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;
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;
{
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)
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
acf2.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 4, 1 },
1, 1));
- List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
+ List<AlignedCodonFrame> mappings = new ArrayList<>();
mappings.add(acf1);
mappings.add(acf2);
af1.getViewport().getAlignment().setCodonFrames(mappings);
*/
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
- assertEquals(2, ssm.getSequenceMappings().size());
- assertTrue(ssm.getSequenceMappings().contains(acf1));
- assertTrue(ssm.getSequenceMappings().contains(acf2));
+ List<AlignedCodonFrame> 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));
}
/**
acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
12 }, 1, 1));
- List<AlignedCodonFrame> mappings1 = new ArrayList<AlignedCodonFrame>();
+ List<AlignedCodonFrame> mappings1 = new ArrayList<>();
mappings1.add(acf1);
af1.getViewport().getAlignment().setCodonFrames(mappings1);
- List<AlignedCodonFrame> mappings2 = new ArrayList<AlignedCodonFrame>();
+ List<AlignedCodonFrame> mappings2 = new ArrayList<>();
mappings2.add(acf2);
mappings2.add(acf3);
af2.getViewport().getAlignment().setCodonFrames(mappings2);
acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
12 }, 1, 1));
- List<AlignedCodonFrame> mappings1 = new ArrayList<AlignedCodonFrame>();
+ List<AlignedCodonFrame> mappings1 = new ArrayList<>();
mappings1.add(acf1);
mappings1.add(acf2);
af1.getViewport().getAlignment().setCodonFrames(mappings1);
- List<AlignedCodonFrame> mappings2 = new ArrayList<AlignedCodonFrame>();
+ List<AlignedCodonFrame> mappings2 = new ArrayList<>();
mappings2.add(acf2);
mappings2.add(acf3);
af2.getViewport().getAlignment().setCodonFrames(mappings2);
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(
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());
+ }
}
git://source.jalview.org / jalview.git / blobdiff