X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignViewportTest.java;h=5ed0cacca927f8c850da8f3c8ac609ae7992af24;hb=2b618ede76f5a9d2f1be7db9aad8bb3a2b10e23b;hp=71a5f3c50ff97f27f83b99ac054ee06da9504b92;hpb=424f6f03e8fb5e40cceca09fc8ffd72b41e3a9e4;p=jalview.git diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java index 71a5f3c..5ed0cac 100644 --- a/test/jalview/gui/AlignViewportTest.java +++ b/test/jalview/gui/AlignViewportTest.java @@ -38,6 +38,7 @@ import jalview.datamodel.PDBEntry.Type; import jalview.datamodel.SearchResults; import jalview.datamodel.SearchResultsI; import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.DataSourceType; import jalview.io.FileLoader; @@ -45,10 +46,12 @@ import jalview.schemes.ColourSchemeI; import jalview.schemes.PIDColourScheme; import jalview.structure.StructureSelectionManager; import jalview.util.MapList; +import jalview.viewmodel.ViewportRanges; import java.util.ArrayList; import java.util.List; +import org.testng.Assert; import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeMethod; import org.testng.annotations.Test; @@ -72,6 +75,13 @@ public class AlignViewportTest { Jalview.main(new String[] { "-nonews", "-props", "test/jalview/testProps.jvprops" }); + + /* + * remove any sequence mappings left lying around by other tests + */ + StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + ssm.resetAll(); } @BeforeMethod(alwaysRun = true) @@ -86,57 +96,6 @@ public class AlignViewportTest testee = new AlignViewport(al); } - @Test(groups = { "Functional" }) - public void testCollateForPdb() - { - // JBP: What behaviour is this supposed to test ? - /* - * Set up sequence pdb ids - */ - PDBEntry pdb1 = new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"); - PDBEntry pdb2 = new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb"); - PDBEntry pdb3 = new PDBEntry("3ABC", "D", Type.PDB, "3ABC.pdb"); - - /* - * seq1 and seq3 refer to 1abcB, seq2 to 2abcC, none to 3abcD - */ - al.getSequenceAt(0).getDatasetSequence() - .addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb")); - al.getSequenceAt(2).getDatasetSequence() - .addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb")); - al.getSequenceAt(1).getDatasetSequence() - .addPDBId(new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb")); - /* - * Add a second chain PDB xref to Seq2 - should not result in a duplicate in - * the results - */ - al.getSequenceAt(1).getDatasetSequence() - .addPDBId(new PDBEntry("2ABC", "D", Type.PDB, "2ABC.pdb")); - /* - * Seq3 refers to 3abc - this does not match 3ABC (as the code stands) - */ - al.getSequenceAt(2).getDatasetSequence() - .addPDBId(new PDBEntry("3abc", "D", Type.PDB, "3ABC.pdb")); - - /* - * run method under test - */ - SequenceI[][] seqs = testee.collateForPDB(new PDBEntry[] { pdb1, pdb2, - pdb3 }); - - // seq1 and seq3 refer to PDBEntry[0] - assertEquals(2, seqs[0].length); - assertSame(al.getSequenceAt(0), seqs[0][0]); - assertSame(al.getSequenceAt(2), seqs[0][1]); - - // seq2 refers to PDBEntry[1] - assertEquals(1, seqs[1].length); - assertSame(al.getSequenceAt(1), seqs[1][0]); - - // no sequence refers to PDBEntry[2] - assertEquals(0, seqs[2].length); - } - /** * Test that a mapping is not deregistered when a second view is closed but * the first still holds a reference to the mapping @@ -158,7 +117,7 @@ public class AlignViewportTest acf2.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 4, 1 }, 1, 1)); - List mappings = new ArrayList(); + List mappings = new ArrayList<>(); mappings.add(acf1); mappings.add(acf2); af1.getViewport().getAlignment().setCodonFrames(mappings); @@ -170,18 +129,19 @@ public class AlignViewportTest */ StructureSelectionManager ssm = StructureSelectionManager .getStructureSelectionManager(Desktop.instance); - assertEquals(2, ssm.getSequenceMappings().size()); - assertTrue(ssm.getSequenceMappings().contains(acf1)); - assertTrue(ssm.getSequenceMappings().contains(acf2)); + List sequenceMappings = ssm.getSequenceMappings(); + assertEquals(2, sequenceMappings.size()); + assertTrue(sequenceMappings.contains(acf1)); + assertTrue(sequenceMappings.contains(acf2)); /* * Close the second view. Verify that mappings are not removed as the first * view still holds a reference to them. */ af1.closeMenuItem_actionPerformed(false); - assertEquals(2, ssm.getSequenceMappings().size()); - assertTrue(ssm.getSequenceMappings().contains(acf1)); - assertTrue(ssm.getSequenceMappings().contains(acf2)); + assertEquals(2, sequenceMappings.size()); + assertTrue(sequenceMappings.contains(acf1)); + assertTrue(sequenceMappings.contains(acf2)); } /** @@ -215,11 +175,11 @@ public class AlignViewportTest acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1, 12 }, 1, 1)); - List mappings1 = new ArrayList(); + List mappings1 = new ArrayList<>(); mappings1.add(acf1); af1.getViewport().getAlignment().setCodonFrames(mappings1); - List mappings2 = new ArrayList(); + List mappings2 = new ArrayList<>(); mappings2.add(acf2); mappings2.add(acf3); af2.getViewport().getAlignment().setCodonFrames(mappings2); @@ -278,12 +238,12 @@ public class AlignViewportTest acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1, 12 }, 1, 1)); - List mappings1 = new ArrayList(); + List mappings1 = new ArrayList<>(); mappings1.add(acf1); mappings1.add(acf2); af1.getViewport().getAlignment().setCodonFrames(mappings1); - List mappings2 = new ArrayList(); + List mappings2 = new ArrayList<>(); mappings2.add(acf2); mappings2.add(acf3); af2.getViewport().getAlignment().setCodonFrames(mappings2); @@ -326,6 +286,8 @@ public class AlignViewportTest Boolean.TRUE.toString()); Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean.FALSE.toString()); + Cache.applicationProperties.setProperty("SHOW_OCCUPANCY", + Boolean.FALSE.toString()); Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean.FALSE.toString()); AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( @@ -355,7 +317,7 @@ public class AlignViewportTest "examples/uniref50.fa", DataSourceType.FILE); ColourSchemeI cs = new PIDColourScheme(); af.getViewport().setGlobalColourScheme(cs); - assertFalse(af.getViewport().getViewportColourScheme() + assertFalse(af.getViewport().getResidueShading() .conservationApplied()); } @@ -382,4 +344,129 @@ public class AlignViewportTest af.getViewport().setSearchResults(null); assertFalse(af.getViewport().hasSearchResults()); } + + /** + * Verify that setting the selection group has the side-effect of setting the + * context on the group, unless it already has one, but does not change + * whether the group is defined or not. + */ + @Test(groups = { "Functional" }) + public void testSetSelectionGroup() + { + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/uniref50.fa", DataSourceType.FILE); + AlignViewport av = af.getViewport(); + SequenceGroup sg1 = new SequenceGroup(); + SequenceGroup sg2 = new SequenceGroup(); + SequenceGroup sg3 = new SequenceGroup(); + + av.setSelectionGroup(sg1); + assertSame(sg1.getContext(), av.getAlignment()); // context set + assertFalse(sg1.isDefined()); // group not defined + + sg2.setContext(sg1, false); + av.setSelectionGroup(sg2); + assertFalse(sg2.isDefined()); // unchanged + assertSame(sg2.getContext(), sg1); // unchanged + + // create a defined group + sg3.setContext(av.getAlignment(), true); + av.setSelectionGroup(sg3); + assertTrue(sg3.isDefined()); // unchanged + } + /** + * Verify that setting/clearing SHOW_OCCUPANCY preference adds or omits occupancy row from viewport + */ + @Test(groups = { "Functional" }) + public void testShowOrDontShowOccupancy() + { + // disable occupancy + jalview.bin.Cache.setProperty("SHOW_OCCUPANCY", Boolean.FALSE.toString()); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/uniref50.fa", DataSourceType.FILE); + AlignViewport av = af.getViewport(); + Assert.assertNull(av.getAlignmentGapAnnotation(), "Preference did not disable occupancy row."); + int c = 0; + for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null, + null, "Occupancy")) + { + c++; + } + Assert.assertEquals(c, 0, "Expected zero occupancy rows."); + + // enable occupancy + jalview.bin.Cache.setProperty("SHOW_OCCUPANCY", Boolean.TRUE.toString()); + af = new FileLoader().LoadFileWaitTillLoaded( + "examples/uniref50.fa", DataSourceType.FILE); + av = af.getViewport(); + Assert.assertNotNull(av.getAlignmentGapAnnotation(), "Preference did not enable occupancy row."); + c = 0; + for (AlignmentAnnotation aa : av.getAlignment().findAnnotations(null, + null, av.getAlignmentGapAnnotation().label)) + { + c++; + } + ; + Assert.assertEquals(c, 1, "Expected to find one occupancy row."); + } + + @Test(groups = { "Functional" }) + public void testGetConsensusSeq() + { + /* + * A-C + * A-C + * A-D + * --D + * consensus expected to be A-C + */ + String fasta = ">s1\nA-C\n>s2\nA-C\n>s3\nA-D\n>s4\n--D\n"; + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta, + DataSourceType.PASTE); + AlignViewport testme = af.getViewport(); + SequenceI cons = testme.getConsensusSeq(); + assertEquals("A-C", cons.getSequenceAsString()); + } + + @Test(groups = { "Functional" }) + public void testHideRevealSequences() + { + ViewportRanges ranges = testee.getRanges(); + assertEquals(3, al.getHeight()); + assertEquals(0, ranges.getStartSeq()); + assertEquals(2, ranges.getEndSeq()); + + /* + * hide first sequence + */ + testee.hideSequence(new SequenceI[] { al.getSequenceAt(0) }); + assertEquals(2, al.getHeight()); + assertEquals(0, ranges.getStartSeq()); + assertEquals(1, ranges.getEndSeq()); + + /* + * reveal hidden sequences above the first + */ + testee.showSequence(0); + assertEquals(3, al.getHeight()); + assertEquals(0, ranges.getStartSeq()); + assertEquals(2, ranges.getEndSeq()); + + /* + * hide first and third sequences + */ + testee.hideSequence(new SequenceI[] { al.getSequenceAt(0), + al.getSequenceAt(2) }); + assertEquals(1, al.getHeight()); + assertEquals(0, ranges.getStartSeq()); + assertEquals(0, ranges.getEndSeq()); + + /* + * reveal all hidden sequences + */ + testee.showAllHiddenSeqs(); + assertEquals(3, al.getHeight()); + assertEquals(0, ranges.getStartSeq()); + assertEquals(2, ranges.getEndSeq()); + } }