X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=8c87aa0d5e5b60d6307dff8f7c7e246bbac66909;hb=a82f1e47eef845557e95e61116e6b34bdd3242f3;hp=fd652b2166e735704d1a3addab4f1650aedebd99;hpb=8c865b34fb48c55582c2c77609cd04f96819ceef;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index fd652b2..8c87aa0 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -33,15 +33,13 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; import jalview.datamodel.DBRefEntry; import jalview.datamodel.HiddenColumns; -import jalview.datamodel.HiddenMarkovModel; import jalview.datamodel.PDBEntry; -import jalview.datamodel.Sequence; +import jalview.datamodel.ResidueCount; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.gui.ColourMenuHelper.ColourChangeListener; -import jalview.hmmer.HMMAlignThread; -import jalview.hmmer.HMMBuildThread; +import jalview.io.CountReader; import jalview.io.FileFormatI; import jalview.io.FileFormats; import jalview.io.FormatAdapter; @@ -50,16 +48,21 @@ import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemes; import jalview.schemes.PIDColourScheme; +import jalview.schemes.ResidueColourScheme; 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.io.IOException; +import java.net.MalformedURLException; import java.util.ArrayList; import java.util.Arrays; +import java.util.BitSet; import java.util.Collection; import java.util.Collections; import java.util.Hashtable; @@ -70,17 +73,17 @@ 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; /** - * 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 { @@ -94,6 +97,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); + protected JRadioButtonMenuItem annotationColour; + protected JMenuItem modifyConservation = new JMenuItem(); AlignmentPanel ap; @@ -160,7 +165,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener JMenuItem sequenceFeature = new JMenuItem(); - JMenuItem hmmBuildGroup = new JMenuItem(); JMenuItem textColour = new JMenuItem(); @@ -177,28 +181,215 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener JMenuItem hideInsertions = 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 + */ + 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) + { + 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. * * @param ap - * DOCUMENT ME! * @param seq - * DOCUMENT ME! + * @param features + * non-positional features (for seq not null), or positional features + * at residue (for seq equal to null) */ - public PopupMenu(final AlignmentPanel ap, Sequence seq, - List links) + public PopupMenu(final AlignmentPanel ap, SequenceI seq, + List features) { - this(ap, seq, links, null); + this(ap, seq, features, null); } /** + * Constructor * - * @param ap + * @param alignPanel * @param seq - * @param links + * 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 * @param groupLinks */ - public PopupMenu(final AlignmentPanel ap, final SequenceI seq, - List links, List groupLinks) + public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq, + List features, List groupLinks) { // ///////////////////////////////////////////////////////// // If this is activated from the sequence panel, the user may want to @@ -206,7 +397,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener // // If from the IDPanel, we must display the sequence menu // //////////////////////////////////////////////////////// - this.ap = ap; + this.ap = alignPanel; sequence = seq; for (String ff : FileFormats.getInstance().getWritableFormats(true)) @@ -232,6 +423,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener */ final List selectedSequence = (seq == null ? Collections. emptyList() : Arrays.asList(seq)); + buildAnnotationTypesMenus(seqShowAnnotationsMenu, seqHideAnnotationsMenu, selectedSequence); configureReferenceAnnotationsMenu(seqAddReferenceAnnotations, @@ -240,9 +432,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener /* * And repeat for the current selection group (if there is one): */ - final List selectedGroup = (ap.av.getSelectionGroup() == null + final List selectedGroup = (alignPanel.av.getSelectionGroup() == null ? Collections. emptyList() - : ap.av.getSelectionGroup().getSequences()); + : alignPanel.av.getSelectionGroup().getSequences()); buildAnnotationTypesMenus(groupShowAnnotationsMenu, groupHideAnnotationsMenu, selectedGroup); configureReferenceAnnotationsMenu(groupAddReferenceAnnotations, @@ -260,7 +452,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener if (seq != null) { sequenceMenu.setText(sequence.getName()); - if (seq == ap.av.getAlignment().getSeqrep()) + if (seq == alignPanel.av.getAlignment().getSeqrep()) { makeReferenceSeq.setText( MessageManager.getString("action.unmark_as_reference")); @@ -271,7 +463,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener MessageManager.getString("action.set_as_reference")); } - if (!ap.av.getAlignment().isNucleotide()) + if (!alignPanel.av.getAlignment().isNucleotide()) { remove(rnaStructureMenu); } @@ -282,7 +474,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener * add menu items to 2D-render any alignment or sequence secondary * structure annotation */ - AlignmentAnnotation[] aas = ap.av.getAlignment() + AlignmentAnnotation[] aas = alignPanel.av.getAlignment() .getAlignmentAnnotation(); if (aas != null) { @@ -295,15 +487,14 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener */ menuItem = new JMenuItem(); menuItem.setText(MessageManager.formatMessage( - "label.2d_rna_structure_line", - new Object[] - { aa.label })); + "label.2d_rna_structure_line", new Object[] + { aa.label })); menuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { - new AppVarna(seq, aa, ap); + new AppVarna(seq, aa, alignPanel); } }); rnaStructureMenu.add(menuItem); @@ -324,16 +515,15 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener // TODO: make rnastrucF a bit more nice menuItem = new JMenuItem(); menuItem.setText(MessageManager.formatMessage( - "label.2d_rna_sequence_name", - new Object[] - { seq.getName() })); + "label.2d_rna_sequence_name", new Object[] + { seq.getName() })); menuItem.addActionListener(new ActionListener() { @Override public void actionPerformed(ActionEvent e) { // TODO: VARNA does'nt print gaps in the sequence - new AppVarna(seq, aa, ap); + new AppVarna(seq, aa, alignPanel); } }); rnaStructureMenu.add(menuItem); @@ -346,6 +536,36 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } } + if (seq.hasHMMProfile()) + { + menuItem = new JMenuItem(MessageManager + .getString("action.add_background_frequencies")); + menuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + try + { + ResidueCount counts = CountReader.getBackgroundFrequencies(ap, + seq); + if (counts != null) + { + seq.getHMM().setBackgroundFrequencies(counts); + ap.alignFrame.buildColourMenu(); + } + } catch (MalformedURLException e1) + { + e1.printStackTrace(); + } catch (IOException e1) + { + e1.printStackTrace(); + } + } + }); + add(menuItem); + } + menuItem = new JMenuItem( MessageManager.getString("action.hide_sequences")); menuItem.addActionListener(new ActionListener() @@ -358,41 +578,11 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener }); add(menuItem); - if (sequence.isHMMConsensusSequence()) + if (alignPanel.av.getSelectionGroup() != null + && alignPanel.av.getSelectionGroup().getSize() > 1) { - JMenuItem selectHMM = new JCheckBoxMenuItem(); - selectHMM.setText(MessageManager.getString("label.select_hmm")); - selectHMM.addActionListener(new ActionListener() - { - - @Override - public void actionPerformed(ActionEvent e) - { - selectHMM_actionPerformed(e); - } - }); - add(selectHMM); - - JMenuItem hmmAlign = new JCheckBoxMenuItem(); - hmmAlign.setText(MessageManager.getString("label.hmmalign")); - hmmAlign.addActionListener(new ActionListener() - { - - @Override - public void actionPerformed(ActionEvent e) - { - hmmAlign_actionPerformed(e); - } - }); - add(hmmAlign); - } - - if (ap.av.getSelectionGroup() != null - && ap.av.getSelectionGroup().getSize() > 1) - { - menuItem = new JMenuItem( - MessageManager.formatMessage("label.represent_group_with", - new Object[] + menuItem = new JMenuItem(MessageManager + .formatMessage("label.represent_group_with", new Object[] { seq.getName() })); menuItem.addActionListener(new ActionListener() { @@ -405,12 +595,12 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener sequenceMenu.add(menuItem); } - if (ap.av.hasHiddenRows()) + if (alignPanel.av.hasHiddenRows()) { - final int index = ap.av.getAlignment().findIndex(seq); + final int index = alignPanel.av.getAlignment().findIndex(seq); - if (ap.av.adjustForHiddenSeqs(index) - - ap.av.adjustForHiddenSeqs(index - 1) > 1) + if (alignPanel.av.adjustForHiddenSeqs(index) + - alignPanel.av.adjustForHiddenSeqs(index - 1) > 1) { menuItem = new JMenuItem( MessageManager.getString("action.reveal_sequences")); @@ -419,10 +609,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener @Override public void actionPerformed(ActionEvent e) { - ap.av.showSequence(index); - if (ap.overviewPanel != null) + alignPanel.av.showSequence(index); + if (alignPanel.overviewPanel != null) { - ap.overviewPanel.updateOverviewImage(); + alignPanel.overviewPanel.updateOverviewImage(); } } }); @@ -430,9 +620,20 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } } } - // for the case when no sequences are even visible - if (ap.av.hasHiddenRows()) + + /* + * 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) + { + addOption = true; + } + if (addOption) { menuItem = new JMenuItem( MessageManager.getString("action.reveal_all")); @@ -441,21 +642,21 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener @Override public void actionPerformed(ActionEvent e) { - ap.av.showAllHiddenSeqs(); - if (ap.overviewPanel != null) + alignPanel.av.showAllHiddenSeqs(); + if (alignPanel.overviewPanel != null) { - ap.overviewPanel.updateOverviewImage(); + alignPanel.overviewPanel.updateOverviewImage(); } } }); - add(menuItem); } } - SequenceGroup sg = ap.av.getSelectionGroup(); + SequenceGroup sg = alignPanel.av.getSelectionGroup(); boolean isDefinedGroup = (sg != null) - ? ap.av.getAlignment().getGroups().contains(sg) : false; + ? alignPanel.av.getAlignment().getGroups().contains(sg) + : false; if (sg != null && sg.getSize() > 0) { @@ -489,10 +690,11 @@ 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<>(); + Hashtable reppdb = new Hashtable<>(); + SequenceI sqass = null; - for (SequenceI sq : ap.av.getSequenceSelection()) + for (SequenceI sq : alignPanel.av.getSequenceSelection()) { Vector pes = sq.getDatasetSequence().getAllPDBEntries(); if (pes != null && pes.size() > 0) @@ -542,65 +744,118 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener rnaStructureMenu.setVisible(false); } - if (links != null && links.size() > 0) + addLinks(seq, features); + + if (seq == null) { - addFeatureLinks(seq, links); + addFeatureDetails(features); } } /** - * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided. + * Add a link to show feature details for each sequence feature * - * @param seq - * @param links + * @param features */ - void addFeatureLinks(final SequenceI seq, List links) + protected void addFeatureDetails(List features) { - JMenu linkMenu = new JMenu(MessageManager.getString("action.link")); - Map> linkset = new LinkedHashMap<>(); + if (features == null || features.isEmpty()) + { + return; + } + JMenu details = new JMenu( + MessageManager.getString("label.feature_details")); + add(details); - for (String link : links) + for (final SequenceFeature sf : features) { - UrlLink urlLink = null; - try + int start = sf.getBegin(); + int end = sf.getEnd(); + String desc = null; + if (start == end) { - urlLink = new UrlLink(link); - } catch (Exception foo) + desc = String.format("%s %d", sf.getType(), start); + } + else { - Cache.log.error("Exception for URLLink '" + link + "'", foo); - continue; + desc = String.format("%s %d-%d", sf.getType(), start, end); } - - if (!urlLink.isValid()) + String tooltip = desc; + String description = sf.getDescription(); + if (description != null) { - Cache.log.error(urlLink.getInvalidMessage()); - continue; + description = StringUtils.stripHtmlTags(description); + if (description.length() > 12) + { + desc = desc + " " + description.substring(0, 12) + ".."; + } + else + { + desc = desc + " " + description; + } + tooltip = tooltip + " " + description; } - - urlLink.createLinksFromSeq(seq, linkset); + if (sf.getFeatureGroup() != null) + { + tooltip = tooltip + (" (" + sf.getFeatureGroup() + ")"); + } + JMenuItem item = new JMenuItem(desc); + item.setToolTipText(tooltip); + item.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showFeatureDetails(sf); + } + }); + details.add(item); } + } - addshowLinks(linkMenu, linkset.values()); + /** + * Opens a panel showing a text report of feature dteails + * + * @param sf + */ + protected void showFeatureDetails(SequenceFeature sf) + { + CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer(); + // it appears Java's CSS does not support border-collaps :-( + cap.addStylesheetRule("table { border-collapse: collapse;}"); + cap.addStylesheetRule("table, td, th {border: 1px solid black;}"); + cap.setText(sf.getDetailsReport()); - // disable link menu if there are no valid entries - if (linkMenu.getItemCount() > 0) - { - linkMenu.setEnabled(true); - } - else - { - linkMenu.setEnabled(false); - } + Desktop.addInternalFrame(cap, + MessageManager.getString("label.feature_details"), 500, 500); + } - if (sequence != null) - { - sequenceMenu.add(linkMenu); - } - else + /** + * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided. + * 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. If no links are found, the menu is not added. + * + * @param seq + * @param features + */ + void addLinks(final SequenceI seq, List features) + { + JMenu linkMenu = buildLinkMenu(seq, features); + + // only add link menu if it has entries + if (linkMenu.getItemCount() > 0) { - add(linkMenu); + if (sequence != null) + { + sequenceMenu.add(linkMenu); + } + else + { + add(linkMenu); + } } - } /** @@ -626,7 +881,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener final List all = Arrays .asList(new String[] - { MessageManager.getString("label.all") }); + { MessageManager.getString("label.all") }); addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true); addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true, @@ -855,8 +1110,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener int type = urlLink.getGroupURLType() & 3; // first two bits ofurlLink type bitfield are sequenceids and sequences // TODO: FUTURE: ensure the groupURL menu structure can be generalised - addshowLink(linkMenus[type], label + (((type & 1) == 1) - ? ("(" + (usingNames ? "Names" : ltarget) + ")") : ""), + addshowLink(linkMenus[type], + label + (((type & 1) == 1) + ? ("(" + (usingNames ? "Names" : ltarget) + ")") + : ""), urlLink, urlset); addMenu = true; } @@ -878,99 +1135,6 @@ 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! * @@ -1167,15 +1331,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener sequenceFeature_actionPerformed(); } }); - hmmBuildGroup.setText(MessageManager.getString("label.group_hmmbuild")); - hmmBuildGroup.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - hmmBuildGroup_actionPerformed(); - } - }); jMenu1.setText(MessageManager.getString("label.group")); pdbStructureDialog.setText( MessageManager.getString("label.show_pdbstruct_dialog")); @@ -1285,26 +1440,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener jMenu1.add(displayNonconserved); } - protected void hmmBuildGroup_actionPerformed() - { - new Thread(new HMMBuildThread(ap.alignFrame)).start(); - ap.repaint(); - - } - - protected void selectHMM_actionPerformed(ActionEvent e) - { - HiddenMarkovModel hmm = ap.av.getSequenceSelection()[0].getHMM(); - ap.av.setSelectedHMM(hmm); - } - - protected void hmmAlign_actionPerformed(ActionEvent e) - { - ap.av.setSelectedHMM(this.sequence.getHMM()); - new Thread(new HMMAlignThread(ap.alignFrame, true)).start(); - ap.repaint(); - } - /** * Constructs the entries for the colour menu */ @@ -1355,6 +1490,13 @@ 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() @@ -1385,7 +1527,10 @@ 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); @@ -1515,23 +1660,37 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener protected void hideInsertions_actionPerformed(ActionEvent actionEvent) { - if (sequence != null) + HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns(); + BitSet inserts = new BitSet(); + + boolean markedPopup = false; + // mark inserts in current selection + if (ap.av.getSelectionGroup() != null) { - /* ColumnSelection cs = ap.av.getColumnSelection(); - if (cs == null) - { - cs = new ColumnSelection(); - } - cs.hideInsertionsFor(sequence); - ap.av.setColumnSelection(cs);*/ + // mark just the columns in the selection group to be hidden + inserts.set(ap.av.getSelectionGroup().getStartRes(), + ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1? - HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns(); - if (hidden == null) + // now clear columns without gaps + for (SequenceI sq : ap.av.getSelectionGroup().getSequences()) { - hidden = new HiddenColumns(); + if (sq == sequence) + { + markedPopup = true; + } + inserts.and(sq.getInsertionsAsBits()); } - hidden.hideInsertionsFor(sequence); - ap.av.getAlignment().setHiddenColumns(hidden); + hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(), + ap.av.getSelectionGroup().getEndRes()); + } + + // now mark for sequence under popup if we haven't already done it + else if (!markedPopup && sequence != null) + { + inserts.or(sequence.getInsertionsAsBits()); + + // and set hidden columns accordingly + hidden.hideColumns(inserts); } refresh(); } @@ -1552,28 +1711,24 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener StringBuilder contents = new StringBuilder(128); for (SequenceI seq : sequences) { - contents.append("

" - + MessageManager.formatMessage( - "label.create_sequence_details_report_annotation_for", - new Object[] - { seq.getDisplayId(true) }) - + "

"); - new SequenceAnnotationReport(null) - .createSequenceAnnotationReport(contents, seq, true, true, - (ap.getSeqPanel().seqCanvas.fr != null) - ? ap.getSeqPanel().seqCanvas.fr.getMinMax() - : null); + contents.append("

" + 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); contents.append("

"); } cap.setText("" + contents.toString() + ""); - Desktop.addInternalFrame(cap, MessageManager.formatMessage( - "label.sequence_details_for", - (sequences.length == 1 - ? new Object[] + Desktop.addInternalFrame(cap, + MessageManager.formatMessage("label.sequence_details_for", + (sequences.length == 1 ? new Object[] { sequences[0].getDisplayId(true) } - : new Object[] - { MessageManager.getString("label.selection") })), 500, 400); + : new Object[] + { MessageManager + .getString("label.selection") })), + 500, 400); } @@ -1589,7 +1744,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener void refresh() { ap.updateAnnotation(); - ap.paintAlignment(true); + // removed paintAlignment(true) here: + // updateAnnotation calls paintAlignment already, so don't need to call + // again PaintRefresher.Refresh(this, ap.av.getSequenceSetId()); } @@ -1747,8 +1904,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener " " + MessageManager.getString("label.sequence_name") + " ", MessageManager.getString("label.sequence_description") + " ", - MessageManager - .getString("label.edit_sequence_name_description"), + MessageManager.getString( + "label.edit_sequence_name_description"), ap.alignFrame); if (!dialog.accept) @@ -1769,7 +1926,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } sequence.setName(dialog.getName().replace(' ', '_')); - ap.paintAlignment(false); + ap.paintAlignment(false, false); } sequence.setDescription(dialog.getDescription()); @@ -1857,22 +2014,6 @@ 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); @@ -1933,9 +2074,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener { CutAndPasteTransfer cap = new CutAndPasteTransfer(); cap.setForInput(null); - Desktop.addInternalFrame(cap, - MessageManager.formatMessage("label.alignment_output_command", - new Object[] + Desktop.addInternalFrame(cap, MessageManager + .formatMessage("label.alignment_output_command", new Object[] { e.getActionCommand() }), 600, 500); String[] omitHidden = null; @@ -1973,16 +2113,22 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener if (start <= end) { seqs.add(sg.getSequenceAt(i).getDatasetSequence()); - features.add( - new SequenceFeature(null, null, null, start, end, null)); + features.add(new SequenceFeature(null, null, start, end, null)); } } - if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs, - features, true, ap)) + /* + * an entirely gapped region will generate empty lists of sequence / features + */ + if (!seqs.isEmpty()) { - ap.alignFrame.setShowSeqFeatures(true); - ap.highlightSearchResults(null); + 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 + } } } @@ -2063,7 +2209,7 @@ 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