if (closeAllTabs)
{
+ /*
+ * this will raise an INTERNAL_FRAME_CLOSED event and this method will
+ * be called recursively, with the frame now in 'closed' state
+ */
this.setClosed(true);
}
} catch (Exception ex)
}
/*
- * Views share the same edits, undo and redo stacks, mappings.
+ * Views share the same edits undo and redo stacks
*/
newap.av.setHistoryList(viewport.getHistoryList());
newap.av.setRedoList(viewport.getRedoList());
- newap.av.getAlignment().setCodonFrames(
- viewport.getAlignment().getCodonFrames());
+
+ /*
+ * Views share the same mappings; need to deregister any new mappings
+ * created by copyAlignPanel, and register the new reference to the shared
+ * mappings
+ */
+ newap.av.replaceMappings(viewport.getAlignment());
newap.av.viewName = getNewViewName(viewTitle);
"Exception during translation. Please report this !", ex);
final String msg = MessageManager
.getString("label.error_when_translating_sequences_submit_bug_report");
- final String title = MessageManager
+ final String errorTitle = MessageManager
.getString("label.implementation_error")
+ MessageManager.getString("translation_failed");
- JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
+ JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
JOptionPane.ERROR_MESSAGE);
return;
}
{
final String msg = MessageManager
.getString("label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
- final String title = MessageManager
+ final String errorTitle = MessageManager
.getString("label.translation_failed");
- JOptionPane.showMessageDialog(Desktop.desktop, msg, title,
+ JOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
JOptionPane.WARNING_MESSAGE);
}
else
if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
{
final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
- viewport.openSplitFrame(af, new Alignment(seqs),
- al.getCodonFrames());
+ viewport.openSplitFrame(af, new Alignment(seqs));
}
else
{
sf.setComplementVisible(this, show);
}
}
-
}
class PrintThread extends Thread
import jalview.api.ViewStyleI;
import jalview.bin.Cache;
import jalview.commands.CommandI;
-import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.List;
-import java.util.Set;
import java.util.Vector;
import javax.swing.JInternalFrame;
*/
public void setAlignment(AlignmentI align)
{
- if (alignment != null && alignment.getCodonFrames() != null)
+ replaceMappings(align);
+ this.alignment = align;
+ }
+
+ /**
+ * Replace any codon mappings for this viewport with those for the given
+ * viewport
+ *
+ * @param align
+ */
+ public void replaceMappings(AlignmentI align)
+ {
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+
+ /*
+ * Deregister current mappings (if any)
+ */
+ if (alignment != null)
{
- StructureSelectionManager.getStructureSelectionManager(
- Desktop.instance).removeMappings(alignment.getCodonFrames());
+ ssm.removeMappings(alignment.getCodonFrames());
}
- this.alignment = align;
- if (alignment != null && alignment.getCodonFrames() != null)
+
+ /*
+ * Register new mappings (if any)
+ */
+ if (align != null)
{
- StructureSelectionManager.getStructureSelectionManager(
- Desktop.instance).addMappings(alignment.getCodonFrames());
+ ssm.addMappings(align.getCodonFrames());
+ }
+
+ /*
+ * replace mappings on our alignment
+ */
+ if (alignment != null && align != null)
+ {
+ alignment.setCodonFrames(align.getCodonFrames());
}
}
AlignmentUtils.mapProteinToCdna(protein, cdna);
/*
- * Create the AlignFrame for the added alignment. Note this will include the
- * cDNA consensus annotation if it is protein (because the alignment holds
- * mappings to nucleotide)
+ * Create the AlignFrame for the added alignment. If it is protein, mappings
+ * are registered with StructureSelectionManager as a side-effect.
*/
AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
if (openSplitPane)
{
al.alignAs(thisAlignment);
- protein = openSplitFrame(newAlignFrame, thisAlignment,
- protein.getCodonFrames());
+ protein = openSplitFrame(newAlignFrame, thisAlignment);
}
- /*
- * Register the mappings (held on the protein alignment) with the
- * StructureSelectionManager (for mouseover linking).
- */
- final StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
- ssm.addMappings(protein.getCodonFrames());
-
return true;
}
* containing a new alignment to be shown
* @param complement
* cdna/protein complement alignment to show in the other split half
- * @param mappings
* @return the protein alignment in the split frame
*/
protected AlignmentI openSplitFrame(AlignFrame newAlignFrame,
- AlignmentI complement, Set<AlignedCodonFrame> mappings)
+ AlignmentI complement)
{
/*
* Make a new frame with a copy of the alignment we are adding to. If this
- * is protein, the new frame will have a cDNA consensus annotation row
- * added.
+ * is protein, the mappings to cDNA will be registered with StructureSelectionManager as a side-effect.
*/
AlignFrame copyMe = new AlignFrame(complement,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
: newAlignFrame;
final AlignFrame cdnaFrame = al.isNucleotide() ? newAlignFrame
: copyMe;
- AlignmentI protein = proteinFrame.viewport.getAlignment();
- protein.setCodonFrames(mappings);
-
cdnaFrame.setVisible(true);
proteinFrame.setVisible(true);
String linkedTitle = MessageManager
JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
- return protein;
+ return proteinFrame.viewport.getAlignment();
}
public AnnotationColumnChooser getAnnotationColumnSelectionState()
delegate.openFrame(f);
}
+ @Override
public void resizeFrame(JComponent f, int newX, int newY, int newWidth,
int newHeight)
{
- Rectangle b = desktop.getBounds();
if (newY < 0)
{
newY = 0;
if (v_client != null)
{
// TODO clear binding to vamsas document objects on close_all
+ }
+ /*
+ * reset state of singleton objects as appropriate (clear down session state
+ * when all windows are closed)
+ */
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(this);
+ if (ssm != null)
+ {
+ ssm.resetAll();
}
}
}
}
+ @Override
public void paintComponent(Graphics g)
{
if (showMemoryUsage && g != null && df != null)
*/
package jalview.structure;
+import jalview.analysis.AlignSeq;
+import jalview.api.StructureSelectionManagerProvider;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.OrderCommand;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
+
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.Arrays;
import MCview.PDBChain;
import MCview.PDBfile;
-import jalview.analysis.AlignSeq;
-import jalview.api.StructureSelectionManagerProvider;
-import jalview.commands.CommandI;
-import jalview.commands.EditCommand;
-import jalview.commands.OrderCommand;
-import jalview.datamodel.AlignedCodonFrame;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.Annotation;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
-import jalview.util.MappingUtils;
-import jalview.util.MessageManager;
-
public class StructureSelectionManager
{
public final static String NEWLINE = System.lineSeparator();
* Reference counters for the above mappings. Remove mappings when ref count
* goes to zero.
*/
- Map<AlignedCodonFrame, Integer> seqMappingRefCounts = new HashMap<AlignedCodonFrame, Integer>();
+ private Map<AlignedCodonFrame, Integer> seqMappingRefCounts = new HashMap<AlignedCodonFrame, Integer>();
private List<CommandListener> commandListeners = new ArrayList<CommandListener>();
{
results = MappingUtils.buildSearchResults(seq, index,
seqmappings);
- }
+ }
if (handlingVamsasMo)
{
results.addResult(seq, index, index);
}
- seqListener.highlightSequence(results);
+ if (!results.isEmpty())
+ {
+ seqListener.highlightSequence(results);
+ }
}
}
}
{
seqmappings.remove(acf);
seqMappingRefCounts.remove(acf);
+ if (seqmappings.isEmpty())
+ { // debug
+ System.out.println("All mappings removed");
+ }
}
}
}
}
}
+ /**
+ * Resets this object to its initial state by removing all registered
+ * listeners, codon mappings, PDB file mappings
+ */
+ public void resetAll()
+ {
+ if (mappings != null)
+ {
+ mappings.clear();
+ }
+ if (seqmappings != null)
+ {
+ seqmappings.clear();
+ }
+ if (seqMappingRefCounts != null)
+ {
+ seqMappingRefCounts.clear();
+ }
+ if (sel_listeners != null)
+ {
+ sel_listeners.clear();
+ }
+ if (listeners != null)
+ {
+ listeners.clear();
+ }
+ if (commandListeners != null)
+ {
+ commandListeners.clear();
+ }
+ if (view_listeners != null)
+ {
+ view_listeners.clear();
+ }
+ if (pdbFileNameId != null)
+ {
+ pdbFileNameId.clear();
+ }
+ if (pdbIdFileName != null)
+ {
+ pdbIdFileName.clear();
+ }
+ }
+
public void addSelectionListener(SelectionListener selecter)
{
if (!sel_listeners.contains(selecter))
}
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());
+ }
}
ssm.addMapping(acf1);
assertEquals(1, ssm.seqmappings.size());
assertTrue(ssm.seqmappings.contains(acf1));
- assertEquals(1, ssm.seqMappingRefCounts.size());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf1).intValue());
+ assertEquals(1, ssm.getMappingReferenceCount(acf1));
/*
* A second mapping.
assertEquals(2, ssm.seqmappings.size());
assertTrue(ssm.seqmappings.contains(acf1));
assertTrue(ssm.seqmappings.contains(acf2));
- assertEquals(2, ssm.seqMappingRefCounts.size());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf1).intValue());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf2).intValue());
+ assertEquals(1, ssm.getMappingReferenceCount(acf1));
+ assertEquals(1, ssm.getMappingReferenceCount(acf2));
/*
* A second reference to the first mapping.
assertEquals(2, ssm.seqmappings.size());
assertTrue(ssm.seqmappings.contains(acf1));
assertTrue(ssm.seqmappings.contains(acf2));
- assertEquals(2, ssm.seqMappingRefCounts.size());
- assertEquals(2, ssm.seqMappingRefCounts.get(acf1).intValue());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf2).intValue());
+ assertEquals(2, ssm.getMappingReferenceCount(acf1));
+ assertEquals(1, ssm.getMappingReferenceCount(acf2));
}
@Test(groups ={ "Functional" })
assertTrue(ssm.seqmappings.contains(acf1));
assertTrue(ssm.seqmappings.contains(acf2));
assertTrue(ssm.seqmappings.contains(acf3));
- assertEquals(3, ssm.seqMappingRefCounts.size());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf1).intValue());
- assertEquals(2, ssm.seqMappingRefCounts.get(acf2).intValue());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf3).intValue());
+ assertEquals(1, ssm.getMappingReferenceCount(acf1));
+ assertEquals(2, ssm.getMappingReferenceCount(acf2));
+ assertEquals(1, ssm.getMappingReferenceCount(acf3));
}
@Test(groups ={ "Functional" })
{
AlignedCodonFrame acf1 = new AlignedCodonFrame();
AlignedCodonFrame acf2 = new AlignedCodonFrame();
- ssm.addMapping(acf1);
/*
* Add one and remove it.
*/
+ ssm.addMapping(acf1);
ssm.removeMapping(acf1);
ssm.removeMapping(acf2);
assertEquals(0, ssm.seqmappings.size());
- assertEquals(0, ssm.seqMappingRefCounts.size());
+ assertEquals(0, ssm.getMappingReferenceCount(acf1));
+ assertEquals(0, ssm.getMappingReferenceCount(acf2));
/*
* Add one twice and remove it once.
assertEquals(2, ssm.seqmappings.size());
assertTrue(ssm.seqmappings.contains(acf1));
assertTrue(ssm.seqmappings.contains(acf2));
- assertEquals(2, ssm.seqMappingRefCounts.size());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf1).intValue());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf2).intValue());
+ assertEquals(1, ssm.getMappingReferenceCount(acf1));
+ assertEquals(1, ssm.getMappingReferenceCount(acf2));
/*
* Remove both once more to clear the set.
ssm.removeMapping(acf1);
ssm.removeMapping(acf2);
assertEquals(0, ssm.seqmappings.size());
- assertEquals(0, ssm.seqMappingRefCounts.size());
+ assertEquals(0, ssm.getMappingReferenceCount(acf1));
+ assertEquals(0, ssm.getMappingReferenceCount(acf2));
}
@Test(groups ={ "Functional" })
assertTrue(ssm.seqmappings.contains(acf1));
assertTrue(ssm.seqmappings.contains(acf2));
assertTrue(ssm.seqmappings.contains(acf3));
- assertEquals(3, ssm.seqMappingRefCounts.size());
- assertEquals(2, ssm.seqMappingRefCounts.get(acf1).intValue());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf2).intValue());
- assertEquals(1, ssm.seqMappingRefCounts.get(acf3).intValue());
+ 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
ssm.removeMappings(set2);
assertEquals(1, ssm.seqmappings.size());
assertTrue(ssm.seqmappings.contains(acf1));
- assertEquals(1, ssm.seqMappingRefCounts.size());
- assertEquals(2, ssm.seqMappingRefCounts.get(acf1).intValue());
+ assertEquals(2, ssm.getMappingReferenceCount(acf1));
}
}
git://source.jalview.org / jalview.git / commitdiff