X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FPopupMenuTest.java;fp=test%2Fjalview%2Fgui%2FPopupMenuTest.java;h=335240b3d9a05e8128b2dfab41c990a5ea321ec6;hb=2595e9d4ee0dbbd3406a98c4e49a61ccde806479;hp=edf320277fc35fe5d30c58cc9ac789862c627604;hpb=e20075ba805d744d7cc4976e2b8d5e5840fb0a8d;p=jalview.git diff --git a/test/jalview/gui/PopupMenuTest.java b/test/jalview/gui/PopupMenuTest.java index edf3202..335240b 100644 --- a/test/jalview/gui/PopupMenuTest.java +++ b/test/jalview/gui/PopupMenuTest.java @@ -20,6 +20,8 @@ */ package jalview.gui; +import static jalview.util.UrlConstants.DB_ACCESSION; +import static jalview.util.UrlConstants.SEQUENCE_ID; import static org.testng.AssertJUnit.assertEquals; import static org.testng.AssertJUnit.assertFalse; import static org.testng.AssertJUnit.assertTrue; @@ -27,8 +29,12 @@ import static org.testng.AssertJUnit.assertTrue; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.DBRefSource; +import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; -import jalview.io.AppletFormatAdapter; +import jalview.io.DataSourceType; +import jalview.io.FileFormat; import jalview.io.FormatAdapter; import jalview.util.MessageManager; @@ -42,11 +48,20 @@ import javax.swing.JMenuItem; import javax.swing.JPopupMenu; import javax.swing.JSeparator; +import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; public class PopupMenuTest { + + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + // 4 sequences x 13 positions final static String TEST_DATA = ">FER_CAPAA Ferredoxin\n" + "TIETHKEAELVG-\n" @@ -66,7 +81,7 @@ public class PopupMenuTest public void setUp() throws IOException { alignment = new FormatAdapter().readFile(TEST_DATA, - AppletFormatAdapter.PASTE, "FASTA"); + DataSourceType.PASTE, FileFormat.Fasta); AlignFrame af = new AlignFrame(alignment, 700, 500); parentPanel = new AlignmentPanel(af, af.getViewport()); testee = new PopupMenu(parentPanel, null, null); @@ -306,7 +321,8 @@ public class PopupMenuTest assertEquals(4, showOptions.length); // includes 'All' and separator assertEquals(4, hideOptions.length); - assertEquals("All", ((JMenuItem) showOptions[0]).getText()); + String all = MessageManager.getString("label.all"); + assertEquals(all, ((JMenuItem) showOptions[0]).getText()); assertTrue(showOptions[1] instanceof JPopupMenu.Separator); assertEquals(JSeparator.HORIZONTAL, ((JSeparator) showOptions[1]).getOrientation()); @@ -316,7 +332,7 @@ public class PopupMenuTest assertEquals("SSP", ((JMenuItem) showOptions[3]).getText()); assertEquals("JPred", ((JMenuItem) showOptions[3]).getToolTipText()); - assertEquals("All", ((JMenuItem) hideOptions[0]).getText()); + assertEquals(all, ((JMenuItem) hideOptions[0]).getText()); assertTrue(hideOptions[1] instanceof JPopupMenu.Separator); assertEquals(JSeparator.HORIZONTAL, ((JSeparator) hideOptions[1]).getOrientation()); @@ -368,12 +384,13 @@ public class PopupMenuTest assertEquals(2, showOptions.length); // includes 'All' and separator assertEquals(4, hideOptions.length); - assertEquals("All", ((JMenuItem) showOptions[0]).getText()); + String all = MessageManager.getString("label.all"); + assertEquals(all, ((JMenuItem) showOptions[0]).getText()); assertTrue(showOptions[1] instanceof JPopupMenu.Separator); assertEquals(JSeparator.HORIZONTAL, ((JSeparator) showOptions[1]).getOrientation()); - assertEquals("All", ((JMenuItem) hideOptions[0]).getText()); + assertEquals(all, ((JMenuItem) hideOptions[0]).getText()); assertTrue(hideOptions[1] instanceof JPopupMenu.Separator); assertEquals(JSeparator.HORIZONTAL, ((JSeparator) hideOptions[1]).getOrientation()); @@ -425,7 +442,8 @@ public class PopupMenuTest assertEquals(4, showOptions.length); // includes 'All' and separator assertEquals(2, hideOptions.length); - assertEquals("All", ((JMenuItem) showOptions[0]).getText()); + String all = MessageManager.getString("label.all"); + assertEquals(all, ((JMenuItem) showOptions[0]).getText()); assertTrue(showOptions[1] instanceof JPopupMenu.Separator); assertEquals(JSeparator.HORIZONTAL, ((JSeparator) showOptions[1]).getOrientation()); @@ -435,9 +453,110 @@ public class PopupMenuTest assertEquals("Temp", ((JMenuItem) showOptions[3]).getText()); assertEquals("PDB2", ((JMenuItem) showOptions[3]).getToolTipText()); - assertEquals("All", ((JMenuItem) hideOptions[0]).getText()); + assertEquals(all, ((JMenuItem) hideOptions[0]).getText()); assertTrue(hideOptions[1] instanceof JPopupMenu.Separator); assertEquals(JSeparator.HORIZONTAL, ((JSeparator) hideOptions[1]).getOrientation()); } + + /** + * Test for adding feature links + */ + @Test(groups = { "Functional" }) + public void testAddFeatureLinks() + { + // 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 + seqs.get(0).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)); + + 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); + Component[] seqItems = testee.sequenceMenu.getMenuComponents(); + JMenu linkMenu = (JMenu) seqItems[6]; + Component[] linkItems = linkMenu.getMenuComponents(); + + // check the number of links are the expected number + 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()); + + // 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]) + .getText().split("\\|")[0]); + assertEquals(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); + seqItems = testee.sequenceMenu.getMenuComponents(); + linkMenu = (JMenu) seqItems[6]; + 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()); + + // 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]) + .getText().split("\\|")[0].toUpperCase()); + assertEquals(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/$" + + DB_ACCESSION + "$"); + + testee = new PopupMenu(parentPanel, (Sequence) seqs.get(0), + nomatchlinks); + seqItems = testee.sequenceMenu.getMenuComponents(); + linkMenu = (JMenu) seqItems[6]; + assertFalse(linkMenu.isEnabled()); + + } }