From bfb35471fbb8dd6cc4252b9a12b81057922e8f5e Mon Sep 17 00:00:00 2001 From: gmungoc Date: Fri, 4 Jan 2019 10:32:21 +0000 Subject: [PATCH] JAL-3181 refactor: extracted buildLinkMenu() for testability --- src/jalview/gui/PopupMenu.java | 349 +++++++++++++++++++---------------- test/jalview/gui/PopupMenuTest.java | 18 +- 2 files changed, 191 insertions(+), 176 deletions(-) diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 473ac3a..4e02d21 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -75,10 +75,8 @@ import javax.swing.JMenuItem; import javax.swing.JPopupMenu; /** - * 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 { @@ -173,6 +171,187 @@ 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 @@ -605,64 +784,14 @@ 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(); - 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); - } - } - } - } - - 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) @@ -955,98 +1084,6 @@ 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! * @@ -1916,22 +1953,6 @@ 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); diff --git a/test/jalview/gui/PopupMenuTest.java b/test/jalview/gui/PopupMenuTest.java index e04be68..df30935 100644 --- a/test/jalview/gui/PopupMenuTest.java +++ b/test/jalview/gui/PopupMenuTest.java @@ -492,7 +492,7 @@ public class PopupMenuTest * Test for adding sequence id, dbref and feature links */ @Test(groups = { "Functional" }) - public void testConstructor_links() + public void testBuildLinkMenu() { List seqs = parentPanel.getAlignment().getSequences(); final SequenceI seq0 = seqs.get(0); @@ -509,11 +509,9 @@ public class PopupMenuTest seq1.addDBRef(new DBRefEntry("GENE3D", "1", "3.10.20.30")); /* - * check the Popup Menu for the first sequence + * check the Link Menu for the first sequence */ - testee = new PopupMenu(parentPanel, seq0, noFeatures); - Component[] seqItems = testee.sequenceMenu.getMenuComponents(); - JMenu linkMenu = (JMenu) seqItems[6]; + JMenu linkMenu = PopupMenu.buildLinkMenu(seq0, noFeatures); assertEquals(linkText, linkMenu.getText()); Component[] linkItems = linkMenu.getMenuComponents(); @@ -532,12 +530,10 @@ public class PopupMenuTest assertEquals("UNIPROT|P83527", ((JMenuItem) linkItems[4]).getText()); /* - * check the Popup Menu for second sequence + * check the Link Menu for the second sequence * note dbref GENE3D is matched to link Gene3D, the latter is displayed */ - testee = new PopupMenu(parentPanel, seq1, noFeatures); - seqItems = testee.sequenceMenu.getMenuComponents(); - linkMenu = (JMenu) seqItems[6]; + linkMenu = PopupMenu.buildLinkMenu(seq1, noFeatures); assertEquals(linkText, linkMenu.getText()); linkItems = linkMenu.getMenuComponents(); assertEquals(3, linkItems.length); @@ -556,9 +552,7 @@ public class PopupMenuTest unmatched, ""); Preferences.sequenceUrlLinks = factory.createUrlProvider(); - testee = new PopupMenu(parentPanel, seq1, noFeatures); - seqItems = testee.sequenceMenu.getMenuComponents(); - linkMenu = (JMenu) seqItems[6]; + linkMenu = PopupMenu.buildLinkMenu(seq1, noFeatures); assertEquals(linkText, linkMenu.getText()); linkItems = linkMenu.getMenuComponents(); assertEquals(1, linkItems.length); -- 1.7.10.2