package jalview.structure;
import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertTrue;
import jalview.datamodel.AlignedCodonFrame;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
+import jalview.io.FileLoader;
+import jalview.io.FormatAdapter;
import java.util.HashSet;
+import java.util.LinkedHashSet;
import java.util.Set;
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
{
private StructureSelectionManager ssm;
+ @BeforeClass(alwaysRun = true)
+ public static void setUpBeforeClass() throws Exception
+ {
+ jalview.bin.Jalview.main(new String[] { "-props",
+ "test/jalview/testProps.jvprops" });
+ }
+
@BeforeMethod(alwaysRun = true)
public void setUp()
{
}
@Test(groups ={ "Functional" })
- public void testAddMapping()
+ public void testRegisterMapping()
{
AlignedCodonFrame acf1 = new AlignedCodonFrame();
AlignedCodonFrame acf2 = new AlignedCodonFrame();
- /*
- * One mapping only.
- */
- ssm.addMapping(acf1);
+ ssm.registerMapping(acf1);
assertEquals(1, ssm.seqmappings.size());
assertTrue(ssm.seqmappings.contains(acf1));
- assertEquals(1, ssm.getMappingReferenceCount(acf1));
- /*
- * A second mapping.
- */
- ssm.addMapping(acf2);
+ ssm.registerMapping(acf2);
assertEquals(2, ssm.seqmappings.size());
assertTrue(ssm.seqmappings.contains(acf1));
assertTrue(ssm.seqmappings.contains(acf2));
- assertEquals(1, ssm.getMappingReferenceCount(acf1));
- assertEquals(1, ssm.getMappingReferenceCount(acf2));
/*
- * A second reference to the first mapping.
+ * Re-adding the first mapping does nothing
*/
- ssm.addMapping(acf1);
+ ssm.registerMapping(acf1);
assertEquals(2, ssm.seqmappings.size());
assertTrue(ssm.seqmappings.contains(acf1));
assertTrue(ssm.seqmappings.contains(acf2));
- assertEquals(2, ssm.getMappingReferenceCount(acf1));
- assertEquals(1, ssm.getMappingReferenceCount(acf2));
}
@Test(groups ={ "Functional" })
- public void testAddMappings()
+ public void testRegisterMappings()
{
AlignedCodonFrame acf1 = new AlignedCodonFrame();
AlignedCodonFrame acf2 = new AlignedCodonFrame();
set2.add(acf3);
/*
- * Adding both sets adds acf2 twice and acf1 and acf3 once each.
+ * Add both sets twice; each mapping should be added once only
*/
- ssm.addMappings(set1);
- ssm.addMappings(set2);
+ ssm.registerMappings(set1);
+ ssm.registerMappings(set1);
+ ssm.registerMappings(set2);
+ ssm.registerMappings(set2);
assertEquals(3, ssm.seqmappings.size());
assertTrue(ssm.seqmappings.contains(acf1));
assertTrue(ssm.seqmappings.contains(acf2));
assertTrue(ssm.seqmappings.contains(acf3));
- assertEquals(1, ssm.getMappingReferenceCount(acf1));
- assertEquals(2, ssm.getMappingReferenceCount(acf2));
- assertEquals(1, ssm.getMappingReferenceCount(acf3));
}
+ /**
+ * Test that a mapping is not deregistered if an alignment holds a reference
+ * to it
+ */
@Test(groups ={ "Functional" })
- public void testRemoveMapping()
+ public void testDeregisterMapping_withAlignmentReference()
{
+ Desktop d = Desktop.instance;
+ assertNotNull(d);
+
+ /*
+ * alignment with reference to mappings
+ */
+ AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
+ ">Seq1\nCAGT\n", FormatAdapter.PASTE);
+
AlignedCodonFrame acf1 = new AlignedCodonFrame();
AlignedCodonFrame acf2 = new AlignedCodonFrame();
+ Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
+ mappings.add(acf1);
+ mappings.add(acf2);
+ af1.getViewport().getAlignment().setCodonFrames(mappings);
+
/*
* Add one and remove it.
*/
- ssm.addMapping(acf1);
- ssm.removeMapping(acf1);
- ssm.removeMapping(acf2);
- assertEquals(0, ssm.seqmappings.size());
- assertEquals(0, ssm.getMappingReferenceCount(acf1));
- assertEquals(0, ssm.getMappingReferenceCount(acf2));
+ ssm.registerMapping(acf1);
+ ssm.deregisterMapping(acf1);
+ assertEquals(1, ssm.seqmappings.size());
+ assertTrue(ssm.seqmappings.contains(acf1));
+ }
+ /**
+ * Test that a mapping is deregistered if no alignment holds a reference to it
+ */
+ @Test(groups ={ "Functional" })
+ public void testDeregisterMapping_withNoReference()
+ {
+ Desktop d = Desktop.instance;
+ assertNotNull(d);
+
/*
- * Add one twice and remove it once.
+ * alignment with reference to mappings
*/
- ssm.addMapping(acf1);
- ssm.addMapping(acf2);
- ssm.addMapping(acf1);
- ssm.removeMapping(acf1);
- assertEquals(2, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
- assertTrue(ssm.seqmappings.contains(acf2));
- assertEquals(1, ssm.getMappingReferenceCount(acf1));
- assertEquals(1, ssm.getMappingReferenceCount(acf2));
-
+ AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
+ ">Seq1\nCAGT\n", FormatAdapter.PASTE);
+
+ AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ AlignedCodonFrame acf2 = new AlignedCodonFrame();
+
+ Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
+ mappings.add(acf2);
+ af1.getViewport().getAlignment().setCodonFrames(mappings);
+
/*
- * Remove both once more to clear the set.
+ * Add one and remove it.
*/
- ssm.removeMapping(acf1);
- ssm.removeMapping(acf2);
+ ssm.registerMapping(acf1);
+ assertEquals(1, ssm.seqmappings.size());
+ assertTrue(ssm.seqmappings.contains(acf1));
+ ssm.deregisterMapping(acf1);
assertEquals(0, ssm.seqmappings.size());
- assertEquals(0, ssm.getMappingReferenceCount(acf1));
- assertEquals(0, ssm.getMappingReferenceCount(acf2));
}
+ /**
+ * 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" })
- public void testRemoveMappings()
+ public void testDeregisterMapping_onCloseView()
{
- AlignedCodonFrame acf1 = new AlignedCodonFrame();
- AlignedCodonFrame acf2 = new AlignedCodonFrame();
- AlignedCodonFrame acf3 = new AlignedCodonFrame();
-
/*
- * Initial ref counts are 3/2/1:
+ * alignment with reference to mappings
*/
- ssm.addMapping(acf1);
- ssm.addMapping(acf1);
- ssm.addMapping(acf1);
- ssm.addMapping(acf2);
- ssm.addMapping(acf2);
- ssm.addMapping(acf3);
-
- Set<AlignedCodonFrame> set1 = new HashSet<AlignedCodonFrame>();
- set1.add(acf1);
- set1.add(acf2);
- Set<AlignedCodonFrame> set2 = new HashSet<AlignedCodonFrame>();
- set2.add(acf2);
- set2.add(acf3);
+ AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
+ ">Seq1\nCAGT\n", FormatAdapter.PASTE);
+
+ AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ AlignedCodonFrame acf2 = new AlignedCodonFrame();
+
+ Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
+ mappings.add(acf1);
+ mappings.add(acf2);
+ af1.getViewport().getAlignment().setCodonFrames(mappings);
+ af1.newView_actionPerformed(null);
/*
- * Remove one ref each to acf1, acf2, counts are now 2/1/1:
+ * Verify that creating the alignment for the new View has registered the
+ * mappings
*/
- ssm.removeMappings(set1);
- assertEquals(3, ssm.seqmappings.size());
+ ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ assertEquals(2, ssm.seqmappings.size());
assertTrue(ssm.seqmappings.contains(acf1));
assertTrue(ssm.seqmappings.contains(acf2));
- assertTrue(ssm.seqmappings.contains(acf3));
- assertEquals(2, ssm.getMappingReferenceCount(acf1));
- assertEquals(1, ssm.getMappingReferenceCount(acf2));
- assertEquals(1, ssm.getMappingReferenceCount(acf3));
/*
- * Remove one ref each to acf2, acf3 - they are removed
+ * Close the second view. Verify that mappings are not removed as the first
+ * view still holds a reference to them.
*/
- ssm.removeMappings(set2);
- assertEquals(1, ssm.seqmappings.size());
+ af1.closeMenuItem_actionPerformed(false);
+ assertEquals(2, ssm.seqmappings.size());
assertTrue(ssm.seqmappings.contains(acf1));
- assertEquals(2, ssm.getMappingReferenceCount(acf1));
+ assertTrue(ssm.seqmappings.contains(acf2));
}
}
git://source.jalview.org / jalview.git / blobdiff