGroup sg = getGroup(); + if (sg != null) + { + new TextColourChooser().chooseColour(ap, sg); + } + } + + public void colourByStructure(String pdbid) + { + Annotation[] anots = jalview.structure.StructureSelectionManager + .getStructureSelectionManager().colourSequenceFromStructure( + sequence, pdbid); + + AlignmentAnnotation an = new AlignmentAnnotation("Structure", + "Coloured by " + pdbid, anots); + + ap.av.alignment.addAnnotation(an); + an.createSequenceMapping(sequence, 0, true); + // an.adjustForAlignment(); + ap.av.alignment.setAnnotationIndex(an, 0); + + ap.adjustAnnotationHeight(); + + sequence.addAlignmentAnnotation(an); + + } + + public void editSequence_actionPerformed(ActionEvent actionEvent) + { + SequenceGroup sg = ap.av.getSelectionGroup(); + + if (sg != null) + { + if (sequence == null) + sequence = (Sequence) sg.getSequenceAt(0); + + EditNameDialog dialog = new EditNameDialog(sequence + .getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1), + null, "Edit Sequence ", null, "Edit Sequence"); + + if (dialog.accept) + { + EditCommand editCommand = new EditCommand("Edit Sequences", + EditCommand.REPLACE, dialog.getName().replace(' ', + ap.av.getGapCharacter()), sg + .getSequencesAsArray(ap.av.hiddenRepSequences), sg + .getStartRes(), sg.getEndRes() + 1, ap.av.alignment); + + ap.alignFrame.addHistoryItem(editCommand); + + ap.av.firePropertyChange("alignment", null, ap.av.getAlignment() + .getSequences()); + } + } + } + +}