X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FPopupMenuTest.java;h=e04be685a979d2bb7e1529b00afa02d4d4ecbad6;hp=6f605883970a754380cd89201f80d4e127434d52;hb=b22e1863f9c10dbff13ca8bc889255b91f0c4d1c;hpb=1554f4bd8e8ee6dd985251c1591793e23d89aad7 diff --git a/test/jalview/gui/PopupMenuTest.java b/test/jalview/gui/PopupMenuTest.java index 6f60588..e04be68 100644 --- a/test/jalview/gui/PopupMenuTest.java +++ b/test/jalview/gui/PopupMenuTest.java @@ -489,115 +489,82 @@ public class PopupMenuTest } /** - * Test for adding feature links + * Test for adding sequence id, dbref and feature links */ @Test(groups = { "Functional" }) - public void testAddFeatureLinks() + public void testConstructor_links() { - // sequences from the alignment List seqs = parentPanel.getAlignment().getSequences(); - - // create list of links and list of DBRefs - List links = new ArrayList<>(); - List refs = new ArrayList<>(); - - // links as might be added into Preferences | Connections dialog - links.add("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$" - + SEQUENCE_ID + "$"); - links.add("UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION - + "$"); - links.add("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$" - + DB_ACCESSION + "$"); - // Gene3D entry tests for case (in)sensitivity - links.add("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$" - + DB_ACCESSION + "$&mode=protein"); - - // make seq0 dbrefs - refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527")); - refs.add(new DBRefEntry("INTERPRO", "1", "IPR001041")); - refs.add(new DBRefEntry("INTERPRO", "1", "IPR006058")); - refs.add(new DBRefEntry("INTERPRO", "1", "IPR012675")); - - // make seq1 dbrefs - refs.add(new DBRefEntry(DBRefSource.UNIPROT, "1", "Q9ZTS2")); - refs.add(new DBRefEntry("GENE3D", "1", "3.10.20.30")); - - // add all the dbrefs to the sequences: Uniprot 1 each, Interpro all 3 to - // seq0, Gene3D to seq1 - SequenceI seq = seqs.get(0); - seq.addDBRef(refs.get(0)); - - seq.addDBRef(refs.get(1)); - seq.addDBRef(refs.get(2)); - seq.addDBRef(refs.get(3)); + final SequenceI seq0 = seqs.get(0); + final SequenceI seq1 = seqs.get(1); + final List noFeatures = Collections + . emptyList(); + final String linkText = MessageManager.getString("action.link"); + + seq0.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, "1", "P83527")); + seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR001041")); + seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR012675")); + seq0.addDBRef(new DBRefEntry("INTERPRO", "1", "IPR006058")); + seq1.addDBRef(new DBRefEntry(DBRefSource.UNIPROT, "1", "Q9ZTS2")); + seq1.addDBRef(new DBRefEntry("GENE3D", "1", "3.10.20.30")); - seqs.get(1).addDBRef(refs.get(4)); - seqs.get(1).addDBRef(refs.get(5)); - - // get the Popup Menu for first sequence - List noFeatures = Collections. emptyList(); - testee = new PopupMenu(parentPanel, seq, noFeatures); + /* + * check the Popup Menu for the first sequence + */ + testee = new PopupMenu(parentPanel, seq0, noFeatures); Component[] seqItems = testee.sequenceMenu.getMenuComponents(); JMenu linkMenu = (JMenu) seqItems[6]; + assertEquals(linkText, linkMenu.getText()); Component[] linkItems = linkMenu.getMenuComponents(); - // check the number of links are the expected number + /* + * menu items are ordered: SEQUENCE_ID search first, then dbrefs in order + * of database name (and within that by order of dbref addition) + */ assertEquals(5, linkItems.length); - - // first entry is EMBL-EBI which just uses sequence id not accession id? assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText()); + assertEquals("INTERPRO|IPR001041", + ((JMenuItem) linkItems[1]).getText()); + assertEquals("INTERPRO|IPR012675", + ((JMenuItem) linkItems[2]).getText()); + assertEquals("INTERPRO|IPR006058", + ((JMenuItem) linkItems[3]).getText()); + assertEquals("UNIPROT|P83527", ((JMenuItem) linkItems[4]).getText()); - // sequence id for each link should match corresponding DB accession id - for (int i = 1; i < 4; i++) - { - String msg = seq.getName() + " link[" + i + "]"; - assertEquals(msg, refs.get(i - 1).getSource(), - ((JMenuItem) linkItems[i]) - .getText().split("\\|")[0]); - assertEquals(msg, refs.get(i - 1).getAccessionId(), - ((JMenuItem) linkItems[i]) - .getText().split("\\|")[1]); - } - - // get the Popup Menu for second sequence - seq = seqs.get(1); - testee = new PopupMenu(parentPanel, seq, noFeatures); + /* + * check the Popup Menu for 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]; + assertEquals(linkText, linkMenu.getText()); linkItems = linkMenu.getMenuComponents(); - - // check the number of links are the expected number assertEquals(3, linkItems.length); - - // first entry is EMBL-EBI which just uses sequence id not accession id? assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText()); + assertEquals("Gene3D|3.10.20.30", ((JMenuItem) linkItems[1]).getText()); + assertEquals("UNIPROT|Q9ZTS2", ((JMenuItem) linkItems[2]).getText()); - // sequence id for each link should match corresponding DB accession id - for (int i = 1; i < 3; i++) - { - String msg = seq.getName() + " link[" + i + "]"; - assertEquals(msg, refs.get(i + 3).getSource(), - ((JMenuItem) linkItems[i]) - .getText().split("\\|")[0].toUpperCase()); - assertEquals(msg, refs.get(i + 3).getAccessionId(), - ((JMenuItem) linkItems[i]).getText().split("\\|")[1]); - } - - // if there are no valid links the Links submenu is disabled - List nomatchlinks = new ArrayList<>(); - nomatchlinks.add("NOMATCH | http://www.uniprot.org/uniprot/$" - + DB_ACCESSION + "$"); + /* + * if there are no valid links the Links submenu is still shown, but + * reduced to the EMBL-EBI lookup only (inserted by + * CustomUrlProvider.choosePrimaryUrl()) + */ + String unmatched = "NOMATCH|http://www.uniprot.org/uniprot/$" + + DB_ACCESSION + "$"; + UrlProviderFactoryI factory = new DesktopUrlProviderFactory(null, + unmatched, ""); + Preferences.sequenceUrlLinks = factory.createUrlProvider(); - testee = new PopupMenu(parentPanel, seq, noFeatures); + testee = new PopupMenu(parentPanel, seq1, noFeatures); seqItems = testee.sequenceMenu.getMenuComponents(); linkMenu = (JMenu) seqItems[6]; - assertFalse(linkMenu.isEnabled()); - + assertEquals(linkText, linkMenu.getText()); + linkItems = linkMenu.getMenuComponents(); + assertEquals(1, linkItems.length); + assertEquals("EMBL-EBI Search", ((JMenuItem) linkItems[0]).getText()); } - /** - * Test for adding feature links - */ @Test(groups = { "Functional" }) public void testHideInsertions() {