X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=6903034f1ca18d5f08e7adff8fb5b85e9040b3b6;hb=70a6730dba4ab0af6906fd8f874fe853c02efef0;hp=40f576497ea39071878ee0d858a0d7e7c846b6bd;hpb=a57976ba40e1abe6d7c1940386e1a25419ef9c9d;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 40f5764..6903034 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -20,24 +20,57 @@ */ package jalview.gui; +import java.util.Locale; + +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.BitSet; +import java.util.Collection; +import java.util.Collections; +import java.util.Hashtable; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; +import java.util.Objects; +import java.util.SortedMap; +import java.util.TreeMap; +import java.util.Vector; + +import javax.swing.ButtonGroup; +import javax.swing.JCheckBoxMenuItem; +import javax.swing.JInternalFrame; +import javax.swing.JLabel; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JPanel; +import javax.swing.JPopupMenu; +import javax.swing.JRadioButtonMenuItem; +import javax.swing.JScrollPane; + import jalview.analysis.AAFrequency; import jalview.analysis.AlignmentAnnotationUtils; import jalview.analysis.AlignmentUtils; import jalview.analysis.Conservation; -import jalview.bin.Cache; +import jalview.api.AlignViewportI; +import jalview.bin.Console; import jalview.commands.ChangeCaseCommand; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; -import jalview.datamodel.Annotation; import jalview.datamodel.DBRefEntry; import jalview.datamodel.HiddenColumns; +import jalview.datamodel.MappedFeatures; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.gui.ColourMenuHelper.ColourChangeListener; +import jalview.gui.JalviewColourChooser.ColourChooserListener; import jalview.io.FileFormatI; import jalview.io.FileFormats; import jalview.io.FormatAdapter; @@ -46,41 +79,40 @@ import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemes; import jalview.schemes.PIDColourScheme; +import jalview.schemes.ResidueColourScheme; +import jalview.util.Comparison; import jalview.util.GroupUrlLink; import jalview.util.GroupUrlLink.UrlStringTooLongException; import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.util.StringUtils; import jalview.util.UrlLink; - -import java.awt.Color; -import java.awt.event.ActionEvent; -import java.awt.event.ActionListener; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.BitSet; -import java.util.Collection; -import java.util.Collections; -import java.util.Hashtable; -import java.util.LinkedHashMap; -import java.util.List; -import java.util.Map; -import java.util.SortedMap; -import java.util.TreeMap; -import java.util.Vector; - -import javax.swing.JCheckBoxMenuItem; -import javax.swing.JColorChooser; -import javax.swing.JMenu; -import javax.swing.JMenuItem; -import javax.swing.JPopupMenu; +import jalview.viewmodel.seqfeatures.FeatureRendererModel; /** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision: 1.118 $ + * The popup menu that is displayed on right-click on a sequence id, or in the + * sequence alignment. */ public class PopupMenu extends JPopupMenu implements ColourChangeListener { + /* + * maximum length of feature description to include in popup menu item text + */ + private static final int FEATURE_DESC_MAX = 40; + + /* + * true for ID Panel menu, false for alignment panel menu + */ + private final boolean forIdPanel; + + private final AlignmentPanel ap; + + /* + * the sequence under the cursor when clicked + * (additional sequences may be selected) + */ + private final SequenceI sequence; + JMenu groupMenu = new JMenu(); JMenuItem groupName = new JMenuItem(); @@ -91,30 +123,18 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); - protected JMenuItem modifyConservation = new JMenuItem(); + protected JRadioButtonMenuItem annotationColour; - AlignmentPanel ap; + protected JMenuItem modifyConservation = new JMenuItem(); JMenu sequenceMenu = new JMenu(); - JMenuItem sequenceName = new JMenuItem(); - - JMenuItem sequenceDetails = new JMenuItem(); - - JMenuItem sequenceSelDetails = new JMenuItem(); - JMenuItem makeReferenceSeq = new JMenuItem(); - JMenuItem chooseAnnotations = new JMenuItem(); - - SequenceI sequence; - JMenuItem createGroupMenuItem = new JMenuItem(); JMenuItem unGroupMenuItem = new JMenuItem(); - JMenuItem outline = new JMenuItem(); - JMenu colourMenu = new JMenu(); JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem(); @@ -127,18 +147,12 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener JMenu editMenu = new JMenu(); - JMenuItem cut = new JMenuItem(); - - JMenuItem copy = new JMenuItem(); - JMenuItem upperCase = new JMenuItem(); JMenuItem lowerCase = new JMenuItem(); JMenuItem toggle = new JMenuItem(); - JMenu pdbMenu = new JMenu(); - JMenu outputMenu = new JMenu(); JMenu seqShowAnnotationsMenu = new JMenu(); @@ -155,58 +169,245 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener JMenuItem groupAddReferenceAnnotations = new JMenuItem( MessageManager.getString("label.add_reference_annotations")); - JMenuItem sequenceFeature = new JMenuItem(); - JMenuItem textColour = new JMenuItem(); - JMenu jMenu1 = new JMenu(); + JMenu editGroupMenu = new JMenu(); - JMenuItem pdbStructureDialog = new JMenuItem(); + JMenuItem chooseStructure = new JMenuItem(); JMenu rnaStructureMenu = new JMenu(); - JMenuItem editSequence = new JMenuItem(); + /** + * Constructs a menu with sub-menu items for any hyperlinks for the sequence + * and/or features provided. Hyperlinks may include a lookup by sequence id, + * or database cross-references, depending on which links are enabled in user + * preferences. + * + * @param seq + * @param features + * @return + */ + protected static JMenu buildLinkMenu(final SequenceI seq, + List features) + { + JMenu linkMenu = new JMenu(MessageManager.getString("action.link")); + + List nlinks = null; + if (seq != null) + { + nlinks = Preferences.sequenceUrlLinks.getLinksForMenu(); + UrlLink.sort(nlinks); + } + else + { + nlinks = new ArrayList<>(); + } + + if (features != null) + { + for (SequenceFeature sf : features) + { + if (sf.links != null) + { + for (String link : sf.links) + { + nlinks.add(link); + } + } + } + } + + /* + * instantiate the hyperlinklink templates from sequence data; + * note the order of the templates is preserved in the map + */ + Map> linkset = new LinkedHashMap<>(); + for (String link : nlinks) + { + UrlLink urlLink = null; + try + { + urlLink = new UrlLink(link); + } catch (Exception foo) + { + Console.error("Exception for URLLink '" + link + "'", foo); + continue; + } + + if (!urlLink.isValid()) + { + Console.error(urlLink.getInvalidMessage()); + continue; + } + + urlLink.createLinksFromSeq(seq, linkset); + } + + /* + * construct menu items for the hyperlinks (still preserving + * the order of the sorted templates) + */ + addUrlLinks(linkMenu, linkset.values()); + + return linkMenu; + } + + /** + * A helper method that builds menu items from the given links, with action + * handlers to open the link URL, and adds them to the linkMenu. Each provided + * link should be a list whose second item is the menu text, and whose fourth + * item is the URL to open when the menu item is selected. + * + * @param linkMenu + * @param linkset + */ + static private void addUrlLinks(JMenu linkMenu, + Collection> linkset) + { + for (List linkstrset : linkset) + { + final String url = linkstrset.get(3); + JMenuItem item = new JMenuItem(linkstrset.get(1)); + 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); + } + } + + /** + * Opens the provided url in the default web browser, or shows an error + * message if this fails + * + * @param url + */ + static 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); - JMenu groupLinksMenu; + ex.printStackTrace(); + } + } - JMenuItem hideInsertions = new JMenuItem(); + /** + * 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. + */ + static 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); + } /** - * Creates a new PopupMenu object. + * Constructor for a PopupMenu for a click in the alignment panel (on a + * residue) * * @param ap + * the panel in which the mouse is clicked * @param seq - * @param features - * non-positional features (for seq not null), or positional features - * at residue (for seq equal to null) + * the sequence under the mouse + * @throws NullPointerException + * if seq is null */ - public PopupMenu(final AlignmentPanel ap, SequenceI seq, - List features) + public PopupMenu(final AlignmentPanel ap, SequenceI seq, int column) { - this(ap, seq, features, null); + this(false, ap, seq, column, null); } /** - * Constructor + * Constructor for a PopupMenu for a click in the sequence id panel * * @param alignPanel + * the panel in which the mouse is clicked * @param seq - * the sequence under the cursor if in the Id panel, null if in the - * sequence panel - * @param features - * non-positional features if in the Id panel, features at the - * clicked residue if in the sequence panel + * the sequence under the mouse click * @param groupLinks + * templates for sequence external links + * @throws NullPointerException + * if seq is null */ public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq, - List features, List groupLinks) + List groupLinks) + { + this(true, alignPanel, seq, -1, groupLinks); + } + + /** + * Private constructor that constructs a popup menu for either sequence ID + * Panel, or alignment context + * + * @param fromIdPanel + * @param alignPanel + * @param seq + * @param column + * aligned column position (0...) + * @param groupLinks + */ + private PopupMenu(boolean fromIdPanel, final AlignmentPanel alignPanel, + final SequenceI seq, final int column, List groupLinks) { - // ///////////////////////////////////////////////////////// - // 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 - // //////////////////////////////////////////////////////// + Objects.requireNonNull(seq); + this.forIdPanel = fromIdPanel; this.ap = alignPanel; sequence = seq; @@ -231,9 +432,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener * 'reference annotations' that may be added to the alignment. First for the * currently selected sequence (if there is one): */ - final List selectedSequence = (seq == null - ? Collections. emptyList() - : Arrays.asList(seq)); + final List selectedSequence = (forIdPanel && seq != null + ? Arrays.asList(seq) + : Collections. emptyList()); buildAnnotationTypesMenus(seqShowAnnotationsMenu, seqHideAnnotationsMenu, selectedSequence); configureReferenceAnnotationsMenu(seqAddReferenceAnnotations, @@ -242,9 +443,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener /* * And repeat for the current selection group (if there is one): */ - final List selectedGroup = (alignPanel.av.getSelectionGroup() == null - ? Collections. emptyList() - : alignPanel.av.getSelectionGroup().getSequences()); + final List selectedGroup = (alignPanel.av + .getSelectionGroup() == null + ? Collections. emptyList() + : alignPanel.av.getSelectionGroup().getSequences()); buildAnnotationTypesMenus(groupShowAnnotationsMenu, groupHideAnnotationsMenu, selectedGroup); configureReferenceAnnotationsMenu(groupAddReferenceAnnotations, @@ -258,9 +460,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener e.printStackTrace(); } - JMenuItem menuItem; - if (seq != null) + if (forIdPanel) { + JMenuItem menuItem; sequenceMenu.setText(sequence.getName()); if (seq == alignPanel.av.getAlignment().getSeqrep()) { @@ -400,11 +602,22 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } } } - // for the case when no sequences are even visible + + /* + * offer 'Reveal All' + * - in the IdPanel (seq not null) if any sequence is hidden + * - in the IdPanel or SeqPanel if all sequences are hidden (seq is null) + */ if (alignPanel.av.hasHiddenRows()) { + boolean addOption = seq != null; + if (!addOption && alignPanel.av.getAlignment().getHeight() == 0) { - menuItem = new JMenuItem( + addOption = true; + } + if (addOption) + { + JMenuItem menuItem = new JMenuItem( MessageManager.getString("action.reveal_all")); menuItem.addActionListener(new ActionListener() { @@ -418,7 +631,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } } }); - add(menuItem); } } @@ -460,7 +672,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener buildGroupURLMenu(sg, groupLinks); } // Add a 'show all structures' for the current selection - Hashtable pdbe = new Hashtable<>(), reppdb = new Hashtable<>(); + Hashtable pdbe = new Hashtable<>(), + reppdb = new Hashtable<>(); SequenceI sqass = null; for (SequenceI sq : alignPanel.av.getSequenceSelection()) @@ -497,97 +710,231 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener { createGroupMenuItem.setVisible(true); unGroupMenuItem.setVisible(false); - jMenu1.setText(MessageManager.getString("action.edit_new_group")); + editGroupMenu + .setText(MessageManager.getString("action.edit_new_group")); } else { createGroupMenuItem.setVisible(false); unGroupMenuItem.setVisible(true); - jMenu1.setText(MessageManager.getString("action.edit_group")); + editGroupMenu.setText(MessageManager.getString("action.edit_group")); } - if (seq == null) + if (!forIdPanel) { sequenceMenu.setVisible(false); - pdbStructureDialog.setVisible(false); + chooseStructure.setVisible(false); rnaStructureMenu.setVisible(false); } + addLinksAndFeatures(seq, column); + } + + /** + * Adds + *
    + *
  • configured sequence database links (ID panel popup menu)
    • + *
  • non-positional feature links (ID panel popup menu)
    • + *
  • positional feature links (alignment panel popup menu)
    • + *
  • feature details links (alignment panel popup menu)
    • + *
+ * If this panel is also showed complementary (CDS/protein) features, then + * links to their feature details are also added. + * + * @param seq + * @param column + */ + void addLinksAndFeatures(final SequenceI seq, final int column) + { + List features = null; + if (forIdPanel) + { + features = sequence.getFeatures().getNonPositionalFeatures(); + } + else + { + features = ap.getFeatureRenderer().findFeaturesAtColumn(sequence, + column + 1); + } + addLinks(seq, features); - if (seq == null) + if (!forIdPanel) { - addFeatureDetails(features); + addFeatureDetails(features, seq, column); } } /** - * Add a link to show feature details for each sequence feature + * Add a menu item to show feature details for each sequence feature. Any + * linked 'virtual' features (CDS/protein) are also optionally found and + * included. * * @param features + * @param seq + * @param column */ - protected void addFeatureDetails(List features) + protected void addFeatureDetails(List features, + final SequenceI seq, final int column) { - if (features == null || features.isEmpty()) + /* + * add features in CDS/protein complement at the corresponding + * position if configured to do so + */ + MappedFeatures mf = null; + if (ap.av.isShowComplementFeatures()) { + if (!Comparison.isGap(sequence.getCharAt(column))) + { + AlignViewportI complement = ap.getAlignViewport() + .getCodingComplement(); + AlignFrame af = Desktop.getAlignFrameFor(complement); + FeatureRendererModel fr2 = af.getFeatureRenderer(); + int seqPos = sequence.findPosition(column); + mf = fr2.findComplementFeaturesAtResidue(sequence, seqPos); + } + } + + if (features.isEmpty() && mf == null) + { + /* + * no features to show at this position + */ return; } + JMenu details = new JMenu( MessageManager.getString("label.feature_details")); add(details); + String name = seq.getName(); for (final SequenceFeature sf : features) { - int start = sf.getBegin(); - int end = sf.getEnd(); - String desc = null; - if (start == end) + addFeatureDetailsMenuItem(details, name, sf, null); + } + + if (mf != null) + { + for (final SequenceFeature sf : mf.features) { - desc = String.format("%s %d", sf.getType(), start); + addFeatureDetailsMenuItem(details, name, sf, mf); } - else + } + } + + /** + * A helper method to add one menu item whose action is to show details for + * one feature. The menu text includes feature description, but this may be + * truncated. + * + * @param details + * @param seqName + * @param sf + * @param mf + */ + void addFeatureDetailsMenuItem(JMenu details, final String seqName, + final SequenceFeature sf, MappedFeatures mf) + { + int start = sf.getBegin(); + int end = sf.getEnd(); + if (mf != null) + { + /* + * show local rather than linked feature coordinates + */ + int[] localRange = mf.getMappedPositions(start, end); + if (localRange == null) { - desc = String.format("%s %d-%d", sf.getType(), start, end); + // e.g. variant extending to stop codon so not mappable + return; } - String description = sf.getDescription(); - if (description != null) + start = localRange[0]; + end = localRange[localRange.length - 1]; + } + StringBuilder desc = new StringBuilder(); + desc.append(sf.getType()).append(" ").append(String.valueOf(start)); + if (start != end) + { + desc.append(sf.isContactFeature() ? ":" : "-"); + desc.append(String.valueOf(end)); + } + String description = sf.getDescription(); + if (description != null) + { + desc.append(" "); + description = StringUtils.stripHtmlTags(description); + + /* + * truncate overlong descriptions unless they contain an href + * (as truncation could leave corrupted html) + */ + boolean hasLink = description.indexOf("a href") > -1; + if (description.length() > FEATURE_DESC_MAX && !hasLink) { - if (description.length() <= 6) - { - desc = desc + " " + description; - } - else - { - desc = desc + " " + description.substring(0, 6) + ".."; - } + description = description.substring(0, FEATURE_DESC_MAX) + "..."; } - if (sf.getFeatureGroup() != null) + desc.append(description); + } + String featureGroup = sf.getFeatureGroup(); + if (featureGroup != null) + { + desc.append(" (").append(featureGroup).append(")"); + } + String htmlText = JvSwingUtils.wrapTooltip(true, desc.toString()); + JMenuItem item = new JMenuItem(htmlText); + item.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) { - desc = desc + " (" + sf.getFeatureGroup() + ")"; + showFeatureDetails(sf, seqName, mf); } - JMenuItem item = new JMenuItem(desc); - item.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - showFeatureDetails(sf); - } - }); - details.add(item); - } + }); + details.add(item); } /** - * Opens a panel showing a text report of feature dteails + * Opens a panel showing a text report of feature details * * @param sf + * @param seqName + * @param mf */ - protected void showFeatureDetails(SequenceFeature sf) + protected void showFeatureDetails(SequenceFeature sf, String seqName, + MappedFeatures mf) { - CutAndPasteTransfer cap = new CutAndPasteTransfer(); - cap.setText(sf.getDetailsReport()); - Desktop.addInternalFrame(cap, + JInternalFrame details; + if (Platform.isJS()) + { + details = new JInternalFrame(); + JPanel panel = new JPanel(new BorderLayout()); + panel.setOpaque(true); + panel.setBackground(Color.white); + // TODO JAL-3026 set style of table correctly for feature details + JLabel reprt = new JLabel(MessageManager + .formatMessage("label.html_content", new Object[] + { sf.getDetailsReport(seqName, mf) })); + reprt.setBackground(Color.WHITE); + reprt.setOpaque(true); + panel.add(reprt, BorderLayout.CENTER); + details.setContentPane(panel); + details.pack(); + } + else + /** + * Java only + * + * @j2sIgnore + */ + { + CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer(); + // it appears Java's CSS does not support border-collapse :-( + cap.addStylesheetRule("table { border-collapse: collapse;}"); + cap.addStylesheetRule("table, td, th {border: 1px solid black;}"); + cap.setText(sf.getDetailsReport(seqName, mf)); + details = cap; + } + Desktop.addInternalFrame(details, MessageManager.getString("label.feature_details"), 500, 500); } @@ -596,68 +943,19 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener * When seq is not null, these are links for the sequence id, which may be to * external web sites for the sequence accession, and/or links embedded in * non-positional features. When seq is null, only links embedded in the - * provided features are added. + * provided features are added. If no links are found, the menu is not added. * * @param seq * @param features */ void addLinks(final SequenceI seq, List features) { - JMenu linkMenu = new JMenu(MessageManager.getString("action.link")); - - List nlinks = null; - if (seq != null) - { - nlinks = Preferences.sequenceUrlLinks.getLinksForMenu(); - } - else - { - nlinks = new ArrayList<>(); - } - - if (features != null) - { - for (SequenceFeature sf : features) - { - if (sf.links != null) - { - for (String link : sf.links) - { - nlinks.add(link); - } - } - } - } - - Map> linkset = new LinkedHashMap<>(); - - for (String link : nlinks) - { - 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()); + JMenu linkMenu = buildLinkMenu(forIdPanel ? seq : null, features); // only add link menu if it has entries if (linkMenu.getItemCount() > 0) { - if (sequence != null) + if (forIdPanel) { sequenceMenu.add(linkMenu); } @@ -805,7 +1103,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener // menu appears asap // sequence only URLs // ID/regex match URLs - groupLinksMenu = new JMenu( + JMenu groupLinksMenu = new JMenu( MessageManager.getString("action.group_link")); // three types of url that might be created. JMenu[] linkMenus = new JMenu[] { null, @@ -829,12 +1127,14 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener { sqi = sqi.getDatasetSequence(); } - DBRefEntry[] dbr = sqi.getDBRefs(); - if (dbr != null && dbr.length > 0) + List dbr = sqi.getDBRefs(); + int nd; + if (dbr != null && (nd = dbr.size()) > 0) { - for (int d = 0; d < dbr.length; d++) + for (int d = 0; d < nd; d++) { - String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(); + DBRefEntry e = dbr.get(d); + String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(Locale.ROOT); Object[] sarray = commonDbrefs.get(src); if (sarray == null) { @@ -847,10 +1147,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener if (((String[]) sarray[1])[sq] == null) { - if (!dbr[d].hasMap() || (dbr[d].getMap() - .locateMappedRange(start, end) != null)) + if (!e.hasMap() + || (e.getMap().locateMappedRange(start, end) != null)) { - ((String[]) sarray[1])[sq] = dbr[d].getAccessionId(); + ((String[]) sarray[1])[sq] = e.getAccessionId(); ((int[]) sarray[0])[0]++; } } @@ -868,20 +1168,19 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener urlLink = new GroupUrlLink(link); } catch (Exception foo) { - Cache.log.error("Exception for GroupURLLink '" + link + "'", foo); + Console.error("Exception for GroupURLLink '" + link + "'", foo); continue; } - ; if (!urlLink.isValid()) { - Cache.log.error(urlLink.getInvalidMessage()); + Console.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()); + Object[] idset = commonDbrefs.get(ltarget.toUpperCase(Locale.ROOT)); String[] seqstr, ids; // input to makeUrl if (idset != null) { @@ -945,98 +1244,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } } - 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! * @@ -1056,7 +1263,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } }); sequenceMenu.setText(MessageManager.getString("label.sequence")); - sequenceName.setText( + + JMenuItem sequenceName = new JMenuItem( MessageManager.getString("label.edit_name_description")); sequenceName.addActionListener(new ActionListener() { @@ -1066,8 +1274,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener sequenceName_actionPerformed(); } }); - chooseAnnotations - .setText(MessageManager.getString("action.choose_annotations")); + JMenuItem chooseAnnotations = new JMenuItem( + MessageManager.getString("action.choose_annotations")); chooseAnnotations.addActionListener(new ActionListener() { @Override @@ -1076,24 +1284,24 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener chooseAnnotations_actionPerformed(e); } }); - sequenceDetails - .setText(MessageManager.getString("label.sequence_details")); + JMenuItem sequenceDetails = new JMenuItem( + MessageManager.getString("label.sequence_details")); sequenceDetails.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - sequenceDetails_actionPerformed(); + createSequenceDetailsReport(new SequenceI[] { sequence }); } }); - sequenceSelDetails - .setText(MessageManager.getString("label.sequence_details")); + JMenuItem sequenceSelDetails = new JMenuItem( + MessageManager.getString("label.sequence_details")); sequenceSelDetails.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - sequenceSelectionDetails_actionPerformed(); + createSequenceDetailsReport(ap.av.getSequenceSelection()); } }); @@ -1118,7 +1326,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } }); - outline.setText(MessageManager.getString("action.border_colour")); + JMenuItem outline = new JMenuItem( + MessageManager.getString("action.border_colour")); outline.addActionListener(new ActionListener() { @Override @@ -1168,7 +1377,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } }); editMenu.setText(MessageManager.getString("action.edit")); - cut.setText(MessageManager.getString("action.cut")); + JMenuItem cut = new JMenuItem(MessageManager.getString("action.cut")); cut.addActionListener(new ActionListener() { @Override @@ -1186,7 +1395,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener changeCase(e); } }); - copy.setText(MessageManager.getString("action.copy")); + JMenuItem copy = new JMenuItem(MessageManager.getString("action.copy")); copy.addActionListener(new ActionListener() { @Override @@ -1223,7 +1432,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener .setText(MessageManager.getString("label.show_annotations")); groupHideAnnotationsMenu .setText(MessageManager.getString("label.hide_annotations")); - sequenceFeature.setText( + JMenuItem sequenceFeature = new JMenuItem( MessageManager.getString("label.create_sequence_feature")); sequenceFeature.addActionListener(new ActionListener() { @@ -1233,10 +1442,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener sequenceFeature_actionPerformed(); } }); - jMenu1.setText(MessageManager.getString("label.group")); - pdbStructureDialog.setText( + editGroupMenu.setText(MessageManager.getString("label.group")); + chooseStructure.setText( MessageManager.getString("label.show_pdbstruct_dialog")); - pdbStructureDialog.addActionListener(new ActionListener() + chooseStructure.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) @@ -1254,14 +1463,14 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener .setText(MessageManager.getString("label.view_rna_structure")); // colStructureMenu.setText("Colour By Structure"); - editSequence.setText( + JMenuItem editSequence = new JMenuItem( MessageManager.getString("label.edit_sequence") + "..."); editSequence.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent actionEvent) { - editSequence_actionPerformed(actionEvent); + editSequence_actionPerformed(); } }); makeReferenceSeq.setText( @@ -1276,25 +1485,25 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } }); - 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(chooseStructure); + if (forIdPanel) { + JMenuItem hideInsertions = new JMenuItem( + MessageManager.getString("label.hide_insertions")); + hideInsertions.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + hideInsertions_actionPerformed(e); + } + }); add(hideInsertions); } // annotations configuration panel suppressed for now @@ -1315,7 +1524,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener groupMenu.add(sequenceFeature); groupMenu.add(createGroupMenuItem); groupMenu.add(unGroupMenuItem); - groupMenu.add(jMenu1); + groupMenu.add(editGroupMenu); sequenceMenu.add(sequenceName); sequenceMenu.add(sequenceDetails); sequenceMenu.add(makeReferenceSeq); @@ -1329,17 +1538,13 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener 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); + editGroupMenu.add(groupName); + editGroupMenu.add(colourMenu); + editGroupMenu.add(showBoxes); + editGroupMenu.add(showText); + editGroupMenu.add(showColourText); + editGroupMenu.add(outline); + editGroupMenu.add(displayNonconserved); } /** @@ -1392,6 +1597,13 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } }); + annotationColour = new JRadioButtonMenuItem( + MessageManager.getString("action.by_annotation")); + annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR); + annotationColour.setEnabled(false); + annotationColour.setToolTipText( + MessageManager.getString("label.by_annotation_tooltip")); + modifyConservation.setText(MessageManager .getString("label.modify_conservation_threshold")); modifyConservation.addActionListener(new ActionListener() @@ -1422,7 +1634,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener colourMenu.add(textColour); colourMenu.addSeparator(); - ColourMenuHelper.addMenuItems(colourMenu, this, sg, false); + ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, sg, + false); + bg.add(annotationColour); + colourMenu.add(annotationColour); colourMenu.addSeparator(); colourMenu.add(conservationMenuItem); @@ -1552,15 +1767,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener 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); - } + HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns(); + BitSet inserts = new BitSet(); boolean markedPopup = false; // mark inserts in current selection @@ -1568,10 +1776,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener { // 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); + ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1? // now clear columns without gaps for (SequenceI sq : ap.av.getSelectionGroup().getSequences()) @@ -1582,29 +1787,19 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } 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(); + hidden.clearAndHideColumns(inserts, + ap.av.getSelectionGroup().getStartRes(), + ap.av.getSelectionGroup().getEndRes()); } // now mark for sequence under popup if we haven't already done it - if (!markedPopup && sequence != null) + else 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); + inserts.or(sequence.getInsertionsAsBits()); - ap.av.getAlignment().setHiddenColumns(hidden); + // and set hidden columns accordingly + hidden.hideColumns(inserts); + } refresh(); } @@ -1613,31 +1808,49 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener 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); + contents.append(""); 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); + { seq.getDisplayId(true) }) + "

\n

"); + new SequenceAnnotationReport(false).createSequenceAnnotationReport( + contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr); contents.append("

"); } - cap.setText("" + contents.toString() + ""); + contents.append(""); + String report = contents.toString(); + + JInternalFrame frame; + if (Platform.isJS()) + { + JLabel textLabel = new JLabel(); + textLabel.setText(report); + textLabel.setBackground(Color.WHITE); + JPanel pane = new JPanel(new BorderLayout()); + pane.setOpaque(true); + pane.setBackground(Color.WHITE); + pane.add(textLabel, BorderLayout.NORTH); + frame = new JInternalFrame(); + frame.getContentPane().add(new JScrollPane(pane)); + } + else + /** + * Java only + * + * @j2sIgnore + */ + { + CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer(); + cap.setText(report); + frame = cap; + } - Desktop.addInternalFrame(cap, + Desktop.addInternalFrame(frame, MessageManager.formatMessage("label.sequence_details_for", (sequences.length == 1 ? new Object[] { sequences[0].getDisplayId(true) } @@ -1645,7 +1858,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener { MessageManager .getString("label.selection") })), 500, 400); - } protected void showNonconserved_actionPerformed() @@ -1764,30 +1976,27 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Shows a dialog where group name and description may be edited */ 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.group_name"), + MessageManager.getString("label.group_description")); + dialog.showDialog(ap.alignFrame, MessageManager.getString("label.edit_group_name_description"), - ap.alignFrame); - - if (!dialog.accept) - { - return; - } - - sg.setName(dialog.getName()); - sg.setDescription(dialog.getDescription()); - refresh(); + new Runnable() + { + @Override + public void run() + { + sg.setName(dialog.getName()); + sg.setDescription(dialog.getDescription()); + refresh(); + } + }); } /** @@ -1808,48 +2017,41 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Shows a dialog where the sequence name and description may be edited. If a + * name containing spaces is entered, these are converted to underscores, with + * a warning message. */ 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, false); - } - - sequence.setDescription(dialog.getDescription()); - - ap.av.firePropertyChange("alignment", null, - ap.av.getAlignment().getSequences()); - + MessageManager.getString("label.sequence_name"), + MessageManager.getString("label.sequence_description")); + dialog.showDialog(ap.alignFrame, MessageManager.getString( + "label.edit_sequence_name_description"), new Runnable() + { + @Override + public void run() + { + if (dialog.getName() != null) + { + if (dialog.getName().indexOf(" ") > -1) + { + JvOptionPane.showMessageDialog(ap, + MessageManager.getString( + "label.spaces_converted_to_underscores"), + MessageManager.getString( + "label.no_spaces_allowed_sequence_name"), + JvOptionPane.WARNING_MESSAGE); + } + sequence.setName(dialog.getName().replace(' ', '_')); + ap.paintAlignment(false, false); + } + sequence.setDescription(dialog.getDescription()); + ap.av.firePropertyChange("alignment", null, + ap.av.getAlignment().getSequences()); + } + }); } /** @@ -1874,24 +2076,22 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } /** - * DOCUMENT ME! - * - * @param e - * DOCUMENT ME! + * Offers a colour chooser and sets the selected colour as the group outline */ protected void outline_actionPerformed() { - SequenceGroup sg = getGroup(); - Color col = JColorChooser.showDialog(this, - MessageManager.getString("label.select_outline_colour"), - Color.BLUE); - - if (col != null) + String title = MessageManager.getString("label.select_outline_colour"); + ColourChooserListener listener = new ColourChooserListener() { - sg.setOutlineColour(col); - } - - refresh(); + @Override + public void colourSelected(Color c) + { + getGroup().setOutlineColour(c); + refresh(); + } + }; + JalviewColourChooser.showColourChooser(Desktop.getDesktop(), title, + Color.BLUE, listener); } /** @@ -1930,22 +2130,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener 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); @@ -1953,12 +2137,12 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener public void copy_actionPerformed() { - ap.alignFrame.copy_actionPerformed(null); + ap.alignFrame.copy_actionPerformed(); } public void cut_actionPerformed() { - ap.alignFrame.cut_actionPerformed(null); + ap.alignFrame.cut_actionPerformed(); } void changeCase(ActionEvent e) @@ -2054,13 +2238,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener */ if (!seqs.isEmpty()) { - if (ap.getSeqPanel().seqCanvas.getFeatureRenderer() - .amendFeatures(seqs, features, true, ap)) - { - ap.alignFrame.setShowSeqFeatures(true); - ap.av.setSearchResults(null); // clear highlighting - ap.repaint(); // draw new/amended features - } + new FeatureEditor(ap, seqs, features, true).showDialog(); } } @@ -2073,57 +2251,47 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } } - 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) + /** + * Shows a dialog where sequence characters may be edited. Any changes are + * applied, and added as an available 'Undo' item in the edit commands + * history. + */ + public void editSequence_actionPerformed() { SequenceGroup sg = ap.av.getSelectionGroup(); + SequenceI seq = sequence; if (sg != null) { - if (sequence == null) + if (seq == null) { - sequence = sg.getSequenceAt(0); + seq = sg.getSequenceAt(0); } EditNameDialog dialog = new EditNameDialog( - sequence.getSequenceAsString(sg.getStartRes(), - sg.getEndRes() + 1), - null, MessageManager.getString("label.edit_sequence"), null, + seq.getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1), + null, MessageManager.getString("label.edit_sequence"), null); + dialog.showDialog(ap.alignFrame, 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()); - } + new Runnable() + { + @Override + public void run() + { + 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()); + } + }); } } @@ -2141,7 +2309,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener * switch to the chosen colour scheme (or null for None) */ ColourSchemeI colourScheme = ColourSchemes.getInstance() - .getColourScheme(colourSchemeName, sg, + .getColourScheme(colourSchemeName, ap.av, sg, ap.av.getHiddenRepSequences()); sg.setColourScheme(colourScheme); if (colourScheme instanceof Blosum62ColourScheme