X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=702773b6af1cf47e727f2a63bb6877513f20580c;hb=383fd91269f510b189450fbe174e9c051103c7eb;hp=6da7d4fbb99d77236f62832fb9577eab4869eb60;hpb=14193747f3831242bc7dfac12394eb20eb0ba480;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 6da7d4f..702773b 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -46,6 +46,7 @@ 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; @@ -68,17 +69,17 @@ 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 { @@ -92,6 +93,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem(); + protected JRadioButtonMenuItem annotationColour; + protected JMenuItem modifyConservation = new JMenuItem(); AlignmentPanel ap; @@ -173,6 +176,187 @@ 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 @@ -401,9 +585,20 @@ 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) + { + addOption = true; + } + if (addOption) { menuItem = new JMenuItem( MessageManager.getString("action.reveal_all")); @@ -419,7 +614,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener } } }); - add(menuItem); } } @@ -550,24 +744,27 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener { desc = String.format("%s %d-%d", sf.getType(), start, end); } + String tooltip = desc; String description = sf.getDescription(); if (description != null) { description = StringUtils.stripHtmlTags(description); - if (description.length() <= 6) + if (description.length() > 12) { - desc = desc + " " + description; + desc = desc + " " + description.substring(0, 12) + ".."; } else { - desc = desc + " " + description.substring(0, 6) + ".."; + desc = desc + " " + description; } + tooltip = tooltip + " " + description; } if (sf.getFeatureGroup() != null) { - desc = desc + " (" + sf.getFeatureGroup() + ")"; + tooltip = tooltip + (" (" + sf.getFeatureGroup() + ")"); } JMenuItem item = new JMenuItem(desc); + item.setToolTipText(tooltip); item.addActionListener(new ActionListener() { @Override @@ -602,63 +799,14 @@ 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(seq, features); // only add link menu if it has entries if (linkMenu.getItemCount() > 0) @@ -951,98 +1099,6 @@ 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! * @@ -1398,6 +1454,13 @@ 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 +1491,10 @@ 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 +1624,8 @@ 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 +1633,7 @@ 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 +1644,18 @@ 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()); - } - - // 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(); } @@ -1635,10 +1680,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener 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, seq, true, true, ap.getSeqPanel().seqCanvas.fr); contents.append("

"); } cap.setText("" + contents.toString() + ""); @@ -1936,22 +1978,6 @@ 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); @@ -2147,7 +2173,7 @@ 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