import jalview.api.StructureSelectionManagerProvider;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
-import jalview.commands.EditCommand.Action;
-import jalview.commands.EditCommand.Edit;
+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.Sequence;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
+import jalview.util.MappingUtils;
import jalview.util.MessageManager;
-import jalview.util.StringUtils;
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.HashMap;
import java.util.IdentityHashMap;
-import java.util.Iterator;
import java.util.LinkedHashSet;
import java.util.List;
-import java.util.Map;
import java.util.Set;
import java.util.Vector;
{
static IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> instances;
- StructureMapping[] mappings;
+ private List<StructureMapping> mappings = new ArrayList<StructureMapping>();
private boolean processSecondaryStructure = false;
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
* structure
*/
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)
- {
- for (AlignedCodonFrame acf : seqmappings)
- {
- acf.markMappedRegion(mappings[j].sequence, indexpos,
- results);
- }
- }
+ acf.markMappedRegion(sm.sequence, indexpos, results);
}
}
}
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)
{
{
if (results == null)
{
- results = buildSearchResults(seq, index);
+ results = MappingUtils.buildSearchResults(seq, index,
+ seqmappings);
+ }
+ if (handlingVamsasMo)
+ {
+ results.addResult(seq, index, index);
+
}
seqListener.highlightSequence(results);
}
}
/**
- * Returns a SearchResults object describing the mapped region corresponding
- * to the specified sequence position.
- *
- * @param seq
- * @param index
- * @return
- */
- protected SearchResults buildSearchResults(SequenceI seq, int index)
- {
- SearchResults results;
- results = new SearchResults();
- if (index >= seq.getStart() && index <= seq.getEnd())
- {
- if (seqmappings != null)
- {
- for (AlignedCodonFrame acf : seqmappings)
- {
- acf.markMappedRegion(seq, index, results);
- }
- }
- // hasSequenceListeners = results.getSize() > 0;
- if (handlingVamsasMo)
- {
- // maybe have to resolve seq to a dataset sequence...
- // add in additional direct sequence and/or dataset sequence
- // highlighting
- results.addResult(seq, index, index);
- }
- }
- return results;
- }
-
- /**
* Send suitable messages to a StructureListener to highlight atoms
* corresponding to the given sequence position.
*
int index)
{
int atomNo;
- if (mappings != null)
+ List<AtomSpec> atoms = new ArrayList<AtomSpec>();
+ for (StructureMapping sm : mappings)
{
- List<AtomSpec> atoms = new ArrayList<AtomSpec>();
- for (int j = 0; j < mappings.length; j++)
+ if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence())
{
- if (mappings[j].sequence == seq
- || mappings[j].sequence == seq.getDatasetSequence())
- {
- atomNo = mappings[j].getAtomNum(index);
+ atomNo = sm.getAtomNum(index);
- if (atomNo > 0)
- {
- atoms.add(new AtomSpec(mappings[j].pdbfile,
- mappings[j].pdbchain, mappings[j].getPDBResNum(index),
- atomNo));
- }
+ if (atomNo > 0)
+ {
+ atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, sm
+ .getPDBResNum(index), atomNo));
}
}
- sl.highlightAtoms(atoms);
}
+ sl.highlightAtoms(atoms);
}
/**
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);
}
}
}
}
- 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);
}
}
}
{
for (CommandListener listener : commandListeners)
{
- if (listener.getVamsasSource() != source)
- {
- listener.mirrorCommand(command, undo, this);
- }
+ listener.mirrorCommand(command, undo, this, source);
}
}
/**
- * Returns a new EditCommand representing the given command as mapped to the
- * given sequences. If there is no mapping, returns an empty EditCommand.
+ * 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 targetSeqs
+ * @param alignmentI
* @param gapChar
* @return
*/
- public EditCommand mapEditCommand(EditCommand command, boolean undo,
- final List<SequenceI> targetSeqs, char gapChar)
+ public CommandI mapCommand(CommandI command,
+ boolean undo,
+ final AlignmentI alignmentI, char gapChar)
{
- /*
- * Cache a copy of the target sequences so we can mimic successive edits on
- * them. This lets us compute mappings for all edits in the set.
- */
- Map<SequenceI, SequenceI> targetCopies = new HashMap<SequenceI, SequenceI>();
- for (SequenceI seq : targetSeqs)
+ if (command instanceof EditCommand)
{
- SequenceI ds = seq.getDatasetSequence();
- if (ds != null)
- {
- final Sequence copy = new Sequence("", new String(seq.getSequence()));
- copy.setDatasetSequence(ds);
- targetCopies.put(ds, copy);
- }
+ return MappingUtils.mapEditCommand((EditCommand) command, undo,
+ alignmentI, gapChar,
+ seqmappings);
}
-
- /*
- * Compute 'source' sequences as they were before applying edits:
- */
- Map<SequenceI, SequenceI> originalSequences = command.priorState(undo);
-
- EditCommand result = new EditCommand();
- Iterator<Edit> edits = command.getEditIterator(!undo);
- while (edits.hasNext())
+ else if (command instanceof OrderCommand)
{
- Edit edit = edits.next();
- Action action = edit.getAction();
-
- /*
- * Invert sense of action if an Undo.
- */
- if (undo)
- {
- action = action == Action.INSERT_GAP ? Action.DELETE_GAP
- : (action == Action.DELETE_GAP ? Action.INSERT_GAP : action);
- }
- final int count = edit.getNumber();
- final int editPos = edit.getPosition();
- for (SequenceI seq : edit.getSequences())
- {
- /*
- * Get residue position at (or to right of) edit location. Note we use
- * our 'copy' of the sequence before editing for this.
- */
- SequenceI ds = seq.getDatasetSequence();
- if (ds == null)
- {
- continue;
- }
- final SequenceI actedOn = originalSequences.get(ds);
- final int seqpos = actedOn.findPosition(editPos);
-
- /*
- * Determine all mappings from this position to mapped sequences.
- */
- SearchResults sr = buildSearchResults(seq, seqpos);
-
- if (!sr.isEmpty())
- {
- for (SequenceI targetSeq : targetSeqs)
- {
- ds = targetSeq.getDatasetSequence();
- if (ds == null)
- {
- continue;
- }
- SequenceI copyTarget = targetCopies.get(ds);
- final int[] match = sr.getResults(copyTarget, 0,
- copyTarget.getLength());
- if (match != null)
- {
- final int ratio = 3; // TODO: compute this - how?
- final int mappedCount = count * ratio;
-
- /*
- * Shift Delete start position left, as it acts on positions to
- * its right.
- */
- int mappedEditPos = action == Action.DELETE_GAP ? match[0]
- - mappedCount : match[0];
- Edit e = new EditCommand().new Edit(action, new SequenceI[]
- { targetSeq }, mappedEditPos, mappedCount, gapChar);
- result.addEdit(e);
-
- /*
- * and 'apply' the edit to our copy of its target sequence
- */
- if (action == Action.INSERT_GAP)
- {
- copyTarget.setSequence(new String(StringUtils.insertCharAt(
- copyTarget.getSequence(), mappedEditPos,
- mappedCount,
- gapChar)));
- }
- else if (action == Action.DELETE_GAP)
- {
- copyTarget.setSequence(new String(StringUtils.deleteChars(
- copyTarget.getSequence(), mappedEditPos,
- mappedEditPos + mappedCount)));
- }
- }
- }
- }
- /*
- * and 'apply' the edit to our copy of its source sequence
- */
- if (action == Action.INSERT_GAP) {
- actedOn.setSequence(new String(StringUtils.insertCharAt(
- actedOn.getSequence(), editPos, count, gapChar)));
- }
- else if (action == Action.DELETE_GAP)
- {
- actedOn.setSequence(new String(StringUtils.deleteChars(
- actedOn.getSequence(), editPos, editPos + count)));
- }
- }
+ return MappingUtils.mapOrderCommand((OrderCommand) command, undo,
+ alignmentI, seqmappings);
}
- return result;
+ return null;
}
}
git://source.jalview.org / jalview.git / blobdiff