X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=abe9835d3911bc5b89bc82b33191f77108e220c1;hp=6da7d4fbb99d77236f62832fb9577eab4869eb60;hb=c6018dc0dc12720e13b75850a5303279ac7094b7;hpb=14193747f3831242bc7dfac12394eb20eb0ba480 diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 6da7d4f..abe9835 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -20,19 +20,45 @@ */ package jalview.gui; +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.JColorChooser; +import javax.swing.JMenu; +import javax.swing.JMenuItem; +import javax.swing.JPopupMenu; +import javax.swing.JRadioButtonMenuItem; + import jalview.analysis.AAFrequency; import jalview.analysis.AlignmentAnnotationUtils; import jalview.analysis.AlignmentUtils; import jalview.analysis.Conservation; +import jalview.api.AlignViewportI; import jalview.bin.Cache; 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; @@ -46,42 +72,39 @@ 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.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(); @@ -92,30 +115,18 @@ 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(); @@ -128,18 +139,12 @@ 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(); @@ -156,58 +161,245 @@ 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")); - JMenu groupLinksMenu; + List nlinks = null; + if (seq != null) + { + nlinks = Preferences.sequenceUrlLinks.getLinksForMenu(); + UrlLink.sort(nlinks); + } + else + { + nlinks = new ArrayList<>(); + } - JMenuItem hideInsertions = new JMenuItem(); + 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) + { + Cache.log.error("Exception for URLLink '" + link + "'", foo); + continue; + } + + if (!urlLink.isValid()) + { + Cache.log.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); + + ex.printStackTrace(); + } + } + + /** + * 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) { - // ///////////////////////////////////////////////////////// - // If this is activated from the sequence panel, the user may want to - // edit or annotate a particular residue. Therefore display the residue menu - // - // If from the IDPanel, we must display the sequence menu - // //////////////////////////////////////////////////////// + this(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) + { + Objects.requireNonNull(seq); + this.forIdPanel = fromIdPanel; this.ap = alignPanel; sequence = seq; @@ -232,9 +424,9 @@ 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, @@ -259,9 +451,9 @@ 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()) { @@ -401,11 +593,22 @@ 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() { @@ -419,7 +622,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } } }); - add(menuItem); } } @@ -498,100 +700,211 @@ 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[] beginRange = mf.getMappedPositions(start, start); + int[] endRange = mf.getMappedPositions(end, end); + if (beginRange == null || endRange == 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 = beginRange[0]; + end = endRange[endRange.length - 1]; + int[] localRange = mf.getMappedPositions(start, end); + if (localRange == null) { - description = StringUtils.stripHtmlTags(description); - if (description.length() <= 6) - { - desc = desc + " " + description; - } - else - { - desc = desc + " " + description.substring(0, 6) + ".."; - } + return; } - if (sf.getFeatureGroup() != 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) { - desc = desc + " (" + sf.getFeatureGroup() + ")"; + description = description.substring(0, FEATURE_DESC_MAX) + "..."; } - JMenuItem item = new JMenuItem(desc); - item.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - showFeatureDetails(sf); - } - }); - details.add(item); + 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) + { + showFeatureDetails(sf, seqName, mf); + } + }); + 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) { CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer(); - // it appears Java's CSS does not support border-collaps :-( + // 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()); + cap.setText(sf.getDetailsReport(seqName, mf)); Desktop.addInternalFrame(cap, MessageManager.getString("label.feature_details"), 500, 500); @@ -602,68 +915,19 @@ 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); } @@ -811,7 +1075,7 @@ 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, @@ -951,98 +1215,6 @@ 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! * @@ -1062,7 +1234,8 @@ 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() { @@ -1072,8 +1245,8 @@ 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 @@ -1082,24 +1255,24 @@ 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()); } }); @@ -1124,7 +1297,8 @@ 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 @@ -1174,7 +1348,7 @@ 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 @@ -1192,7 +1366,7 @@ 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 @@ -1229,7 +1403,7 @@ 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() { @@ -1239,10 +1413,10 @@ 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) @@ -1260,7 +1434,7 @@ 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() { @@ -1282,25 +1456,25 @@ 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 @@ -1321,7 +1495,7 @@ 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); @@ -1335,17 +1509,13 @@ 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); } /** @@ -1398,6 +1568,13 @@ 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() @@ -1428,7 +1605,10 @@ 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); @@ -1558,15 +1738,8 @@ 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 @@ -1574,10 +1747,7 @@ 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()) @@ -1588,29 +1758,18 @@ 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()); - } + inserts.or(sequence.getInsertionsAsBits()); - // finally, preserve hidden regions outside selection - inserts.or(mask); - - // and set hidden columns accordingly - hidden.hideMarkedBits(inserts); - - ap.av.getAlignment().setHiddenColumns(hidden); + // and set hidden columns accordingly + hidden.hideColumns(inserts); + } refresh(); } @@ -1619,11 +1778,6 @@ 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(); @@ -1634,11 +1788,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener "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); + new SequenceAnnotationReport(false).createSequenceAnnotationReport( + contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr); contents.append("

"); } cap.setText("" + contents.toString() + ""); @@ -1814,10 +1965,9 @@ 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() { @@ -1835,9 +1985,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener return; } - if (dialog.getName() != null) + String name = dialog.getName(); + if (name != null) { - if (dialog.getName().indexOf(" ") > -1) + if (name.indexOf(" ") > -1) { JvOptionPane.showMessageDialog(ap, MessageManager @@ -1845,9 +1996,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener MessageManager .getString("label.no_spaces_allowed_sequence_name"), JvOptionPane.WARNING_MESSAGE); + name = name.replace(' ', '_'); } - sequence.setName(dialog.getName().replace(' ', '_')); + sequence.setName(name); ap.paintAlignment(false, false); } @@ -1936,22 +2088,6 @@ 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); @@ -2079,38 +2215,20 @@ 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) { 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(), + seq.getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null, MessageManager.getString("label.edit_sequence"), @@ -2147,7 +2265,7 @@ 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