X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignViewportTest.java;h=fa71b2eaa35b75ac48806965d2d1d9b615485494;hb=8e1be43e250107a4d86898bd554cf03098fa5957;hp=6f514874221b329a0847a1f3ab37042619cf9a9f;hpb=e81459b192f4d635c1cd96befa7b14992d12ee5e;p=jalview.git diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java index 6f51487..fa71b2e 100644 --- a/test/jalview/gui/AlignViewportTest.java +++ b/test/jalview/gui/AlignViewportTest.java @@ -1,23 +1,53 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.gui; import static org.testng.AssertJUnit.assertEquals; +import static org.testng.AssertJUnit.assertFalse; 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.SearchResults; +import jalview.datamodel.SearchResultsI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceI; +import jalview.io.DataSourceType; 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.LinkedHashSet; -import java.util.Set; +import java.util.ArrayList; +import java.util.List; import org.testng.annotations.BeforeClass; import org.testng.annotations.BeforeMethod; @@ -26,51 +56,55 @@ import org.testng.annotations.Test; public class AlignViewportTest { + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + AlignmentI al; + AlignViewport testee; @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) + @BeforeMethod(alwaysRun = true) public void setUp() { SequenceI seq1 = new Sequence("Seq1", "ABC"); SequenceI seq2 = new Sequence("Seq2", "ABC"); SequenceI seq3 = new Sequence("Seq3", "ABC"); - SequenceI[] seqs = new SequenceI[] - { seq1, seq2, seq3 }; + SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3 }; al = new Alignment(seqs); al.setDataset(null); testee = new AlignViewport(al); } - @Test(groups ={ "Functional" }) + @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")); + .addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb")); al.getSequenceAt(2).getDatasetSequence() - .addPDBId( - new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb")); + .addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb")); al.getSequenceAt(1).getDatasetSequence() - .addPDBId( - new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb")); + .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 @@ -86,8 +120,8 @@ public class AlignViewportTest /* * run method under test */ - SequenceI[][] seqs = testee.collateForPDB(new PDBEntry[] - { pdb1, pdb2, pdb3 }); + SequenceI[][] seqs = testee.collateForPDB(new PDBEntry[] { pdb1, pdb2, + pdb3 }); // seq1 and seq3 refer to PDBEntry[0] assertEquals(2, seqs[0].length); @@ -106,110 +140,245 @@ public class AlignViewportTest * Test that a mapping is not deregistered when a second view is closed but * the first still holds a reference to the mapping */ - @Test(groups ={ "Functional" }) + @Test(groups = { "Functional" }) public void testDeregisterMapping_onCloseView() { /* * alignment with reference to mappings */ AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded( - ">Seq1\nCAGT\n", FormatAdapter.PASTE); - + ">Seq1\nCAGT\n", DataSourceType.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(); - - Set mappings = new LinkedHashSet(); + acf2.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 4, 1 }, + 1, 1)); + + List mappings = new ArrayList(); mappings.add(acf1); mappings.add(acf2); af1.getViewport().getAlignment().setCodonFrames(mappings); af1.newView_actionPerformed(null); - + /* * Verify that creating the alignment for the new View has registered the * mappings */ StructureSelectionManager ssm = StructureSelectionManager .getStructureSelectionManager(Desktop.instance); - assertEquals(2, ssm.seqmappings.size()); - assertTrue(ssm.seqmappings.contains(acf1)); - assertTrue(ssm.seqmappings.contains(acf2)); - + assertEquals(2, ssm.getSequenceMappings().size()); + assertTrue(ssm.getSequenceMappings().contains(acf1)); + assertTrue(ssm.getSequenceMappings().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.seqmappings.size()); - assertTrue(ssm.seqmappings.contains(acf1)); - assertTrue(ssm.seqmappings.contains(acf2)); + assertEquals(2, ssm.getSequenceMappings().size()); + assertTrue(ssm.getSequenceMappings().contains(acf1)); + assertTrue(ssm.getSequenceMappings().contains(acf2)); } /** - * Test that a mapping is not deregistered if an alignment holds a reference - * to it + * Test that a mapping is deregistered if no alignment holds a reference to it */ - @Test(groups ={ "Functional" }) - public void testDeregisterMapping_withAlignmentReference() + @Test(groups = { "Functional" }) + public void testDeregisterMapping_withNoReference() { Desktop d = Desktop.instance; assertNotNull(d); - - /* - * alignment with reference to mappings - */ + StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + ssm.resetAll(); + AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded( - ">Seq1\nCAGT\n", FormatAdapter.PASTE); - + ">Seq1\nRSVQ\n", DataSourceType.PASTE); + AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded( + ">Seq2\nDGEL\n", DataSourceType.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(); - - Set mappings = new LinkedHashSet(); - mappings.add(acf1); - mappings.add(acf2); - af1.getViewport().getAlignment().setCodonFrames(mappings); - StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); + 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); + af1.getViewport().getAlignment().setCodonFrames(mappings1); + + List mappings2 = new ArrayList(); + mappings2.add(acf2); + mappings2.add(acf3); + af2.getViewport().getAlignment().setCodonFrames(mappings2); /* - * Add one and remove it. + * AlignFrame1 has mapping acf1, AlignFrame2 has acf2 and acf3 */ + + List ssmMappings = ssm.getSequenceMappings(); + assertEquals(0, ssmMappings.size()); ssm.registerMapping(acf1); - ssm.deregisterMapping(acf1); - assertEquals(1, ssm.seqmappings.size()); - assertTrue(ssm.seqmappings.contains(acf1)); + assertEquals(1, ssmMappings.size()); + ssm.registerMapping(acf2); + assertEquals(2, ssmMappings.size()); + ssm.registerMapping(acf3); + assertEquals(3, ssmMappings.size()); + + /* + * Closing AlignFrame2 should remove its mappings from + * StructureSelectionManager, since AlignFrame1 has no reference to them + */ + af2.closeMenuItem_actionPerformed(true); + assertEquals(1, ssmMappings.size()); + assertTrue(ssmMappings.contains(acf1)); } /** - * Test that a mapping is deregistered if no alignment holds a reference to it + * Test that a mapping is not deregistered if another alignment holds a + * reference to it */ - @Test(groups ={ "Functional" }) - public void testDeregisterMapping_withNoReference() + @Test(groups = { "Functional" }) + public void testDeregisterMapping_withReference() { Desktop d = Desktop.instance; assertNotNull(d); - - /* - * alignment with reference to mappings - */ + StructureSelectionManager ssm = StructureSelectionManager + .getStructureSelectionManager(Desktop.instance); + ssm.resetAll(); + AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded( - ">Seq1\nCAGT\n", FormatAdapter.PASTE); - + ">Seq1\nRSVQ\n", DataSourceType.PASTE); + AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded( + ">Seq2\nDGEL\n", DataSourceType.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(); - - Set mappings = new LinkedHashSet(); - mappings.add(acf2); - af1.getViewport().getAlignment().setCodonFrames(mappings); - StructureSelectionManager ssm = StructureSelectionManager - .getStructureSelectionManager(Desktop.instance); - + 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); + mappings1.add(acf2); + af1.getViewport().getAlignment().setCodonFrames(mappings1); + + List mappings2 = new ArrayList(); + mappings2.add(acf2); + mappings2.add(acf3); + af2.getViewport().getAlignment().setCodonFrames(mappings2); + /* - * Add one and remove it. + * AlignFrame1 has mappings acf1 and acf2, AlignFrame2 has acf2 and acf3 */ + + List ssmMappings = ssm.getSequenceMappings(); + assertEquals(0, ssmMappings.size()); ssm.registerMapping(acf1); - assertEquals(1, ssm.seqmappings.size()); - assertTrue(ssm.seqmappings.contains(acf1)); - ssm.deregisterMapping(acf1); - assertEquals(0, ssm.seqmappings.size()); + assertEquals(1, ssmMappings.size()); + ssm.registerMapping(acf2); + assertEquals(2, ssmMappings.size()); + ssm.registerMapping(acf3); + assertEquals(3, ssmMappings.size()); + + /* + * Closing AlignFrame2 should remove mapping acf3 from + * StructureSelectionManager, but not acf2, since AlignFrame1 still has a + * reference to it + */ + af2.closeMenuItem_actionPerformed(true); + assertEquals(2, ssmMappings.size()); + assertTrue(ssmMappings.contains(acf1)); + 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", DataSourceType.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("DEFAULT_COLOUR_PROT", "None"); + Cache.applicationProperties.setProperty("SHOW_CONSERVATION", + Boolean.TRUE.toString()); + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/uniref50.fa", DataSourceType.FILE); + ColourSchemeI cs = new PIDColourScheme(); + af.getViewport().setGlobalColourScheme(cs); + assertFalse(af.getViewport().getViewportColourScheme() + .conservationApplied()); + } + + @Test(groups = { "Functional" }) + public void testSetGetHasSearchResults() + { + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded( + "examples/uniref50.fa", DataSourceType.FILE); + SearchResultsI sr = new SearchResults(); + SequenceI s1 = af.getViewport().getAlignment().getSequenceAt(0); + + // create arbitrary range on first sequence + sr.addResult(s1, s1.getStart() + 10, s1.getStart() + 15); + + // test set + af.getViewport().setSearchResults(sr); + // has -> true + assertTrue(af.getViewport().hasSearchResults()); + // get == original + assertEquals(sr, af.getViewport().getSearchResults()); + + // set(null) results in has -> false + + af.getViewport().setSearchResults(null); + assertFalse(af.getViewport().hasSearchResults()); } }