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.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
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.structure.StructureSelectionManager;
+import java.util.LinkedHashSet;
+import java.util.Set;
+
+import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
AlignmentI al;
AlignViewport testee;
+ @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()
{
// 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
+ */
+ @Test(groups ={ "Functional" })
+ public void testDeregisterMapping_onCloseView()
+ {
+ /*
+ * 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);
+ 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));
+
+ /*
+ * 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));
+ }
+
+ /**
+ * 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);
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.resetAll();
+
+ AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
+ ">Seq1\nRSVQ\n", FormatAdapter.PASTE);
+ AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
+ ">Seq2\nDGEL\n", FormatAdapter.PASTE);
+
+ AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ AlignedCodonFrame acf2 = new AlignedCodonFrame();
+ AlignedCodonFrame acf3 = new AlignedCodonFrame();
+
+ Set<AlignedCodonFrame> mappings1 = new LinkedHashSet<AlignedCodonFrame>();
+ mappings1.add(acf1);
+ af1.getViewport().getAlignment().setCodonFrames(mappings1);
+
+ Set<AlignedCodonFrame> mappings2 = new LinkedHashSet<AlignedCodonFrame>();
+ mappings2.add(acf2);
+ mappings2.add(acf3);
+ af2.getViewport().getAlignment().setCodonFrames(mappings2);
+
+ /*
+ * AlignFrame1 has mapping acf1, AlignFrame2 has acf2 and acf3
+ */
+
+ Set<AlignedCodonFrame> ssmMappings = ssm.seqmappings;
+ assertEquals(0, ssmMappings.size());
+ ssm.registerMapping(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 not deregistered if another alignment holds a
+ * reference to it
+ */
+ @Test(groups ={ "Functional" })
+ public void testDeregisterMapping_withReference()
+ {
+ Desktop d = Desktop.instance;
+ assertNotNull(d);
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ ssm.resetAll();
+
+ AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
+ ">Seq1\nRSVQ\n", FormatAdapter.PASTE);
+ AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
+ ">Seq2\nDGEL\n", FormatAdapter.PASTE);
+
+ AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ AlignedCodonFrame acf2 = new AlignedCodonFrame();
+ AlignedCodonFrame acf3 = new AlignedCodonFrame();
+
+ Set<AlignedCodonFrame> mappings1 = new LinkedHashSet<AlignedCodonFrame>();
+ mappings1.add(acf1);
+ mappings1.add(acf2);
+ af1.getViewport().getAlignment().setCodonFrames(mappings1);
+
+ Set<AlignedCodonFrame> mappings2 = new LinkedHashSet<AlignedCodonFrame>();
+ mappings2.add(acf2);
+ mappings2.add(acf3);
+ af2.getViewport().getAlignment().setCodonFrames(mappings2);
+
+ /*
+ * AlignFrame1 has mappings acf1 and acf2, AlignFrame2 has acf2 and acf3
+ */
+
+ Set<AlignedCodonFrame> ssmMappings = ssm.seqmappings;
+ assertEquals(0, ssmMappings.size());
+ ssm.registerMapping(acf1);
+ 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));
+ }
}
git://source.jalview.org / jalview.git / blobdiff