pdbs = seq.getAllPDBEntries();
+ if (pdbs != null && !pdbs.isEmpty())
+ {
+ PDBEntry entry = pdbs.firstElement();
+
+ if (ap.av.applet.jmolAvailable)
+ {
+ new AppletJmol(entry, new SequenceI[] { seq }, null, ap,
+ DataSourceType.URL);
+ }
+ else
+ {
+ new mc_view.AppletPDBViewer(entry, new SequenceI[] { seq }, null,
+ ap, DataSourceType.URL);
+ }
+
+ }
+ else
+ {
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true,
+ ap.alignFrame);
+ cap.setText(MessageManager.getString("label.paste_pdb_file"));
+ cap.setPDBImport(seq);
+ Frame frame = new Frame();
+ frame.add(cap);
+ JalviewLite.addFrame(frame, MessageManager.formatMessage(
+ "label.paste_pdb_file_for_sequence", new Object[]
+ { seq.getName() }), 400, 300);
+ }
+ }
+
+ private void jbInit() throws Exception
+ {
+ groupMenu.setLabel(MessageManager.getString("label.selection"));
+ sequenceFeature.addActionListener(this);
+
+ editGroupName.addActionListener(this);
+ unGroupMenuItem
+ .setLabel(MessageManager.getString("action.remove_group"));
+ unGroupMenuItem.addActionListener(this);
+
+ createGroupMenuItem
+ .setLabel(MessageManager.getString("action.create_group"));
+ createGroupMenuItem.addActionListener(this);
+
+ modifyPID.setEnabled(abovePIDColour.getState());
+ modifyConservation.setEnabled(conservationColour.getState());
+ colourMenu.setLabel(MessageManager.getString("label.group_colour"));
+ showBoxes.setLabel(MessageManager.getString("action.boxes"));
+ showBoxes.setState(true);
+ showBoxes.addItemListener(this);
+ sequenceName.addActionListener(this);
+ sequenceDetails.addActionListener(this);
+ selSeqDetails.addActionListener(this);
+ displayNonconserved
+ .setLabel(MessageManager.getString("label.show_non_conserved"));
+ displayNonconserved.setState(false);
+ displayNonconserved.addItemListener(this);
+ showText.setLabel(MessageManager.getString("action.text"));
+ showText.addItemListener(this);
+ showColourText.setLabel(MessageManager.getString("label.colour_text"));
+ showColourText.addItemListener(this);
+ outputmenu.setLabel(MessageManager.getString("label.out_to_textbox"));
+ seqMenu.setLabel(MessageManager.getString("label.sequence"));
+ pdb.setLabel(MessageManager.getString("label.view_pdb_structure"));
+ hideSeqs.setLabel(MessageManager.getString("action.hide_sequences"));
+ repGroup.setLabel(MessageManager
+ .formatMessage("label.represent_group_with", new Object[]
+ { "" }));
+ revealAll.setLabel(MessageManager.getString("action.reveal_all"));
+ revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
+ menu1.setLabel(MessageManager.getString("label.group:"));
+ add(groupMenu);
+ this.add(seqMenu);
+ this.add(hideSeqs);
+ this.add(revealSeq);
+ this.add(revealAll);
+ // groupMenu.add(selSeqDetails);
+ groupMenu.add(groupShowAnnotationsMenu);
+ groupMenu.add(groupHideAnnotationsMenu);
+ groupMenu.add(groupAddReferenceAnnotations);
+ groupMenu.add(editMenu);
+ groupMenu.add(outputmenu);
+ groupMenu.add(sequenceFeature);
+ groupMenu.add(createGroupMenuItem);
+ groupMenu.add(unGroupMenuItem);
+ groupMenu.add(menu1);
+
+ colourMenu.add(noColour);
+ 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(nucleotideColour);
+ colourMenu.add(purinePyrimidineColour);
+ colourMenu.add(userDefinedColour);
+ colourMenu.addSeparator();
+ colourMenu.add(conservationColour);
+ colourMenu.add(modifyConservation);
+ colourMenu.add(abovePIDColour);
+ colourMenu.add(modifyPID);
+
+ noColour.setLabel(MessageManager.getString("label.none"));
+ noColour.addItemListener(this);
+
+ /*
+ * setName allows setSelectedColour to do its thing
+ */
+ clustalColour.setLabel(
+ MessageManager.getString("label.colourScheme_clustal"));
+ clustalColour.setName(JalviewColourScheme.Clustal.toString());
+ clustalColour.addItemListener(this);
+ BLOSUM62Colour.setLabel(
+ MessageManager.getString("label.colourScheme_blosum62"));
+ BLOSUM62Colour.setName(JalviewColourScheme.Blosum62.toString());
+ BLOSUM62Colour.addItemListener(this);
+ PIDColour.setLabel(
+ MessageManager.getString("label.colourScheme_%identity"));
+ PIDColour.setName(JalviewColourScheme.PID.toString());
+ PIDColour.addItemListener(this);
+ zappoColour
+ .setLabel(MessageManager.getString("label.colourScheme_zappo"));
+ zappoColour.setName(JalviewColourScheme.Zappo.toString());
+ zappoColour.addItemListener(this);
+ taylorColour.setLabel(
+ MessageManager.getString("label.colourScheme_taylor"));
+ taylorColour.setName(JalviewColourScheme.Taylor.toString());
+ taylorColour.addItemListener(this);
+ hydrophobicityColour.setLabel(
+ MessageManager.getString("label.colourScheme_hydrophobic"));
+ hydrophobicityColour
+ .setName(JalviewColourScheme.Hydrophobic.toString());
+ hydrophobicityColour.addItemListener(this);
+ helixColour.setLabel(
+ MessageManager.getString("label.colourScheme_helixpropensity"));
+ helixColour.setName(JalviewColourScheme.Helix.toString());
+ helixColour.addItemListener(this);
+ strandColour.setLabel(MessageManager
+ .getString("label.colourScheme_strandpropensity"));
+ strandColour.setName(JalviewColourScheme.Strand.toString());
+ strandColour.addItemListener(this);
+ turnColour.setLabel(
+ MessageManager.getString("label.colourScheme_turnpropensity"));
+ turnColour.setName(JalviewColourScheme.Turn.toString());
+ turnColour.addItemListener(this);
+ buriedColour.setLabel(
+ MessageManager.getString("label.colourScheme_buriedindex"));
+ buriedColour.setName(JalviewColourScheme.Buried.toString());
+ buriedColour.addItemListener(this);
+ nucleotideColour.setLabel(
+ MessageManager.getString("label.colourScheme_nucleotide"));
+ nucleotideColour.setName(JalviewColourScheme.Nucleotide.toString());
+ nucleotideColour.addItemListener(this);
+ purinePyrimidineColour.setLabel(MessageManager
+ .getString("label.colourScheme_purine/pyrimidine"));
+ purinePyrimidineColour
+ .setName(JalviewColourScheme.PurinePyrimidine.toString());
+ purinePyrimidineColour.addItemListener(this);
+
+ userDefinedColour
+ .setLabel(MessageManager.getString("action.user_defined"));
+ userDefinedColour.addActionListener(this);
+
+ abovePIDColour.setLabel(
+ MessageManager.getString("label.above_identity_threshold"));
+ abovePIDColour.addItemListener(this);
+ modifyPID.setLabel(
+ MessageManager.getString("label.modify_identity_threshold"));
+ modifyPID.addActionListener(this);
+ conservationColour
+ .setLabel(MessageManager.getString("action.by_conservation"));
+ conservationColour.addItemListener(this);
+ modifyConservation.setLabel(MessageManager
+ .getString("label.modify_conservation_threshold"));
+ modifyConservation.addActionListener(this);
+
+ PIDColour.addActionListener(this);
+ BLOSUM62Colour.addActionListener(this);
+
+ editMenu.add(copy);
+ copy.addActionListener(this);
+ editMenu.add(cut);
+ cut.addActionListener(this);
+
+ editMenu.add(editSequence);
+ editSequence.addActionListener(this);
+
+ editMenu.add(toUpper);
+ toUpper.addActionListener(this);
+ editMenu.add(toLower);
+ toLower.addActionListener(this);
+ editMenu.add(toggleCase);
+ seqMenu.add(seqShowAnnotationsMenu);
+ seqMenu.add(seqHideAnnotationsMenu);
+ seqMenu.add(seqAddReferenceAnnotations);
+ seqMenu.add(sequenceName);
+ seqMenu.add(makeReferenceSeq);
+ // seqMenu.add(sequenceDetails);
+
+ if (!ap.av.applet.useXtrnalSviewer)
+ {
+ seqMenu.add(pdb);
+ }
+ seqMenu.add(repGroup);
+ menu1.add(editGroupName);
+ menu1.add(colourMenu);
+ menu1.add(showBoxes);
+ menu1.add(showText);
+ menu1.add(showColourText);
+ menu1.add(displayNonconserved);
+ toggleCase.addActionListener(this);
+ pdb.addActionListener(this);
+ hideSeqs.addActionListener(this);
+ repGroup.addActionListener(this);
+ revealAll.addActionListener(this);
+ revealSeq.addActionListener(this);
+ makeReferenceSeq.addActionListener(this);
+ }
+
+ void refresh()
+ {
+ ap.paintAlignment(true, true);
+ }
+
+ protected void clustalColour_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ sg.cs = new ResidueShader(
+ new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences()));
+ refresh();
+ }
+
+ protected void zappoColour_actionPerformed()
+ {
+ getGroup().cs = new ResidueShader(new ZappoColourScheme());
+ refresh();
+ }
+
+ protected void taylorColour_actionPerformed()
+ {
+ getGroup().cs = new ResidueShader(new TaylorColourScheme());
+ refresh();
+ }
+
+ protected void hydrophobicityColour_actionPerformed()
+ {
+ getGroup().cs = new ResidueShader(new HydrophobicColourScheme());
+ refresh();
+ }
+
+ protected void helixColour_actionPerformed()
+ {
+ getGroup().cs = new ResidueShader(new HelixColourScheme());
+ refresh();
+ }
+
+ protected void strandColour_actionPerformed()
+ {
+ getGroup().cs = new ResidueShader(new StrandColourScheme());
+ refresh();
+ }
+
+ protected void turnColour_actionPerformed()
+ {
+ getGroup().cs = new ResidueShader(new TurnColourScheme());
+ refresh();
+ }
+
+ protected void buriedColour_actionPerformed()
+ {
+ getGroup().cs = new ResidueShader(new BuriedColourScheme());
+ refresh();
+ }
+
+ public void nucleotideMenuItem_actionPerformed()
+ {
+ getGroup().cs = new ResidueShader(new NucleotideColourScheme());
+ refresh();
+ }
+
+ public void purinePyrimidineColour_actionPerformed()
+ {
+ getGroup().cs = new ResidueShader(new PurinePyrimidineColourScheme());
+ refresh();
+ }
+
+ protected void abovePIDColour_itemStateChanged()
+ {
+ SequenceGroup sg = getGroup();
+ if (sg.cs == null)
+ {
+ return;
+ }
+
+ if (abovePIDColour.getState())
+ {
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()), 0,
+ ap.av.getAlignment().getWidth()));
+ int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
+ getGroup().getName());
+
+ sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
+
+ SliderPanel.showPIDSlider();
+
+ }
+ else
+ // remove PIDColouring
+ {
+ SliderPanel.hidePIDSlider();
+ sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+ }
+ modifyPID.setEnabled(abovePIDColour.getState());
+ refresh();
+ }
+
+ protected void userDefinedColour_actionPerformed()
+ {
+ new UserDefinedColours(ap, getGroup());
+ }
+
+ protected void PIDColour_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ sg.cs = new ResidueShader(new PIDColourScheme());
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()), 0,
+ ap.av.getAlignment().getWidth()));
+ refresh();
+ }
+
+ protected void BLOSUM62Colour_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+
+ sg.cs = new ResidueShader(new Blosum62ColourScheme());
+
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()), 0,
+ ap.av.getAlignment().getWidth()));
+
+ refresh();
+ }
+
+ protected void noColourmenuItem_actionPerformed()
+ {
+ getGroup().cs = null;
+ refresh();
+ }
+
+ protected void conservationMenuItem_itemStateChanged()
+ {
+ SequenceGroup sg = getGroup();
+ if (sg.cs == null)
+ {
+ return;
+ }
+
+ if (conservationColour.getState())
+ {
+ Conservation conservation = Conservation.calculateConservation(
+ "Group", sg.getSequences(ap.av.getHiddenRepSequences()), 0,
+ ap.av.getAlignment().getWidth(), false,
+ ap.av.getConsPercGaps(), false);
+ sg.getGroupColourScheme().setConservation(conservation);
+ SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+ SliderPanel.showConservationSlider();
+ }
+ else
+ // remove ConservationColouring
+ {
+ SliderPanel.hideConservationSlider();
+ sg.cs.setConservation(null);
+ }
+ modifyConservation.setEnabled(conservationColour.getState());
+ refresh();
+ }
+
+ SequenceGroup getGroup()
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+
+ // this method won't add a new group if it already exists
+ if (sg != null)
+ {
+ ap.av.getAlignment().addGroup(sg);
+ }
+
+ return sg;
+ }
+
+ void unGroupMenuItem_actionPerformed()
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ ap.av.getAlignment().deleteGroup(sg);
+ ap.av.setSelectionGroup(null);
+ ap.paintAlignment(true, true);
+ }
+
+ void createGroupMenuItem_actionPerformed()
+ {
+ getGroup(); // implicitly create group
+ refresh();
+ }
+
+ public void showColourText_itemStateChanged()
+ {
+ getGroup().setColourText(showColourText.getState());
+ refresh();
+ }
+
+ public void showText_itemStateChanged()
+ {
+ getGroup().setDisplayText(showText.getState());
+ refresh();
+ }
+
+ public void makeReferenceSeq_actionPerformed()
+ {
+ if (!ap.av.getAlignment().hasSeqrep())
+ {
+ // initialise the display flags so the user sees something happen
+ ap.av.setDisplayReferenceSeq(true);
+ ap.av.setColourByReferenceSeq(true);
+ ap.av.getAlignment().setSeqrep(seq);
+ }
+ else
+ {
+ if (ap.av.getAlignment().getSeqrep() == seq)
+ {
+ ap.av.getAlignment().setSeqrep(null);
+ }
+ else
+ {
+ ap.av.getAlignment().setSeqrep(seq);
+ }
+ }
+ refresh();
+ }
+
+ public void showNonconserved_itemStateChanged()
+ {
+ getGroup().setShowNonconserved(this.displayNonconserved.getState());
+ refresh();
+ }
+
+ public void showBoxes_itemStateChanged()
+ {
+ getGroup().setDisplayBoxes(showBoxes.getState());
+ refresh();
+ }
+
+ void hideSequences(boolean representGroup)
+ {
+ ap.av.hideSequences(seq, representGroup);
+ }
+
+ /**
+ * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
+ * "All" is added first, followed by a separator. Then add any annotation
+ * types associated with the current selection. Separate menus are built for
+ * the selected sequence group (if any), and the selected sequence.
+ *
+ * Some annotation rows are always rendered together - these can be identified
+ * by a common graphGroup property > -1. Only one of each group will be marked
+ * as visible (to avoid duplication of the display). For such groups we add a
+ * composite type name, e.g.
+ *
+ * IUPredWS (Long), IUPredWS (Short)
+ *
+ * @param seq
+ */
+ protected void buildAnnotationTypesMenus(Menu showMenu, Menu hideMenu,
+ List forSequences)
+ {
+ showMenu.removeAll();
+ hideMenu.removeAll();
+
+ final List all = Arrays
+ .asList(new String[]
+ { MessageManager.getString("label.all") });
+ addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true,
+ true);
+ addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
+ false);
+ showMenu.addSeparator();
+ hideMenu.addSeparator();
+
+ final AlignmentAnnotation[] annotations = ap.getAlignment()
+ .getAlignmentAnnotation();
+
+ /*
+ * Find shown/hidden annotations types, distinguished by source (calcId),
+ * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
+ * the insertion order, which is the order of the annotations on the
+ * alignment.
+ */
+ Map>> shownTypes = new LinkedHashMap<>();
+ Map>> hiddenTypes = new LinkedHashMap<>();
+ AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
+ AlignmentAnnotationUtils.asList(annotations), forSequences);
+
+ for (String calcId : hiddenTypes.keySet())
+ {
+ for (List type : hiddenTypes.get(calcId))
+ {
+ addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
+ false, true);
+ }
+ }
+ // grey out 'show annotations' if none are hidden
+ showMenu.setEnabled(!hiddenTypes.isEmpty());
+
+ for (String calcId : shownTypes.keySet())
+ {
+ for (List type : shownTypes.get(calcId))
+ {
+ addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
+ false, false);
+ }
+ }
+ // grey out 'hide annotations' if none are shown
+ hideMenu.setEnabled(!shownTypes.isEmpty());
+ }
+
+ /**
+ * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
+ * menus.
+ *
+ * @param showOrHideMenu
+ * the menu to add to
+ * @param forSequences
+ * the sequences whose annotations may be shown or hidden
+ * @param calcId
+ * @param types
+ * the label to add
+ * @param allTypes
+ * if true this is a special label meaning 'All'
+ * @param actionIsShow
+ * if true, the select menu item action is to show the annotation
+ * type, else hide
+ */
+ protected void addAnnotationTypeToShowHide(Menu showOrHideMenu,
+ final List forSequences, String calcId,
+ final List types, final boolean allTypes,
+ final boolean actionIsShow)
+ {
+ String label = types.toString(); // [a, b, c]
+ label = label.substring(1, label.length() - 1);
+ final MenuItem item = new MenuItem(label);
+ item.addActionListener(new java.awt.event.ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
+ types, forSequences, allTypes, actionIsShow);
+ refresh();
+ }
+ });
+ showOrHideMenu.add(item);
+ }
+
+}