+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * 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;
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
/*
* 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);
* 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<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
+ acf2.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 4, 1 },
+ 1, 1));
+
+ List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
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<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
- 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<AlignedCodonFrame> mappings1 = new ArrayList<AlignedCodonFrame>();
+ mappings1.add(acf1);
+ af1.getViewport().getAlignment().setCodonFrames(mappings1);
+
+ List<AlignedCodonFrame> mappings2 = new ArrayList<AlignedCodonFrame>();
+ 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<AlignedCodonFrame> 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<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
- 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<AlignedCodonFrame> mappings1 = new ArrayList<AlignedCodonFrame>();
+ mappings1.add(acf1);
+ mappings1.add(acf2);
+ af1.getViewport().getAlignment().setCodonFrames(mappings1);
+
+ List<AlignedCodonFrame> mappings2 = new ArrayList<AlignedCodonFrame>();
+ 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<AlignedCodonFrame> 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());
}
}
git://source.jalview.org / jalview.git / blobdiff