X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FPopupMenuTest.java;fp=test%2Fjalview%2Fgui%2FPopupMenuTest.java;h=6f605883970a754380cd89201f80d4e127434d52;hb=20a4d7ddb86ee996f2b6617a0470922b83354c35;hp=8f60021831eba332bd7c4e0ebad701cdce63b938;hpb=5610d0f46a76d4269d25148d42f92d867fa1061a;p=jalview.git diff --git a/test/jalview/gui/PopupMenuTest.java b/test/jalview/gui/PopupMenuTest.java index 8f60021..6f60588 100644 --- a/test/jalview/gui/PopupMenuTest.java +++ b/test/jalview/gui/PopupMenuTest.java @@ -26,6 +26,7 @@ import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertTrue; +import jalview.bin.Cache; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; @@ -34,16 +35,21 @@ import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; import jalview.datamodel.HiddenColumns; import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.DataSourceType; import jalview.io.FileFormat; import jalview.io.FormatAdapter; +import jalview.urls.api.UrlProviderFactoryI; +import jalview.urls.desktop.DesktopUrlProviderFactory; import jalview.util.MessageManager; +import jalview.util.UrlConstants; import java.awt.Component; import java.io.IOException; import java.util.ArrayList; +import java.util.Collections; import java.util.Iterator; import java.util.List; @@ -84,6 +90,25 @@ public class PopupMenuTest @BeforeMethod(alwaysRun = true) public void setUp() throws IOException { + Cache.loadProperties("test/jalview/io/testProps.jvprops"); + String inMenuString = ("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$" + + SEQUENCE_ID + + "$" + + "|" + + "UNIPROT | http://www.uniprot.org/uniprot/$" + DB_ACCESSION + "$") + + "|" + + ("INTERPRO | http://www.ebi.ac.uk/interpro/entry/$" + + DB_ACCESSION + "$") + + "|" + + + // Gene3D entry tests for case (in)sensitivity + ("Gene3D | http://gene3d.biochem.ucl.ac.uk/Gene3D/search?sterm=$" + + DB_ACCESSION + "$&mode=protein"); + + UrlProviderFactoryI factory = new DesktopUrlProviderFactory( + UrlConstants.DEFAULT_LABEL, inMenuString, ""); + Preferences.sequenceUrlLinks = factory.createUrlProvider(); + alignment = new FormatAdapter().readFile(TEST_DATA, DataSourceType.PASTE, FileFormat.Fasta); AlignFrame af = new AlignFrame(alignment, 700, 500); @@ -499,17 +524,19 @@ public class PopupMenuTest // add all the dbrefs to the sequences: Uniprot 1 each, Interpro all 3 to // seq0, Gene3D to seq1 - seqs.get(0).addDBRef(refs.get(0)); + SequenceI seq = seqs.get(0); + seq.addDBRef(refs.get(0)); - seqs.get(0).addDBRef(refs.get(1)); - seqs.get(0).addDBRef(refs.get(2)); - seqs.get(0).addDBRef(refs.get(3)); + seq.addDBRef(refs.get(1)); + seq.addDBRef(refs.get(2)); + seq.addDBRef(refs.get(3)); seqs.get(1).addDBRef(refs.get(4)); seqs.get(1).addDBRef(refs.get(5)); // get the Popup Menu for first sequence - testee = new PopupMenu(parentPanel, (Sequence) seqs.get(0), links); + List noFeatures = Collections. emptyList(); + testee = new PopupMenu(parentPanel, seq, noFeatures); Component[] seqItems = testee.sequenceMenu.getMenuComponents(); JMenu linkMenu = (JMenu) seqItems[6]; Component[] linkItems = linkMenu.getMenuComponents(); @@ -523,15 +550,18 @@ public class PopupMenuTest // sequence id for each link should match corresponding DB accession id for (int i = 1; i < 4; i++) { - assertEquals(refs.get(i - 1).getSource(), ((JMenuItem) linkItems[i]) + String msg = seq.getName() + " link[" + i + "]"; + assertEquals(msg, refs.get(i - 1).getSource(), + ((JMenuItem) linkItems[i]) .getText().split("\\|")[0]); - assertEquals(refs.get(i - 1).getAccessionId(), + assertEquals(msg, refs.get(i - 1).getAccessionId(), ((JMenuItem) linkItems[i]) .getText().split("\\|")[1]); } // get the Popup Menu for second sequence - testee = new PopupMenu(parentPanel, (Sequence) seqs.get(1), links); + seq = seqs.get(1); + testee = new PopupMenu(parentPanel, seq, noFeatures); seqItems = testee.sequenceMenu.getMenuComponents(); linkMenu = (JMenu) seqItems[6]; linkItems = linkMenu.getMenuComponents(); @@ -545,9 +575,11 @@ public class PopupMenuTest // sequence id for each link should match corresponding DB accession id for (int i = 1; i < 3; i++) { - assertEquals(refs.get(i + 3).getSource(), ((JMenuItem) linkItems[i]) + String msg = seq.getName() + " link[" + i + "]"; + assertEquals(msg, refs.get(i + 3).getSource(), + ((JMenuItem) linkItems[i]) .getText().split("\\|")[0].toUpperCase()); - assertEquals(refs.get(i + 3).getAccessionId(), + assertEquals(msg, refs.get(i + 3).getAccessionId(), ((JMenuItem) linkItems[i]).getText().split("\\|")[1]); } @@ -556,8 +588,7 @@ public class PopupMenuTest nomatchlinks.add("NOMATCH | http://www.uniprot.org/uniprot/$" + DB_ACCESSION + "$"); - testee = new PopupMenu(parentPanel, (Sequence) seqs.get(0), - nomatchlinks); + testee = new PopupMenu(parentPanel, seq, noFeatures); seqItems = testee.sequenceMenu.getMenuComponents(); linkMenu = (JMenu) seqItems[6]; assertFalse(linkMenu.isEnabled()); @@ -597,7 +628,7 @@ public class PopupMenuTest .revealAllHiddenColumns(sel); // get the Popup Menu for 7th sequence - no insertions - testee = new PopupMenu(parentPanel, (Sequence) seqs.get(7), null); + testee = new PopupMenu(parentPanel, seqs.get(7), null); testee.hideInsertions_actionPerformed(null); HiddenColumns hidden = parentPanel.av.getAlignment().getHiddenColumns(); @@ -605,7 +636,7 @@ public class PopupMenuTest assertFalse(it.hasNext()); // get the Popup Menu for GappySeq - this time we have insertions - testee = new PopupMenu(parentPanel, (Sequence) seqs.get(4), null); + testee = new PopupMenu(parentPanel, seqs.get(4), null); testee.hideInsertions_actionPerformed(null); hidden = parentPanel.av.getAlignment().getHiddenColumns(); it = hidden.iterator(); @@ -655,7 +686,7 @@ public class PopupMenuTest hidden.hideColumns(31, 40); // get the Popup Menu for LessGappySeq in the sequence group - testee = new PopupMenu(parentPanel, (Sequence) seqs.get(5), null); + testee = new PopupMenu(parentPanel, seqs.get(5), null); testee.hideInsertions_actionPerformed(null); hidden = parentPanel.av.getAlignment().getHiddenColumns(); it = hidden.iterator();