package jalview.structure;
import jalview.analysis.AlignSeq;
+import jalview.api.AlignmentViewPanel;
import jalview.api.StructureSelectionManagerProvider;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
import jalview.io.AppletFormatAdapter;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
*/
Set<AlignedCodonFrame> seqmappings = new LinkedHashSet<AlignedCodonFrame>();
- /*
- * Reference counters for the above mappings. Remove mappings when ref count
- * goes to zero.
- */
- private Map<AlignedCodonFrame, Integer> seqMappingRefCounts = new HashMap<AlignedCodonFrame, Integer>();
-
private List<CommandListener> commandListeners = new ArrayList<CommandListener>();
private List<SelectionListener> sel_listeners = new ArrayList<SelectionListener>();
if (resNum != tmp.resNumber && tmp.alignmentMapping != -1)
{
resNum = tmp.resNumber;
- mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber;
- mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex;
+ if (tmp.alignmentMapping >= -1)
+ {
+ // TODO (JAL-1836) address root cause: negative residue no in PDB file
+ mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber;
+ mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex;
+ }
}
index++;
}
/**
- * Decrement the reference counter for each of the given mappings, and remove
- * it entirely if its reference counter reduces to zero.
+ * Deregister each mapping in the set, unless there is still an alignment that
+ * holds a reference to it. Note we do not update the set itself, as it may be
+ * shared with an alignment view which is still open.
*
* @param set
*/
- public void removeMappings(Set<AlignedCodonFrame> set)
+ public void deregisterMappings(Set<AlignedCodonFrame> set)
{
if (set != null)
{
for (AlignedCodonFrame acf : set)
{
- removeMapping(acf);
+ deregisterMapping(acf);
}
}
}
/**
- * Decrement the reference counter for the given mapping, and remove it
- * entirely if its reference counter reduces to zero.
+ * Remove the given mapping provided no alignment holds a reference to it
*
* @param acf
*/
- public void removeMapping(AlignedCodonFrame acf)
+ public void deregisterMapping(AlignedCodonFrame acf)
{
- if (acf != null && seqmappings.contains(acf))
+ if (noReferencesTo(acf))
{
- int count = seqMappingRefCounts.get(acf);
- count--;
- if (count > 0)
- {
- seqMappingRefCounts.put(acf, count);
+ boolean removed = seqmappings.remove(acf);
+ if (removed && seqmappings.isEmpty())
+ { // debug
+ System.out.println("All mappings removed");
}
- else
+ }
+ }
+
+ /**
+ * Answers true if no alignment holds a reference to the given mapping
+ *
+ * @param acf
+ * @return
+ */
+ protected boolean noReferencesTo(AlignedCodonFrame acf)
+ {
+ AlignFrame[] frames = Desktop.getAlignFrames();
+ if (frames == null)
+ {
+ return true;
+ }
+ for (AlignFrame af : frames)
+ {
+ for (AlignmentViewPanel ap : af.getAlignPanels())
{
- seqmappings.remove(acf);
- seqMappingRefCounts.remove(acf);
- if (seqmappings.isEmpty())
- { // debug
- System.out.println("All mappings removed");
+ AlignmentI al = ap.getAlignment();
+ if (al != null && al.getCodonFrames().contains(acf))
+ {
+ return false;
}
}
}
+ return true;
}
/**
- * Add each of the given codonFrames to the stored set. If not aready present,
- * increments its reference count instead.
+ * Add each of the given codonFrames to the stored set, if not aready present.
*
* @param set
*/
- public void addMappings(Set<AlignedCodonFrame> set)
+ public void registerMappings(Set<AlignedCodonFrame> set)
{
if (set != null)
{
for (AlignedCodonFrame acf : set)
{
- addMapping(acf);
+ registerMapping(acf);
}
}
}
/**
- * Add the given mapping to the stored set, or if already stored, increment
- * its reference counter.
+ * Add the given mapping to the stored set, unless already stored.
*/
- public void addMapping(AlignedCodonFrame acf)
+ public void registerMapping(AlignedCodonFrame acf)
{
if (acf != null)
{
- if (seqmappings.contains(acf))
- {
- seqMappingRefCounts.put(acf, seqMappingRefCounts.get(acf) + 1);
- }
- else
+ if (!seqmappings.contains(acf))
{
seqmappings.add(acf);
- seqMappingRefCounts.put(acf, 1);
}
}
}
{
seqmappings.clear();
}
- if (seqMappingRefCounts != null)
- {
- seqMappingRefCounts.clear();
- }
if (sel_listeners != null)
{
sel_listeners.clear();
}
return null;
}
-
- /**
- * Returns the reference count for a mapping
- *
- * @param acf
- * @return
- */
- protected int getMappingReferenceCount(AlignedCodonFrame acf)
- {
- if (seqMappingRefCounts == null)
- {
- return 0;
- }
- Integer count = seqMappingRefCounts.get(acf);
- return (count == null ? 0 : count.intValue());
- }
}
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 / commitdiff