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.Enumeration;
import java.util.HashMap;
import java.util.IdentityHashMap;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
import java.util.Vector;
import MCview.Atom;
{
static IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> instances;
- StructureMapping[] mappings;
+ private List<StructureMapping> mappings = new ArrayList<StructureMapping>();
- private boolean processSecondaryStructure = false,
- secStructServices = false, addTempFacAnnot = false;
+ private boolean processSecondaryStructure = false;
+
+ private boolean secStructServices = false;
+
+ private boolean addTempFacAnnot = false;
+
+ /*
+ * Set of any registered mappings between (dataset) sequences.
+ */
+ Set<AlignedCodonFrame> seqmappings = new LinkedHashSet<AlignedCodonFrame>();
+
+ /*
+ * Reference counters for the above mappings. Remove mappings when ref count
+ * goes to zero.
+ */
+ Map<AlignedCodonFrame, Integer> seqMappingRefCounts = new HashMap<AlignedCodonFrame, Integer>();
+
+ private List<CommandListener> commandListeners = new ArrayList<CommandListener>();
+
+ private List<SelectionListener> sel_listeners = new ArrayList<SelectionListener>();
/**
* @return true if will try to use external services for processing secondary
*/
public void reportMapping()
{
- if (mappings == null)
+ if (mappings.isEmpty())
{
System.err.println("reportMapping: No PDB/Sequence mappings.");
}
else
{
- System.err.println("reportMapping: There are " + mappings.length
+ System.err.println("reportMapping: There are " + mappings.size()
+ " mappings.");
- for (int m = 0; m < mappings.length; m++)
+ int i = 0;
+ for (StructureMapping sm : mappings)
{
- System.err.println("mapping " + m + " : " + mappings[m].pdbfile);
+ System.err.println("mapping " + i++ + " : " + sm.pdbfile);
}
}
}
}
}
+ /**
+ * Returns the file name for a mapped PDB id (or null if not mapped).
+ *
+ * @param pdbid
+ * @return
+ */
public String alreadyMappedToFile(String pdbid)
{
- if (mappings != null)
+ for (StructureMapping sm : mappings)
{
- for (int i = 0; i < mappings.length; i++)
+ if (sm.getPdbId().equals(pdbid))
{
- if (mappings[i].getPdbId().equals(pdbid))
- {
- return mappings[i].pdbfile;
- }
+ return sm.pdbfile;
}
}
return null;
mappingDetails.toString());
if (forStructureView)
{
-
- if (mappings == null)
- {
- mappings = new StructureMapping[1];
- }
- else
- {
- StructureMapping[] tmp = new StructureMapping[mappings.length + 1];
- System.arraycopy(mappings, 0, tmp, 0, mappings.length);
- mappings = tmp;
- }
-
- mappings[mappings.length - 1] = newMapping;
+ mappings.add(newMapping);
}
maxChain.transferResidueAnnotation(newMapping, sqmpping);
}
}
}
- if (pdbs.size() > 0 && mappings != null)
+ if (pdbs.size() > 0)
{
- Vector tmp = new Vector();
- for (int i = 0; i < mappings.length; i++)
+ List<StructureMapping> tmp = new ArrayList<StructureMapping>();
+ for (StructureMapping sm : mappings)
{
- if (!pdbs.contains(mappings[i].pdbfile))
+ if (!pdbs.contains(sm.pdbfile))
{
- tmp.addElement(mappings[i]);
+ tmp.add(sm);
}
}
- mappings = new StructureMapping[tmp.size()];
- tmp.copyInto(mappings);
+ mappings = tmp;
}
}
// old or prematurely sent event
return;
}
- boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
SearchResults results = null;
SequenceI lastseq = null;
int lastipos = -1, indexpos;
{
results = new SearchResults();
}
- if (mappings != null)
+ for (StructureMapping sm : mappings)
{
- for (int j = 0; j < mappings.length; j++)
+ if (sm.pdbfile.equals(pdbfile) && sm.pdbchain.equals(chain))
{
- if (mappings[j].pdbfile.equals(pdbfile)
- && mappings[j].pdbchain.equals(chain))
+ indexpos = sm.getSeqPos(pdbResNum);
+ if (lastipos != indexpos && lastseq != sm.sequence)
{
- indexpos = mappings[j].getSeqPos(pdbResNum);
- if (lastipos != indexpos && lastseq != mappings[j].sequence)
+ results.addResult(sm.sequence, indexpos, indexpos);
+ lastipos = indexpos;
+ lastseq = sm.sequence;
+ // construct highlighted sequence list
+ for (AlignedCodonFrame acf : seqmappings)
{
- results.addResult(mappings[j].sequence, indexpos, indexpos);
- lastipos = indexpos;
- lastseq = mappings[j].sequence;
- // construct highlighted sequence list
- if (seqmappings != null)
- {
-
- Enumeration e = seqmappings.elements();
- while (e.hasMoreElements())
-
- {
- ((AlignedCodonFrame) e.nextElement()).markMappedRegion(
- mappings[j].sequence, indexpos, results);
- }
- }
+ acf.markMappedRegion(sm.sequence, indexpos, results);
}
-
}
}
}
}
}
- Vector seqmappings = null; // should be a simpler list of mapped seuqence
-
/**
* highlight regions associated with a position (indexpos) in seq
*
* @param seq
- * the sequeence that the mouse over occured on
+ * the sequence that the mouse over occurred on
* @param indexpos
* the absolute position being mouseovered in seq (0 to seq.length())
* @param index
public void mouseOverSequence(SequenceI seq, int indexpos, int index,
VamsasSource source)
{
- boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
+ boolean hasSequenceListeners = handlingVamsasMo
+ || !seqmappings.isEmpty();
SearchResults results = null;
if (index == -1)
{
index = seq.findPosition(indexpos);
}
- StructureListener sl;
- int atomNo = 0;
for (int i = 0; i < listeners.size(); i++)
{
Object listener = listeners.elementAt(i);
if (listener == source)
{
+ // TODO listener (e.g. SeqPanel) is never == source (AlignViewport)
+ // Temporary fudge with SequenceListener.getVamsasSource()
continue;
}
if (listener instanceof StructureListener)
{
- sl = (StructureListener) listener;
- if (mappings == null)
- {
- continue;
- }
- for (int j = 0; j < mappings.length; j++)
- {
- if (mappings[j].sequence == seq
- || mappings[j].sequence == seq.getDatasetSequence())
- {
- atomNo = mappings[j].getAtomNum(index);
-
- if (atomNo > 0)
- {
- sl.highlightAtom(atomNo, mappings[j].getPDBResNum(index),
- mappings[j].pdbchain, mappings[j].pdbfile);
- }
- }
- }
+ highlightStructure((StructureListener) listener, seq, index);
}
else
{
- if (relaySeqMappings && hasSequenceListeners
- && listener instanceof SequenceListener)
+ if (listener instanceof SequenceListener)
{
- // DEBUG
- // System.err.println("relay Seq " + seq.getDisplayId(false) + " " +
- // index);
-
- if (results == null)
+ final SequenceListener seqListener = (SequenceListener) listener;
+ if (hasSequenceListeners
+ && seqListener.getVamsasSource() != source)
{
- results = new SearchResults();
- if (index >= seq.getStart() && index <= seq.getEnd())
+ if (relaySeqMappings)
{
- // construct highlighted sequence list
-
- if (seqmappings != null)
+ if (results == null)
{
- Enumeration e = seqmappings.elements();
- while (e.hasMoreElements())
-
- {
- ((AlignedCodonFrame) e.nextElement()).markMappedRegion(
- seq, index, results);
- }
+ results = MappingUtils.buildSearchResults(seq, index,
+ seqmappings);
}
- // hasSequenceListeners = results.getSize() > 0;
if (handlingVamsasMo)
{
- // maybe have to resolve seq to a dataset seqeunce...
- // add in additional direct sequence and/or dataset sequence
- // highlighting
results.addResult(seq, index, index);
+
}
+ seqListener.highlightSequence(results);
}
}
- if (hasSequenceListeners)
- {
- ((SequenceListener) listener).highlightSequence(results);
- }
}
else if (listener instanceof VamsasListener && !handlingVamsasMo)
{
- // DEBUG
- // System.err.println("Vamsas from Seq " + seq.getDisplayId(false) + "
- // " +
- // index);
- // pass the mouse over and absolute position onto the
- // VamsasListener(s)
- ((VamsasListener) listener).mouseOver(seq, indexpos, source);
+ ((VamsasListener) listener).mouseOverSequence(seq, indexpos,
+ source);
}
else if (listener instanceof SecondaryStructureListener)
{
}
/**
+ * Send suitable messages to a StructureListener to highlight atoms
+ * corresponding to the given sequence position.
+ *
+ * @param sl
+ * @param seq
+ * @param index
+ */
+ protected void highlightStructure(StructureListener sl, SequenceI seq,
+ int index)
+ {
+ int atomNo;
+ List<AtomSpec> atoms = new ArrayList<AtomSpec>();
+ for (StructureMapping sm : mappings)
+ {
+ if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence())
+ {
+ atomNo = sm.getAtomNum(index);
+
+ if (atomNo > 0)
+ {
+ atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, sm
+ .getPDBResNum(index), atomNo));
+ }
+ }
+ }
+ sl.highlightAtoms(atoms);
+ }
+
+ /**
* true if a mouse over event from an external (ie Vamsas) source is being
* handled
*/
public StructureMapping[] getMapping(String pdbfile)
{
- Vector tmp = new Vector();
- if (mappings != null)
- {
- for (int i = 0; i < mappings.length; i++)
+ List<StructureMapping> tmp = new ArrayList<StructureMapping>();
+ for (StructureMapping sm : mappings)
{
- if (mappings[i].pdbfile.equals(pdbfile))
+ if (sm.pdbfile.equals(pdbfile))
{
- tmp.addElement(mappings[i]);
+ tmp.add(sm);
}
- }
}
- StructureMapping[] ret = new StructureMapping[tmp.size()];
- for (int i = 0; i < tmp.size(); i++)
- {
- ret[i] = (StructureMapping) tmp.elementAt(i);
- }
-
- return ret;
+ return tmp.toArray(new StructureMapping[tmp.size()]);
}
public String printMapping(String pdbfile)
{
- StringBuffer sb = new StringBuffer();
- for (int i = 0; i < mappings.length; i++)
+ StringBuilder sb = new StringBuilder(64);
+ for (StructureMapping sm : mappings)
{
- if (mappings[i].pdbfile.equals(pdbfile))
+ if (sm.pdbfile.equals(pdbfile))
{
- sb.append(mappings[i].mappingDetails);
+ sb.append(sm.mappingDetails);
}
}
return sb.toString();
}
- private int[] seqmappingrefs = null; // refcount for seqmappings elements
-
- private synchronized void modifySeqMappingList(boolean add,
- AlignedCodonFrame[] codonFrames)
+ /**
+ * Decrement the reference counter for each of the given mappings, and remove
+ * it entirely if its reference counter reduces to zero.
+ *
+ * @param set
+ */
+ public void removeMappings(Set<AlignedCodonFrame> set)
{
- if (!add && (seqmappings == null || seqmappings.size() == 0))
- {
- return;
- }
- if (seqmappings == null)
+ if (set != null)
{
- seqmappings = new Vector();
+ for (AlignedCodonFrame acf : set)
+ {
+ removeMapping(acf);
+ }
}
- if (codonFrames != null && codonFrames.length > 0)
+ }
+
+ /**
+ * Decrement the reference counter for the given mapping, and remove it
+ * entirely if its reference counter reduces to zero.
+ *
+ * @param acf
+ */
+ public void removeMapping(AlignedCodonFrame acf)
+ {
+ if (acf != null && seqmappings.contains(acf))
{
- for (int cf = 0; cf < codonFrames.length; cf++)
+ int count = seqMappingRefCounts.get(acf);
+ count--;
+ if (count > 0)
{
- if (seqmappings.contains(codonFrames[cf]))
- {
- if (add)
- {
- seqmappingrefs[seqmappings.indexOf(codonFrames[cf])]++;
- }
- else
- {
- if (--seqmappingrefs[seqmappings.indexOf(codonFrames[cf])] <= 0)
- {
- int pos = seqmappings.indexOf(codonFrames[cf]);
- int[] nr = new int[seqmappingrefs.length - 1];
- if (pos > 0)
- {
- System.arraycopy(seqmappingrefs, 0, nr, 0, pos);
- }
- if (pos < seqmappingrefs.length - 1)
- {
- System.arraycopy(seqmappingrefs, pos + 1, nr, 0,
- seqmappingrefs.length - pos - 2);
- }
- }
- }
- }
- else
- {
- if (add)
- {
- seqmappings.addElement(codonFrames[cf]);
-
- int[] nsr = new int[(seqmappingrefs == null) ? 1
- : seqmappingrefs.length + 1];
- if (seqmappingrefs != null && seqmappingrefs.length > 0)
- {
- System.arraycopy(seqmappingrefs, 0, nsr, 0,
- seqmappingrefs.length);
- }
- nsr[(seqmappingrefs == null) ? 0 : seqmappingrefs.length] = 1;
- seqmappingrefs = nsr;
- }
- }
+ seqMappingRefCounts.put(acf, count);
+ }
+ else
+ {
+ seqmappings.remove(acf);
+ seqMappingRefCounts.remove(acf);
}
}
}
- public void removeMappings(AlignedCodonFrame[] codonFrames)
+ /**
+ * Add each of the given codonFrames to the stored set. If not aready present,
+ * increments its reference count instead.
+ *
+ * @param set
+ */
+ public void addMappings(Set<AlignedCodonFrame> set)
{
- modifySeqMappingList(false, codonFrames);
+ if (set != null)
+ {
+ for (AlignedCodonFrame acf : set)
+ {
+ addMapping(acf);
+ }
+ }
}
- public void addMappings(AlignedCodonFrame[] codonFrames)
+ /**
+ * Add the given mapping to the stored set, or if already stored, increment
+ * its reference counter.
+ */
+ public void addMapping(AlignedCodonFrame acf)
{
- modifySeqMappingList(true, codonFrames);
+ if (acf != null)
+ {
+ if (seqmappings.contains(acf))
+ {
+ seqMappingRefCounts.put(acf, seqMappingRefCounts.get(acf) + 1);
+ }
+ else
+ {
+ seqmappings.add(acf);
+ seqMappingRefCounts.put(acf, 1);
+ }
+ }
}
- Vector<SelectionListener> sel_listeners = new Vector<SelectionListener>();
-
public void addSelectionListener(SelectionListener selecter)
{
if (!sel_listeners.contains(selecter))
{
- sel_listeners.addElement(selecter);
+ sel_listeners.add(selecter);
}
}
{
if (sel_listeners.contains(toremove))
{
- sel_listeners.removeElement(toremove);
+ sel_listeners.remove(toremove);
}
}
jalview.datamodel.SequenceGroup selection,
jalview.datamodel.ColumnSelection colsel, SelectionSource source)
{
- if (sel_listeners != null && sel_listeners.size() > 0)
+ for (SelectionListener slis : sel_listeners)
{
- Enumeration listeners = sel_listeners.elements();
- while (listeners.hasMoreElements())
+ if (slis != source)
{
- SelectionListener slis = ((SelectionListener) listeners
- .nextElement());
- if (slis != source)
- {
- slis.selection(selection, colsel, source);
- }
- ;
+ slis.selection(selection, colsel, source);
}
}
}
}
}
- public void finalize() throws Throwable
- {
- if (listeners != null)
- {
- listeners.clear();
- listeners = null;
- }
- if (pdbIdFileName != null)
- {
- pdbIdFileName.clear();
- pdbIdFileName = null;
- }
- if (sel_listeners != null)
- {
- sel_listeners.clear();
- sel_listeners = null;
- }
- if (view_listeners != null)
- {
- view_listeners.clear();
- view_listeners = null;
- }
- mappings = null;
- seqmappingrefs = null;
- }
-
/**
* release all references associated with this manager provider
*
} catch (Throwable x)
{
}
- ;
}
}
}
}
}
+ public void addCommandListener(CommandListener cl)
+ {
+ if (!commandListeners.contains(cl))
+ {
+ commandListeners.add(cl);
+ }
+ }
+
+ public boolean hasCommandListener(CommandListener cl)
+ {
+ return this.commandListeners.contains(cl);
+ }
+
+ public boolean removeCommandListener(CommandListener l)
+ {
+ return commandListeners.remove(l);
+ }
+
+ /**
+ * Forward a command to any command listeners (except for the command's
+ * source).
+ *
+ * @param command
+ * the command to be broadcast (in its form after being performed)
+ * @param undo
+ * if true, the command was being 'undone'
+ * @param source
+ */
+ public void commandPerformed(CommandI command, boolean undo,
+ VamsasSource source)
+ {
+ for (CommandListener listener : commandListeners)
+ {
+ listener.mirrorCommand(command, undo, this, source);
+ }
+ }
+
+ /**
+ * Returns a new CommandI representing the given command as mapped to the
+ * given sequences. If no mapping could be made, or the command is not of a
+ * mappable kind, returns null.
+ *
+ * @param command
+ * @param undo
+ * @param mapTo
+ * @param gapChar
+ * @return
+ */
+ public CommandI mapCommand(CommandI command, boolean undo,
+ final AlignmentI mapTo, char gapChar)
+ {
+ if (command instanceof EditCommand)
+ {
+ return MappingUtils.mapEditCommand((EditCommand) command, undo,
+ mapTo, gapChar, seqmappings);
+ }
+ else if (command instanceof OrderCommand)
+ {
+ return MappingUtils.mapOrderCommand((OrderCommand) command, undo,
+ mapTo, seqmappings);
+ }
+ return null;
+ }
}
git://source.jalview.org / jalview.git / blobdiff