X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignViewportTest.java;h=d7b26b0213bf757b057f4ab1a875fab12a43017a;hb=ea3d24d953af89ca95d4480371149b70abbfcc67;hp=b39b2bd70bc62bde00a37b8b5c7c5532325d2bef;hpb=49428d3a57e4f4863acbdeb3f77049ed95efd6c3;p=jalview.git diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java index b39b2bd..d7b26b0 100644 --- a/test/jalview/gui/AlignViewportTest.java +++ b/test/jalview/gui/AlignViewportTest.java @@ -26,16 +26,23 @@ import static org.testng.AssertJUnit.assertNotNull; import static org.testng.AssertJUnit.assertSame; import static org.testng.AssertJUnit.assertTrue; +import jalview.bin.Cache; +import jalview.bin.Jalview; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; +import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; +import jalview.datamodel.Annotation; import jalview.datamodel.PDBEntry; import jalview.datamodel.PDBEntry.Type; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; import jalview.io.FileLoader; import jalview.io.FormatAdapter; +import jalview.schemes.ColourSchemeI; +import jalview.schemes.PIDColourScheme; import jalview.structure.StructureSelectionManager; +import jalview.util.MapList; import java.util.ArrayList; import java.util.List; @@ -54,8 +61,7 @@ public class AlignViewportTest @BeforeClass(alwaysRun = true) public static void setUpBeforeClass() throws Exception { - jalview.bin.Jalview.main(new String[] { "-props", - "test/jalview/testProps.jvprops" }); + Jalview.main(new String[] { "-props", "test/jalview/testProps.jvprops" }); } @BeforeMethod(alwaysRun = true) @@ -73,15 +79,16 @@ public class AlignViewportTest @Test(groups = { "Functional" }) public void testCollateForPdb() { + // JBP: What behaviour is this supposed to test ? /* * Set up sequence pdb ids */ - PDBEntry pdb1 = new PDBEntry("1ABC", "A", Type.PDB, "1ABC.pdb"); - PDBEntry pdb2 = new PDBEntry("2ABC", "A", Type.PDB, "2ABC.pdb"); - PDBEntry pdb3 = new PDBEntry("3ABC", "A", Type.PDB, "3ABC.pdb"); + 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 1ABC, seq2 to 2ABC, none to 3ABC + * 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")); @@ -133,8 +140,13 @@ public class AlignViewportTest AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded( ">Seq1\nCAGT\n", FormatAdapter.PASTE); + SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0); AlignedCodonFrame acf1 = new AlignedCodonFrame(); + acf1.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 1, 4 }, + 1, 1)); AlignedCodonFrame acf2 = new AlignedCodonFrame(); + acf2.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 4, 1 }, + 1, 1)); List mappings = new ArrayList(); mappings.add(acf1); @@ -178,10 +190,20 @@ public class AlignViewportTest ">Seq1\nRSVQ\n", FormatAdapter.PASTE); AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded( ">Seq2\nDGEL\n", FormatAdapter.PASTE); - + SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA"); + SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA"); + SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0); + SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0); + // need to be distinct AlignedCodonFrame acf1 = new AlignedCodonFrame(); + acf1.addMap(cs1, s1, new MapList(new int[] { 1, 4 }, + new int[] { 1, 12 }, 1, 3)); AlignedCodonFrame acf2 = new AlignedCodonFrame(); + acf2.addMap(cs2, s2, new MapList(new int[] { 1, 4 }, + new int[] { 1, 12 }, 1, 3)); AlignedCodonFrame acf3 = new AlignedCodonFrame(); + acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1, + 12 }, 1, 1)); List mappings1 = new ArrayList(); mappings1.add(acf1); @@ -231,10 +253,20 @@ public class AlignViewportTest ">Seq1\nRSVQ\n", FormatAdapter.PASTE); AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded( ">Seq2\nDGEL\n", FormatAdapter.PASTE); - + SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA"); + SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA"); + SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0); + SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0); + // need to be distinct AlignedCodonFrame acf1 = new AlignedCodonFrame(); + acf1.addMap(cs1, s1, new MapList(new int[] { 1, 4 }, + new int[] { 1, 12 }, 1, 3)); AlignedCodonFrame acf2 = new AlignedCodonFrame(); + acf2.addMap(cs2, s2, new MapList(new int[] { 1, 4 }, + new int[] { 1, 12 }, 1, 3)); AlignedCodonFrame acf3 = new AlignedCodonFrame(); + acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1, + 12 }, 1, 1)); List mappings1 = new ArrayList(); mappings1.add(acf1); @@ -270,4 +302,51 @@ public class AlignViewportTest assertTrue(ssmMappings.contains(acf2)); assertFalse(ssmMappings.contains(acf3)); } + + /** + * Test for JAL-1306 - conservation thread should run even when only Quality + * (and not Conservation) is enabled in Preferences + */ + @Test(groups = { "Functional" }) + public void testUpdateConservation_qualityOnly() + { + Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", + Boolean.TRUE.toString()); + Cache.applicationProperties.setProperty("SHOW_QUALITY", + Boolean.TRUE.toString()); + Cache.applicationProperties.setProperty("SHOW_CONSERVATION", + Boolean.FALSE.toString()); + Cache.applicationProperties.setProperty("SHOW_IDENTITY", + Boolean.FALSE.toString()); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/uniref50.fa", FormatAdapter.FILE); + AlignmentAnnotation[] anns = af.viewport.getAlignment() + .getAlignmentAnnotation(); + assertNotNull("No annotations found", anns); + assertEquals("More than one annotation found", 1, anns.length); + assertTrue("Annotation is not Quality", + anns[0].description.startsWith("Alignment Quality")); + Annotation[] annotations = anns[0].annotations; + assertNotNull("Quality annotations are null", annotations); + assertNotNull("Quality in column 1 is null", annotations[0]); + assertTrue("No quality value in column 1", annotations[0].value > 10f); + } + + @Test(groups = { "Functional" }) + public void testSetGlobalColourScheme() + { + /* + * test for JAL-2283 don't inadvertently turn on colour by conservation + */ + Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", + Boolean.TRUE.toString()); + Cache.applicationProperties.setProperty("SHOW_CONSERVATION", + Boolean.FALSE.toString()); + Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "NONE"); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/uniref50.fa", FormatAdapter.FILE); + ColourSchemeI cs = new PIDColourScheme(); + af.getViewport().setGlobalColourScheme(cs); + assertFalse(cs.conservationApplied()); + } }