> linkset = new LinkedHashMap<>();
+
+ for (String link : links)
+ {
+ UrlLink urlLink = null;
+ try
+ {
+ urlLink = new UrlLink(link);
+ } catch (Exception foo)
+ {
+ Cache.log.error("Exception for URLLink '" + link + "'", foo);
+ continue;
+ }
+
+ if (!urlLink.isValid())
+ {
+ Cache.log.error(urlLink.getInvalidMessage());
+ continue;
+ }
+
+ urlLink.createLinksFromSeq(seq, linkset);
+ }
+
+ addshowLinks(linkMenu, linkset.values());
+
+ // disable link menu if there are no valid entries
+ if (linkMenu.getItemCount() > 0)
+ {
+ linkMenu.setEnabled(true);
+ }
+ else
+ {
+ linkMenu.setEnabled(false);
+ }
+
+ if (sequence != null)
+ {
+ sequenceMenu.add(linkMenu);
+ }
+ else
+ {
+ add(linkMenu);
+ }
+
+ }
+
+ /**
+ * 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(JMenu showMenu, JMenu 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());
+ }
+
+ /**
+ * Returns a list of sequences - either the current selection group (if there
+ * is one), else the specified single sequence.
+ *
+ * @param seq
+ * @return
+ */
+ protected List getSequenceScope(SequenceI seq)
+ {
+ List forSequences = null;
+ final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
+ if (selectionGroup != null && selectionGroup.getSize() > 0)
+ {
+ forSequences = selectionGroup.getSequences();
+ }
+ else
+ {
+ forSequences = seq == null ? Collections. emptyList()
+ : Arrays.asList(seq);
+ }
+ return forSequences;
+ }
+
+ /**
+ * 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(JMenu 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); // a, b, c
+ final JMenuItem item = new JMenuItem(label);
+ item.setToolTipText(calcId);
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
+ types, forSequences, allTypes, actionIsShow);
+ refresh();
+ }
+ });
+ showOrHideMenu.add(item);
+ }
+
+ private void buildGroupURLMenu(SequenceGroup sg, List groupLinks)
+ {
+
+ // TODO: usability: thread off the generation of group url content so root
+ // menu appears asap
+ // sequence only URLs
+ // ID/regex match URLs
+ groupLinksMenu = new JMenu(
+ MessageManager.getString("action.group_link"));
+ // three types of url that might be created.
+ JMenu[] linkMenus = new JMenu[] { null,
+ new JMenu(MessageManager.getString("action.ids")),
+ new JMenu(MessageManager.getString("action.sequences")),
+ new JMenu(MessageManager.getString("action.ids_sequences")) };
+
+ SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
+ String[][] idandseqs = GroupUrlLink.formStrings(seqs);
+ Hashtable commonDbrefs = new Hashtable<>();
+ for (int sq = 0; sq < seqs.length; sq++)
+ {
+
+ int start = seqs[sq].findPosition(sg.getStartRes()),
+ end = seqs[sq].findPosition(sg.getEndRes());
+ // just collect ids from dataset sequence
+ // TODO: check if IDs collected from selecton group intersects with the
+ // current selection, too
+ SequenceI sqi = seqs[sq];
+ while (sqi.getDatasetSequence() != null)
+ {
+ sqi = sqi.getDatasetSequence();
+ }
+ DBRefEntry[] dbr = sqi.getDBRefs();
+ if (dbr != null && dbr.length > 0)
+ {
+ for (int d = 0; d < dbr.length; d++)
+ {
+ String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
+ Object[] sarray = commonDbrefs.get(src);
+ if (sarray == null)
+ {
+ sarray = new Object[2];
+ sarray[0] = new int[] { 0 };
+ sarray[1] = new String[seqs.length];
+
+ commonDbrefs.put(src, sarray);
+ }
+
+ if (((String[]) sarray[1])[sq] == null)
+ {
+ if (!dbr[d].hasMap() || (dbr[d].getMap()
+ .locateMappedRange(start, end) != null))
+ {
+ ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
+ ((int[]) sarray[0])[0]++;
+ }
+ }
+ }
+ }
+ }
+ // now create group links for all distinct ID/sequence sets.
+ boolean addMenu = false; // indicates if there are any group links to give
+ // to user
+ for (String link : groupLinks)
+ {
+ GroupUrlLink urlLink = null;
+ try
+ {
+ urlLink = new GroupUrlLink(link);
+ } catch (Exception foo)
+ {
+ Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
+ continue;
+ }
+ ;
+ if (!urlLink.isValid())
+ {
+ Cache.log.error(urlLink.getInvalidMessage());
+ continue;
+ }
+ final String label = urlLink.getLabel();
+ boolean usingNames = false;
+ // Now see which parts of the group apply for this URL
+ String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
+ Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
+ String[] seqstr, ids; // input to makeUrl
+ if (idset != null)
+ {
+ int numinput = ((int[]) idset[0])[0];
+ String[] allids = ((String[]) idset[1]);
+ seqstr = new String[numinput];
+ ids = new String[numinput];
+ for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
+ {
+ if (allids[sq] != null)
+ {
+ ids[idcount] = allids[sq];
+ seqstr[idcount++] = idandseqs[1][sq];
+ }
+ }
+ }
+ else
+ {
+ // just use the id/seq set
+ seqstr = idandseqs[1];
+ ids = idandseqs[0];
+ usingNames = true;
+ }
+ // and try and make the groupURL!
+
+ Object[] urlset = null;
+ try
+ {
+ urlset = urlLink.makeUrlStubs(ids, seqstr,
+ "FromJalview" + System.currentTimeMillis(), false);
+ } catch (UrlStringTooLongException e)
+ {
+ }
+ if (urlset != null)
+ {
+ int type = urlLink.getGroupURLType() & 3;
+ // first two bits ofurlLink type bitfield are sequenceids and sequences
+ // TODO: FUTURE: ensure the groupURL menu structure can be generalised
+ addshowLink(linkMenus[type],
+ label + (((type & 1) == 1)
+ ? ("(" + (usingNames ? "Names" : ltarget) + ")")
+ : ""),
+ urlLink, urlset);
+ addMenu = true;
+ }
+ }
+ if (addMenu)
+ {
+ groupLinksMenu = new JMenu(
+ MessageManager.getString("action.group_link"));
+ for (int m = 0; m < linkMenus.length; m++)
+ {
+ if (linkMenus[m] != null
+ && linkMenus[m].getMenuComponentCount() > 0)
+ {
+ groupLinksMenu.add(linkMenus[m]);
+ }
+ }
+
+ groupMenu.add(groupLinksMenu);
+ }
+ }
+
+ private void addshowLinks(JMenu linkMenu,
+ Collection> linkset)
+ {
+ for (List linkstrset : linkset)
+ {
+ // split linkstr into label and url
+ addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
+ }
+ }
+
+ /**
+ * 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(MessageManager.formatMessage("label.open_url_param",
+ new Object[]
+ { url }));
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ showLink(url);
+ }
+
+ }).start();
+ }
+ });
+
+ linkMenu.add(item);
+ }
+
+ /**
+ * add a late bound groupURL item to the given linkMenu
+ *
+ * @param linkMenu
+ * @param label
+ * - menu label string
+ * @param urlgenerator
+ * GroupURLLink used to generate URL
+ * @param urlstub
+ * Object array returned from the makeUrlStubs function.
+ */
+ private void addshowLink(JMenu linkMenu, String label,
+ final GroupUrlLink urlgenerator, final Object[] urlstub)
+ {
+ JMenuItem item = new JMenuItem(label);
+ item.setToolTipText(MessageManager
+ .formatMessage("label.open_url_seqs_param", new Object[]
+ { urlgenerator.getUrl_prefix(),
+ urlgenerator.getNumberInvolved(urlstub) }));
+ // TODO: put in info about what is being sent.
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ try
+ {
+ showLink(urlgenerator.constructFrom(urlstub));
+ } catch (UrlStringTooLongException e2)
+ {
+ }
+ }
+
+ }).start();
+ }
+ });
+
+ linkMenu.add(item);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @throws Exception
+ * DOCUMENT ME!
+ */
+ private void jbInit() throws Exception
+ {
+ groupMenu.setText(MessageManager.getString("label.selection"));
+ groupName.setText(MessageManager.getString("label.name"));
+ groupName.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ groupName_actionPerformed();
+ }
+ });
+ sequenceMenu.setText(MessageManager.getString("label.sequence"));
+ sequenceName.setText(
+ MessageManager.getString("label.edit_name_description"));
+ sequenceName.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceName_actionPerformed();
+ }
+ });
+ chooseAnnotations
+ .setText(MessageManager.getString("action.choose_annotations"));
+ chooseAnnotations.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ chooseAnnotations_actionPerformed(e);
+ }
+ });
+ sequenceDetails
+ .setText(MessageManager.getString("label.sequence_details"));
+ sequenceDetails.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceDetails_actionPerformed();
+ }
+ });
+ sequenceSelDetails
+ .setText(MessageManager.getString("label.sequence_details"));
+ sequenceSelDetails.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceSelectionDetails_actionPerformed();
+ }
+ });
+
+ unGroupMenuItem
+ .setText(MessageManager.getString("action.remove_group"));
+ unGroupMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ unGroupMenuItem_actionPerformed();
+ }
+ });
+ createGroupMenuItem
+ .setText(MessageManager.getString("action.create_group"));
+ createGroupMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ createGroupMenuItem_actionPerformed();
+ }
+ });
+
+ outline.setText(MessageManager.getString("action.border_colour"));
+ outline.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ outline_actionPerformed();
+ }
+ });
+ showBoxes.setText(MessageManager.getString("action.boxes"));
+ showBoxes.setState(true);
+ showBoxes.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showBoxes_actionPerformed();
+ }
+ });
+ showText.setText(MessageManager.getString("action.text"));
+ showText.setState(true);
+ showText.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showText_actionPerformed();
+ }
+ });
+ showColourText.setText(MessageManager.getString("label.colour_text"));
+ showColourText.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showColourText_actionPerformed();
+ }
+ });
+ displayNonconserved
+ .setText(MessageManager.getString("label.show_non_conserved"));
+ displayNonconserved.setState(true);
+ displayNonconserved.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ showNonconserved_actionPerformed();
+ }
+ });
+ editMenu.setText(MessageManager.getString("action.edit"));
+ cut.setText(MessageManager.getString("action.cut"));
+ cut.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ cut_actionPerformed();
+ }
+ });
+ upperCase.setText(MessageManager.getString("label.to_upper_case"));
+ upperCase.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ changeCase(e);
+ }
+ });
+ copy.setText(MessageManager.getString("action.copy"));
+ copy.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ copy_actionPerformed();
+ }
+ });
+ lowerCase.setText(MessageManager.getString("label.to_lower_case"));
+ lowerCase.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ changeCase(e);
+ }
+ });
+ toggle.setText(MessageManager.getString("label.toggle_case"));
+ toggle.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ changeCase(e);
+ }
+ });
+ outputMenu.setText(
+ MessageManager.getString("label.out_to_textbox") + "...");
+ seqShowAnnotationsMenu
+ .setText(MessageManager.getString("label.show_annotations"));
+ seqHideAnnotationsMenu
+ .setText(MessageManager.getString("label.hide_annotations"));
+ groupShowAnnotationsMenu
+ .setText(MessageManager.getString("label.show_annotations"));
+ groupHideAnnotationsMenu
+ .setText(MessageManager.getString("label.hide_annotations"));
+ sequenceFeature.setText(
+ MessageManager.getString("label.create_sequence_feature"));
+ sequenceFeature.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sequenceFeature_actionPerformed();
+ }
+ });
+ jMenu1.setText(MessageManager.getString("label.group"));
+ pdbStructureDialog.setText(
+ MessageManager.getString("label.show_pdbstruct_dialog"));
+ pdbStructureDialog.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ SequenceI[] selectedSeqs = new SequenceI[] { sequence };
+ if (ap.av.getSelectionGroup() != null)
+ {
+ selectedSeqs = ap.av.getSequenceSelection();
+ }
+ new StructureChooser(selectedSeqs, sequence, ap);
+ }
+ });
+
+ rnaStructureMenu
+ .setText(MessageManager.getString("label.view_rna_structure"));
+
+ // colStructureMenu.setText("Colour By Structure");
+ editSequence.setText(
+ MessageManager.getString("label.edit_sequence") + "...");
+ editSequence.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ editSequence_actionPerformed(actionEvent);
+ }
+ });
+ makeReferenceSeq.setText(
+ MessageManager.getString("label.mark_as_representative"));
+ makeReferenceSeq.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ makeReferenceSeq_actionPerformed(actionEvent);
+
+ }
+ });
+ hideInsertions
+ .setText(MessageManager.getString("label.hide_insertions"));
+ hideInsertions.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ hideInsertions_actionPerformed(e);
+ }
+ });
+
+ groupMenu.add(sequenceSelDetails);
+ add(groupMenu);
+ add(sequenceMenu);
+ add(rnaStructureMenu);
+ add(pdbStructureDialog);
+ if (sequence != null)
+ {
+ add(hideInsertions);
+ }
+ // annotations configuration panel suppressed for now
+ // groupMenu.add(chooseAnnotations);
+
+ /*
+ * Add show/hide annotations to the Sequence menu, and to the Selection menu
+ * (if a selection group is in force).
+ */
+ sequenceMenu.add(seqShowAnnotationsMenu);
+ sequenceMenu.add(seqHideAnnotationsMenu);
+ sequenceMenu.add(seqAddReferenceAnnotations);
+ 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(jMenu1);
+ sequenceMenu.add(sequenceName);
+ sequenceMenu.add(sequenceDetails);
+ sequenceMenu.add(makeReferenceSeq);
+
+ initColourMenu();
+ buildColourMenu();
+
+ editMenu.add(copy);
+ editMenu.add(cut);
+ editMenu.add(editSequence);
+ editMenu.add(upperCase);
+ editMenu.add(lowerCase);
+ editMenu.add(toggle);
+ // JBPNote: These shouldn't be added here - should appear in a generic
+ // 'apply web service to this sequence menu'
+ // pdbMenu.add(RNAFold);
+ // pdbMenu.add(ContraFold);
+ jMenu1.add(groupName);
+ jMenu1.add(colourMenu);
+ jMenu1.add(showBoxes);
+ jMenu1.add(showText);
+ jMenu1.add(showColourText);
+ jMenu1.add(outline);
+ jMenu1.add(displayNonconserved);
+ }
+
+ /**
+ * Constructs the entries for the colour menu
+ */
+ protected void initColourMenu()
+ {
+ colourMenu.setText(MessageManager.getString("label.group_colour"));
+ textColour.setText(MessageManager.getString("label.text_colour"));
+ textColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ textColour_actionPerformed();
+ }
+ });
+
+ abovePIDColour.setText(
+ MessageManager.getString("label.above_identity_threshold"));
+ abovePIDColour.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ abovePIDColour_actionPerformed(abovePIDColour.isSelected());
+ }
+ });
+
+ modifyPID.setText(
+ MessageManager.getString("label.modify_identity_threshold"));
+ modifyPID.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyPID_actionPerformed();
+ }
+ });
+
+ conservationMenuItem
+ .setText(MessageManager.getString("action.by_conservation"));
+ conservationMenuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ conservationMenuItem_actionPerformed(
+ conservationMenuItem.isSelected());
+ }
+ });
+
+ modifyConservation.setText(MessageManager
+ .getString("label.modify_conservation_threshold"));
+ modifyConservation.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ modifyConservation_actionPerformed();
+ }
+ });
+ }
+
+ /**
+ * Builds the group colour sub-menu, including any user-defined colours which
+ * were loaded at startup or during the Jalview session
+ */
+ protected void buildColourMenu()
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg == null)
+ {
+ /*
+ * popup menu with no sequence group scope
+ */
+ return;
+ }
+ colourMenu.removeAll();
+ colourMenu.add(textColour);
+ colourMenu.addSeparator();
+
+ ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
+
+ colourMenu.addSeparator();
+ colourMenu.add(conservationMenuItem);
+ colourMenu.add(modifyConservation);
+ colourMenu.add(abovePIDColour);
+ colourMenu.add(modifyPID);
+ }
+
+ protected void modifyConservation_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ if (sg.cs != null)
+ {
+ SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
+ SliderPanel.showConservationSlider();
+ }
+ }
+
+ protected void modifyPID_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ if (sg.cs != null)
+ {
+ // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
+ // .getName());
+ // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
+ SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
+ SliderPanel.showPIDSlider();
+ }
+ }
+
+ /**
+ * Check for any annotations on the underlying dataset sequences (for the
+ * current selection group) which are not 'on the alignment'.If any are found,
+ * enable the option to add them to the alignment. The criteria for 'on the
+ * alignment' is finding an alignment annotation on the alignment, matched on
+ * calcId, label and sequenceRef.
+ *
+ * A tooltip is also constructed that displays the source (calcId) and type
+ * (label) of the annotations that can be added.
+ *
+ * @param menuItem
+ * @param forSequences
+ */
+ protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
+ List forSequences)
+ {
+ menuItem.setEnabled(false);
+
+ /*
+ * Temporary store to hold distinct calcId / type pairs for the tooltip.
+ * Using TreeMap means calcIds are shown in alphabetical order.
+ */
+ SortedMap tipEntries = new TreeMap<>();
+ final Map> candidates = new LinkedHashMap<>();
+ AlignmentI al = this.ap.av.getAlignment();
+ AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
+ candidates, al);
+ if (!candidates.isEmpty())
+ {
+ StringBuilder tooltip = new StringBuilder(64);
+ tooltip.append(MessageManager.getString("label.add_annotations_for"));
+
+ /*
+ * Found annotations that could be added. Enable the menu item, and
+ * configure its tooltip and action.
+ */
+ menuItem.setEnabled(true);
+ for (String calcId : tipEntries.keySet())
+ {
+ tooltip.append("
" + calcId + "/" + tipEntries.get(calcId));
+ }
+ String tooltipText = JvSwingUtils.wrapTooltip(true,
+ tooltip.toString());
+ menuItem.setToolTipText(tooltipText);
+
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ addReferenceAnnotations_actionPerformed(candidates);
+ }
+ });
+ }
+ }
+
+ /**
+ * Add annotations to the sequences and to the alignment.
+ *
+ * @param candidates
+ * a map whose keys are sequences on the alignment, and values a list
+ * of annotations to add to each sequence
+ */
+ protected void addReferenceAnnotations_actionPerformed(
+ Map> candidates)
+ {
+ final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
+ final AlignmentI alignment = this.ap.getAlignment();
+ AlignmentUtils.addReferenceAnnotations(candidates, alignment,
+ selectionGroup);
+ refresh();
+ }
+
+ protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
+ {
+ 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(sequence);
+ }
+ else
+ {
+ if (ap.av.getAlignment().getSeqrep() == sequence)
+ {
+ ap.av.getAlignment().setSeqrep(null);
+ }
+ else
+ {
+ ap.av.getAlignment().setSeqrep(sequence);
+ }
+ }
+ refresh();
+ }
+
+ protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
+ {
+
+ HiddenColumns hidden = new HiddenColumns();
+ BitSet inserts = new BitSet(), mask = new BitSet();
+
+ // set mask to preserve existing hidden columns outside selected group
+ if (ap.av.hasHiddenColumns())
+ {
+ ap.av.getAlignment().getHiddenColumns().markHiddenRegions(mask);
+ }
+
+ boolean markedPopup = false;
+ // mark inserts in current selection
+ if (ap.av.getSelectionGroup() != null)
+ {
+ // mark just the columns in the selection group to be hidden
+ inserts.set(ap.av.getSelectionGroup().getStartRes(),
+ ap.av.getSelectionGroup().getEndRes() + 1);
+
+ // and clear that part of the mask
+ mask.andNot(inserts);
+
+ // now clear columns without gaps
+ for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
+ {
+ if (sq == sequence)
+ {
+ markedPopup = true;
+ }
+ inserts.and(sq.getInsertionsAsBits());
+ }
+ }
+ else
+ {
+ // initially, mark all columns to be hidden
+ inserts.set(0, ap.av.getAlignment().getWidth());
+
+ // and clear out old hidden regions completely
+ mask.clear();
+ }
+
+ // now mark for sequence under popup if we haven't already done it
+ if (!markedPopup && sequence != null)
+ {
+ inserts.and(sequence.getInsertionsAsBits());
+ }
+
+ // finally, preserve hidden regions outside selection
+ inserts.or(mask);
+
+ // and set hidden columns accordingly
+ hidden.hideMarkedBits(inserts);
+
+ ap.av.getAlignment().setHiddenColumns(hidden);
+ refresh();
+ }
+
+ protected void sequenceSelectionDetails_actionPerformed()
+ {
+ createSequenceDetailsReport(ap.av.getSequenceSelection());
+ }
+
+ protected void sequenceDetails_actionPerformed()
+ {
+ createSequenceDetailsReport(new SequenceI[] { sequence });
+ }
+
+ public void createSequenceDetailsReport(SequenceI[] sequences)
+ {
+ CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
+ StringBuilder contents = new StringBuilder(128);
+ for (SequenceI seq : sequences)
+ {
+ contents.append("" + MessageManager.formatMessage(
+ "label.create_sequence_details_report_annotation_for",
+ new Object[]
+ { seq.getDisplayId(true) }) + "
");
+ new SequenceAnnotationReport(null).createSequenceAnnotationReport(
+ contents, seq, true, true,
+ (ap.getSeqPanel().seqCanvas.fr != null)
+ ? ap.getSeqPanel().seqCanvas.fr.getMinMax()
+ : null);
+ contents.append("
");
+ }
+ cap.setText("" + contents.toString() + "");
+
+ Desktop.addInternalFrame(cap,
+ MessageManager.formatMessage("label.sequence_details_for",
+ (sequences.length == 1 ? new Object[]
+ { sequences[0].getDisplayId(true) }
+ : new Object[]
+ { MessageManager
+ .getString("label.selection") })),
+ 500, 400);
+
+ }
+
+ protected void showNonconserved_actionPerformed()
+ {
+ getGroup().setShowNonconserved(displayNonconserved.isSelected());
+ refresh();
+ }
+
+ /**
+ * call to refresh view after settings change
+ */
+ void refresh()
+ {
+ ap.updateAnnotation();
+ // removed paintAlignment(true) here:
+ // updateAnnotation calls paintAlignment already, so don't need to call
+ // again
+
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
+ }
+
+ /*
+ * protected void covariationColour_actionPerformed() { getGroup().cs = new
+ * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
+ */
+ /**
+ * DOCUMENT ME!
+ *
+ * @param selected
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void abovePIDColour_actionPerformed(boolean selected)
+ {
+ SequenceGroup sg = getGroup();
+ if (sg.cs == null)
+ {
+ return;
+ }
+
+ if (selected)
+ {
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
+
+ int threshold = SliderPanel.setPIDSliderSource(ap,
+ sg.getGroupColourScheme(), getGroup().getName());
+
+ sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
+
+ SliderPanel.showPIDSlider();
+ }
+ else
+ // remove PIDColouring
+ {
+ sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
+ SliderPanel.hidePIDSlider();
+ }
+ modifyPID.setEnabled(selected);
+
+ refresh();
+ }
+
+ /**
+ * Open a panel where the user can choose which types of sequence annotation
+ * to show or hide.
+ *
+ * @param e
+ */
+ protected void chooseAnnotations_actionPerformed(ActionEvent e)
+ {
+ // todo correct way to guard against opening a duplicate panel?
+ new AnnotationChooser(ap);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void conservationMenuItem_actionPerformed(boolean selected)
+ {
+ SequenceGroup sg = getGroup();
+ if (sg.cs == null)
+ {
+ return;
+ }
+
+ if (selected)
+ {
+ // JBPNote: Conservation name shouldn't be i18n translated
+ Conservation c = new Conservation("Group",
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1);
+
+ c.calculate();
+ c.verdict(false, ap.av.getConsPercGaps());
+ sg.cs.setConservation(c);
+
+ SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
+ sg.getName());
+ SliderPanel.showConservationSlider();
+ }
+ else
+ // remove ConservationColouring
+ {
+ sg.cs.setConservation(null);
+ SliderPanel.hideConservationSlider();
+ }
+ modifyConservation.setEnabled(selected);
+
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void groupName_actionPerformed()
+ {
+
+ SequenceGroup sg = getGroup();
+ EditNameDialog dialog = new EditNameDialog(sg.getName(),
+ sg.getDescription(),
+ " " + MessageManager.getString("label.group_name") + " ",
+ MessageManager.getString("label.group_description") + " ",
+ MessageManager.getString("label.edit_group_name_description"),
+ ap.alignFrame);
+
+ if (!dialog.accept)
+ {
+ return;
+ }
+
+ sg.setName(dialog.getName());
+ sg.setDescription(dialog.getDescription());
+ refresh();
+ }
+
+ /**
+ * Get selection group - adding it to the alignment if necessary.
+ *
+ * @return sequence group to operate on
+ */
+ 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;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ void sequenceName_actionPerformed()
+ {
+ EditNameDialog dialog = new EditNameDialog(sequence.getName(),
+ sequence.getDescription(),
+ " " + MessageManager.getString("label.sequence_name")
+ + " ",
+ MessageManager.getString("label.sequence_description") + " ",
+ MessageManager.getString(
+ "label.edit_sequence_name_description"),
+ ap.alignFrame);
+
+ if (!dialog.accept)
+ {
+ return;
+ }
+
+ if (dialog.getName() != null)
+ {
+ if (dialog.getName().indexOf(" ") > -1)
+ {
+ JvOptionPane.showMessageDialog(ap,
+ MessageManager
+ .getString("label.spaces_converted_to_backslashes"),
+ MessageManager
+ .getString("label.no_spaces_allowed_sequence_name"),
+ JvOptionPane.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.getAlignment().deleteGroup(sg);
+ ap.av.setSelectionGroup(null);
+ refresh();
+ }
+
+ void createGroupMenuItem_actionPerformed()
+ {
+ getGroup(); // implicitly creates group - note - should apply defaults / use
+ // standard alignment window logic for this
+ refresh();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void outline_actionPerformed()
+ {
+ SequenceGroup sg = getGroup();
+ Color col = JColorChooser.showDialog(this,
+ MessageManager.getString("label.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)
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.web_browser_not_found_unix"),
+ MessageManager.getString("label.web_browser_not_found"),
+ JvOptionPane.WARNING_MESSAGE);
+
+ ex.printStackTrace();
+ }
+ }
+
+ void hideSequences(boolean representGroup)
+ {
+ ap.av.hideSequences(sequence, representGroup);
+ }
+
+ 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)
+ {
+ List startEnd = ap.av.getVisibleRegionBoundaries(
+ sg.getStartRes(), sg.getEndRes() + 1);
+
+ String description;
+ int caseChange;
+
+ if (source == toggle)
+ {
+ description = MessageManager.getString("label.toggle_case");
+ caseChange = ChangeCaseCommand.TOGGLE_CASE;
+ }
+ else if (source == upperCase)
+ {
+ description = MessageManager.getString("label.to_upper_case");
+ caseChange = ChangeCaseCommand.TO_UPPER;
+ }
+ else
+ {
+ description = MessageManager.getString("label.to_lower_case");
+ caseChange = ChangeCaseCommand.TO_LOWER;
+ }
+
+ ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
+ sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
+ 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, MessageManager
+ .formatMessage("label.alignment_output_command", new Object[]
+ { 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
+
+ FileFormatI fileFormat = FileFormats.getInstance()
+ .forName(e.getActionCommand());
+ cap.setText(
+ new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
+ }
+
+ public void sequenceFeature_actionPerformed()
+ {
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg == null)
+ {
+ return;
+ }
+
+ List seqs = new ArrayList<>();
+ List features = new ArrayList<>();
+
+ /*
+ * assemble dataset sequences, and template new sequence features,
+ * for the amend features dialog
+ */
+ int gSize = sg.getSize();
+ 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.add(sg.getSequenceAt(i).getDatasetSequence());
+ features.add(
+ new SequenceFeature(null, null, null, start, end, null));
+ }
+ }
+
+ /*
+ * an entirely gapped region will generate empty lists of sequence / features
+ */
+ if (!seqs.isEmpty())
+ {
+ if (ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .amendFeatures(seqs, features, true, ap))
+ {
+ ap.alignFrame.setShowSeqFeatures(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 = ap.av.getStructureSelectionManager()
+ .colourSequenceFromStructure(sequence, pdbid);
+
+ AlignmentAnnotation an = new AlignmentAnnotation("Structure",
+ "Coloured by " + pdbid, anots);
+
+ ap.av.getAlignment().addAnnotation(an);
+ an.createSequenceMapping(sequence, 0, true);
+ // an.adjustForAlignment();
+ ap.av.getAlignment().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 = sg.getSequenceAt(0);
+ }
+
+ EditNameDialog dialog = new EditNameDialog(
+ sequence.getSequenceAsString(sg.getStartRes(),
+ sg.getEndRes() + 1),
+ null, MessageManager.getString("label.edit_sequence"), null,
+ MessageManager.getString("label.edit_sequence"),
+ ap.alignFrame);
+
+ if (dialog.accept)
+ {
+ EditCommand editCommand = new EditCommand(
+ MessageManager.getString("label.edit_sequences"),
+ Action.REPLACE,
+ dialog.getName().replace(' ', ap.av.getGapCharacter()),
+ sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
+
+ ap.alignFrame.addHistoryItem(editCommand);
+
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
+ }
+ }
+ }
+
+ /**
+ * Action on user selecting an item from the colour menu (that does not have
+ * its bespoke action handler)
+ *
+ * @return
+ */
+ @Override
+ public void changeColour_actionPerformed(String colourSchemeName)
+ {
+ SequenceGroup sg = getGroup();
+ /*
+ * switch to the chosen colour scheme (or null for None)
+ */
+ ColourSchemeI colourScheme = ColourSchemes.getInstance()
+ .getColourScheme(colourSchemeName, sg,
+ ap.av.getHiddenRepSequences());
+ sg.setColourScheme(colourScheme);
+ if (colourScheme instanceof Blosum62ColourScheme
+ || colourScheme instanceof PIDColourScheme)
+ {
+ sg.cs.setConsensus(AAFrequency.calculate(
+ sg.getSequences(ap.av.getHiddenRepSequences()),
+ sg.getStartRes(), sg.getEndRes() + 1));
+ }
+
+ refresh();
+ }
+
+}