X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAPopupMenu.java;h=8c758b3a8ab5c2a1aa64db8ef3fa3cfc1c5fd32d;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=5e72242a9c4e4790d93c4d5e212dd9a3557b4220;hpb=497958b4e5217efaa3ddeece38f38c3a6e98cb96;p=jalview.git diff --git a/src/jalview/appletgui/APopupMenu.java b/src/jalview/appletgui/APopupMenu.java index 5e72242..8c758b3 100644 --- a/src/jalview/appletgui/APopupMenu.java +++ b/src/jalview/appletgui/APopupMenu.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -20,23 +20,58 @@ */ package jalview.appletgui; -import java.util.*; - -import java.awt.*; -import java.awt.event.*; - -import jalview.analysis.*; -import jalview.commands.*; -import jalview.datamodel.*; -import jalview.schemes.*; -import jalview.util.MessageManager; -import jalview.util.UrlLink; +import jalview.analysis.AAFrequency; +import jalview.analysis.AlignmentAnnotationUtils; +import jalview.analysis.AlignmentUtils; +import jalview.analysis.Conservation; +import jalview.commands.ChangeCaseCommand; +import jalview.commands.EditCommand; +import jalview.commands.EditCommand.Action; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; import jalview.io.AppletFormatAdapter; import jalview.io.SequenceAnnotationReport; +import jalview.schemes.Blosum62ColourScheme; +import jalview.schemes.BuriedColourScheme; +import jalview.schemes.ClustalxColourScheme; +import jalview.schemes.HelixColourScheme; +import jalview.schemes.HydrophobicColourScheme; +import jalview.schemes.NucleotideColourScheme; +import jalview.schemes.PIDColourScheme; +import jalview.schemes.ResidueProperties; +import jalview.schemes.StrandColourScheme; +import jalview.schemes.TaylorColourScheme; +import jalview.schemes.TurnColourScheme; +import jalview.schemes.ZappoColourScheme; +import jalview.util.MessageManager; +import jalview.util.UrlLink; + +import java.awt.CheckboxMenuItem; +import java.awt.Frame; +import java.awt.Menu; +import java.awt.MenuItem; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.awt.event.ItemEvent; +import java.awt.event.ItemListener; +import java.util.Arrays; +import java.util.Collections; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; +import java.util.TreeMap; +import java.util.Vector; public class APopupMenu extends java.awt.PopupMenu implements ActionListener, ItemListener { + private static final String ALL_ANNOTATIONS = "All"; + Menu groupMenu = new Menu(); MenuItem editGroupName = new MenuItem(); @@ -87,12 +122,29 @@ public class APopupMenu extends java.awt.PopupMenu implements CheckboxMenuItem displayNonconserved = new CheckboxMenuItem(); + Menu seqShowAnnotationsMenu = new Menu( + MessageManager.getString("label.show_annotations")); + + Menu seqHideAnnotationsMenu = new Menu( + MessageManager.getString("label.hide_annotations")); + + MenuItem seqAddReferenceAnnotations = new MenuItem( + MessageManager.getString("label.add_reference_annotations")); + + Menu groupShowAnnotationsMenu = new Menu( + MessageManager.getString("label.show_annotations")); + + Menu groupHideAnnotationsMenu = new Menu( + MessageManager.getString("label.hide_annotations")); + + MenuItem groupAddReferenceAnnotations = new MenuItem( + MessageManager.getString("label.add_reference_annotations")); + Menu editMenu = new Menu(MessageManager.getString("action.edit")); - MenuItem copy = new MenuItem( - MessageManager.getString("label.jalview_copy")); + MenuItem copy = new MenuItem(MessageManager.getString("action.copy")); - MenuItem cut = new MenuItem(MessageManager.getString("label.jalview_cut")); + MenuItem cut = new MenuItem(MessageManager.getString("action.cut")); MenuItem toUpper = new MenuItem( MessageManager.getString("label.to_upper_case")); @@ -123,12 +175,14 @@ public class APopupMenu extends java.awt.PopupMenu implements MessageManager.getString("label.edit_sequence")); MenuItem sequenceDetails = new MenuItem( - MessageManager.getString("label.sequence_details") + "..."); + MessageManager.getString("label.sequence_details")); MenuItem selSeqDetails = new MenuItem( - MessageManager.getString("label.sequence_details") + "..."); + MessageManager.getString("label.sequence_details")); + + MenuItem makeReferenceSeq = new MenuItem(); - Sequence seq; + SequenceI seq; MenuItem revealAll = new MenuItem(); @@ -141,7 +195,8 @@ public class APopupMenu extends java.awt.PopupMenu implements Menu menu1 = new Menu(); - public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links) + public APopupMenu(AlignmentPanel apanel, final SequenceI seq, + Vector links) { // ///////////////////////////////////////////////////////// // If this is activated from the sequence panel, the user may want to @@ -170,13 +225,13 @@ public class APopupMenu extends java.awt.PopupMenu implements outputmenu.add(item); } - SequenceGroup sg = ap.av.getSelectionGroup(); + buildAnnotationSubmenus(); + SequenceGroup sg = ap.av.getSelectionGroup(); if (sg != null && sg.getSize() > 0) { editGroupName.setLabel(MessageManager.formatMessage( - "label.name_param", new String[] - { sg.getName() })); + "label.name_param", new Object[] { sg.getName() })); showText.setState(sg.getDisplayText()); showColourText.setState(sg.getColourText()); showBoxes.setState(sg.getDisplayBoxes()); @@ -202,10 +257,9 @@ public class APopupMenu extends java.awt.PopupMenu implements if (links != null && links.size() > 0) { Menu linkMenu = new Menu(MessageManager.getString("action.link")); - String link; for (int i = 0; i < links.size(); i++) { - link = links.elementAt(i).toString(); + String link = links.elementAt(i); UrlLink urlLink = new UrlLink(link); if (!urlLink.isValid()) { @@ -220,8 +274,7 @@ public class APopupMenu extends java.awt.PopupMenu implements // collect matching db-refs DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs( - seq.getDBRef(), new String[] - { target }); + seq.getDBRef(), new String[] { target }); // collect id string too String id = seq.getName(); String descr = seq.getDescription(); @@ -323,9 +376,19 @@ public class APopupMenu extends java.awt.PopupMenu implements if (seq != null) { seqMenu.setLabel(seq.getName()); + if (seq == ap.av.getAlignment().getSeqrep()) + { + makeReferenceSeq.setLabel(MessageManager + .getString("action.unmark_as_reference"));// Unmark + // representative"); + } + else + { + makeReferenceSeq.setLabel(MessageManager + .getString("action.set_as_reference")); // ); + } repGroup.setLabel(MessageManager.formatMessage( - "label.represent_group_with", new String[] - { seq.getName() })); + "label.represent_group_with", new Object[] { seq.getName() })); } else { @@ -354,6 +417,95 @@ public class APopupMenu extends java.awt.PopupMenu implements } /** + * Build menus for annotation types that may be shown or hidden, and for + * 'reference annotations' that may be added to the alignment. + */ + private void buildAnnotationSubmenus() + { + /* + * First for the currently selected sequence (if there is one): + */ + final List selectedSequence = (seq == null ? Collections + . emptyList() : Arrays.asList(seq)); + buildAnnotationTypesMenus(seqShowAnnotationsMenu, + seqHideAnnotationsMenu, selectedSequence); + configureReferenceAnnotationsMenu(seqAddReferenceAnnotations, + selectedSequence); + + /* + * and repeat for the current selection group (if there is one): + */ + final List selectedGroup = (ap.av.getSelectionGroup() == null ? Collections + . emptyList() : ap.av.getSelectionGroup() + .getSequences()); + buildAnnotationTypesMenus(groupShowAnnotationsMenu, + groupHideAnnotationsMenu, selectedGroup); + configureReferenceAnnotationsMenu(groupAddReferenceAnnotations, + selectedGroup); + } + + /** + * Determine whether or not to enable 'add reference annotations' menu item. + * It is enable if there are any annotations, on any of the selected + * sequences, which are not yet on the alignment (visible or not). + * + * @param menu + * @param forSequences + */ + private void configureReferenceAnnotationsMenu(MenuItem 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. + */ + Map 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 action. + */ + menuItem.setEnabled(true); + + 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(); + } + + /** * add a show URL menu item to the given linkMenu * * @param linkMenu @@ -491,6 +643,10 @@ public class APopupMenu extends java.awt.PopupMenu implements { editName(); } + else if (source == makeReferenceSeq) + { + makeReferenceSeq_actionPerformed(); + } else if (source == sequenceDetails) { showSequenceDetails(); @@ -549,7 +705,9 @@ public class APopupMenu extends java.awt.PopupMenu implements if (sg != null) { if (seq == null) - seq = (Sequence) sg.getSequenceAt(0); + { + seq = sg.getSequenceAt(0); + } EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString( sg.getStartRes(), sg.getEndRes() + 1), null, @@ -559,8 +717,9 @@ public class APopupMenu extends java.awt.PopupMenu implements if (dialog.accept) { - EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"), - EditCommand.REPLACE, dialog.getName().replace(' ', + 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, @@ -576,10 +735,9 @@ public class APopupMenu extends java.awt.PopupMenu implements else if (source == toUpper || source == toLower || source == toggleCase) { SequenceGroup sg = ap.av.getSelectionGroup(); - Vector regions = new Vector(); if (sg != null) { - int[][] startEnd = ap.av.getVisibleRegionBoundaries( + List startEnd = ap.av.getVisibleRegionBoundaries( sg.getStartRes(), sg.getEndRes() + 1); String description; @@ -647,7 +805,8 @@ public class APopupMenu extends java.awt.PopupMenu implements features, true, ap)) { ap.alignFrame.sequenceFeatures.setState(true); - ap.av.setShowSequenceFeatures(true);; + ap.av.setShowSequenceFeatures(true); + ; ap.highlightSearchResults(null); } } @@ -665,15 +824,14 @@ public class APopupMenu extends java.awt.PopupMenu implements Frame frame = new Frame(); frame.add(cap); jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( - "label.selection_output_command", new String[] - { e.getActionCommand() }), 600, 500); + "label.selection_output_command", + new Object[] { e.getActionCommand() }), 600, 500); // JBPNote: getSelectionAsNewSequence behaviour has changed - this method // now returns a full copy of sequence data // TODO consider using getSequenceSelection instead here cap.setText(new jalview.io.AppletFormatAdapter().formatSequences( - e.getActionCommand(), - ap.av.showJVSuffix, ap.av, true)); + e.getActionCommand(), ap.av.getShowJVSuffix(), ap, true)); } @@ -684,8 +842,7 @@ public class APopupMenu extends java.awt.PopupMenu implements protected void showSequenceDetails() { - createSequenceDetailsReport(new SequenceI[] - { seq }); + createSequenceDetailsReport(new SequenceI[] { seq }); } public void createSequenceDetailsReport(SequenceI[] sequences) @@ -697,17 +854,16 @@ public class APopupMenu extends java.awt.PopupMenu implements for (SequenceI seq : sequences) { contents.append(MessageManager.formatMessage( - "label.annotation_for_displayid", new String[] - { seq.getDisplayId(true) })); - new SequenceAnnotationReport(null) - .createSequenceAnnotationReport( - contents, - seq, - true, - true, - false, - (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.getMinMax() - : null); + "label.annotation_for_displayid", + new Object[] { seq.getDisplayId(true) })); + new SequenceAnnotationReport(null).createSequenceAnnotationReport( + contents, + seq, + true, + true, + false, + (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr + .getMinMax() : null); contents.append("

"); } Frame frame = new Frame(); @@ -716,8 +872,7 @@ public class APopupMenu extends java.awt.PopupMenu implements + (sequences.length == 1 ? sequences[0].getDisplayId(true) : "Selection"), 600, 500); cap.setText(MessageManager.formatMessage("label.html_content", - new String[] - { contents.toString() })); + new Object[] { contents.toString() })); } void editName() @@ -737,16 +892,20 @@ public class APopupMenu extends java.awt.PopupMenu implements void addPDB() { - if (seq.getPDBId() != null) + if (seq.getAllPDBEntries() != null) { - PDBEntry entry = (PDBEntry) seq.getPDBId().firstElement(); + PDBEntry entry = seq.getAllPDBEntries().firstElement(); if (ap.av.applet.jmolAvailable) - new jalview.appletgui.AppletJmol(entry, new Sequence[] - { seq }, null, ap, AppletFormatAdapter.URL); + { + new jalview.appletgui.AppletJmol(entry, new SequenceI[] { seq }, + null, ap, AppletFormatAdapter.URL); + } else - new MCview.AppletPDBViewer(entry, new Sequence[] - { seq }, null, ap, AppletFormatAdapter.URL); + { + new MCview.AppletPDBViewer(entry, new SequenceI[] { seq }, null, + ap, AppletFormatAdapter.URL); + } } else @@ -757,8 +916,8 @@ public class APopupMenu extends java.awt.PopupMenu implements Frame frame = new Frame(); frame.add(cap); jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage( - "label.paste_pdb_file_for_sequence", new String[] - { seq.getName() }), 400, 300); + "label.paste_pdb_file_for_sequence", + new Object[] { seq.getName() }), 400, 300); } } @@ -801,8 +960,7 @@ public class APopupMenu extends java.awt.PopupMenu implements pdb.setLabel(MessageManager.getString("label.view_pdb_structure")); hideSeqs.setLabel(MessageManager.getString("action.hide_sequences")); repGroup.setLabel(MessageManager.formatMessage( - "label.represent_group_with", new String[] - { "" })); + "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") + ":"); @@ -812,6 +970,9 @@ public class APopupMenu extends java.awt.PopupMenu implements 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); @@ -839,31 +1000,39 @@ public class APopupMenu extends java.awt.PopupMenu implements noColourmenuItem.setLabel(MessageManager.getString("label.none")); noColourmenuItem.addActionListener(this); - clustalColour.setLabel(MessageManager.getString("label.clustalx_colours")); + clustalColour.setLabel(MessageManager + .getString("label.clustalx_colours")); clustalColour.addActionListener(this); zappoColour.setLabel(MessageManager.getString("label.zappo")); zappoColour.addActionListener(this); taylorColour.setLabel(MessageManager.getString("label.taylor")); taylorColour.addActionListener(this); - hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity")); + hydrophobicityColour.setLabel(MessageManager + .getString("label.hydrophobicity")); hydrophobicityColour.addActionListener(this); - helixColour.setLabel(MessageManager.getString("label.helix_propensity")); + helixColour + .setLabel(MessageManager.getString("label.helix_propensity")); helixColour.addActionListener(this); - strandColour.setLabel(MessageManager.getString("label.strand_propensity")); + strandColour.setLabel(MessageManager + .getString("label.strand_propensity")); strandColour.addActionListener(this); turnColour.setLabel(MessageManager.getString("label.turn_propensity")); turnColour.addActionListener(this); buriedColour.setLabel(MessageManager.getString("label.buried_index")); buriedColour.addActionListener(this); - abovePIDColour.setLabel(MessageManager.getString("label.above_identity_percentage")); + abovePIDColour.setLabel(MessageManager + .getString("label.above_identity_percentage")); - userDefinedColour.setLabel(MessageManager.getString("action.user_defined")); + userDefinedColour.setLabel(MessageManager + .getString("action.user_defined")); userDefinedColour.addActionListener(this); - PIDColour.setLabel(MessageManager.getString("action.percentage_identity")); + PIDColour.setLabel(MessageManager + .getString("label.percentage_identity")); PIDColour.addActionListener(this); BLOSUM62Colour.setLabel("BLOSUM62"); BLOSUM62Colour.addActionListener(this); - conservationMenuItem.setLabel(MessageManager.getString("label.conservation")); + conservationMenuItem.setLabel(MessageManager + .getString("label.conservation")); editMenu.add(copy); copy.addActionListener(this); @@ -878,7 +1047,11 @@ public class APopupMenu extends java.awt.PopupMenu implements 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) @@ -898,6 +1071,7 @@ public class APopupMenu extends java.awt.PopupMenu implements repGroup.addActionListener(this); revealAll.addActionListener(this); revealSeq.addActionListener(this); + makeReferenceSeq.addActionListener(this); } void refresh() @@ -975,7 +1149,7 @@ public class APopupMenu extends java.awt.PopupMenu implements int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup() .getName()); - sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus()); + sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus()); SliderPanel.showPIDSlider(); @@ -983,7 +1157,7 @@ public class APopupMenu extends java.awt.PopupMenu implements else // remove PIDColouring { - sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus()); + sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus()); } refresh(); @@ -1088,6 +1262,29 @@ public class APopupMenu extends java.awt.PopupMenu implements 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()); @@ -1105,8 +1302,7 @@ public class APopupMenu extends java.awt.PopupMenu implements SequenceGroup sg = ap.av.getSelectionGroup(); if (sg == null || sg.getSize() < 1) { - ap.av.hideSequence(new SequenceI[] - { seq }); + ap.av.hideSequence(new SequenceI[] { seq }); return; } @@ -1134,4 +1330,107 @@ public class APopupMenu extends java.awt.PopupMenu implements ap.av.sendSelection(); } + /** + * 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(ALL_ANNOTATIONS); + 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); + } + }