/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.structure;
import jalview.analysis.AlignSeq;
import jalview.api.StructureSelectionManagerProvider;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
import jalview.commands.EditCommand.Action;
import jalview.commands.EditCommand.Edit;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
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.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.List;
import java.util.Map;
import java.util.Vector;
import MCview.Atom;
import MCview.PDBChain;
public class StructureSelectionManager
{
static IdentityHashMap instances;
StructureMapping[] mappings;
private boolean processSecondaryStructure = false,
secStructServices = false, addTempFacAnnot = false;
List seqmappings = null;
private int[] seqmappingrefs = null; // refcount for seqmappings elements
private List commandListeners = new ArrayList();
/**
* @return true if will try to use external services for processing secondary
* structure
*/
public boolean isSecStructServices()
{
return secStructServices;
}
/**
* control use of external services for processing secondary structure
*
* @param secStructServices
*/
public void setSecStructServices(boolean secStructServices)
{
this.secStructServices = secStructServices;
}
/**
* flag controlling addition of any kind of structural annotation
*
* @return true if temperature factor annotation will be added
*/
public boolean isAddTempFacAnnot()
{
return addTempFacAnnot;
}
/**
* set flag controlling addition of structural annotation
*
* @param addTempFacAnnot
*/
public void setAddTempFacAnnot(boolean addTempFacAnnot)
{
this.addTempFacAnnot = addTempFacAnnot;
}
/**
*
* @return if true, the structure manager will attempt to add secondary
* structure lines for unannotated sequences
*/
public boolean isProcessSecondaryStructure()
{
return processSecondaryStructure;
}
/**
* Control whether structure manager will try to annotate mapped sequences
* with secondary structure from PDB data.
*
* @param enable
*/
public void setProcessSecondaryStructure(boolean enable)
{
processSecondaryStructure = enable;
}
/**
* debug function - write all mappings to stdout
*/
public void reportMapping()
{
if (mappings == null)
{
System.err.println("reportMapping: No PDB/Sequence mappings.");
}
else
{
System.err.println("reportMapping: There are " + mappings.length
+ " mappings.");
for (int m = 0; m < mappings.length; m++)
{
System.err.println("mapping " + m + " : " + mappings[m].pdbfile);
}
}
}
/**
* map between the PDB IDs (or structure identifiers) used by Jalview and the
* absolute filenames for PDB data that corresponds to it
*/
HashMap pdbIdFileName = new HashMap(),
pdbFileNameId = new HashMap();
public void registerPDBFile(String idForFile, String absoluteFile)
{
pdbIdFileName.put(idForFile, absoluteFile);
pdbFileNameId.put(absoluteFile, idForFile);
}
public String findIdForPDBFile(String idOrFile)
{
String id = pdbFileNameId.get(idOrFile);
return id;
}
public String findFileForPDBId(String idOrFile)
{
String id = pdbIdFileName.get(idOrFile);
return id;
}
public boolean isPDBFileRegistered(String idOrFile)
{
return pdbFileNameId.containsKey(idOrFile)
|| pdbIdFileName.containsKey(idOrFile);
}
private static StructureSelectionManager nullProvider = null;
public static StructureSelectionManager getStructureSelectionManager(
StructureSelectionManagerProvider context)
{
if (context == null)
{
if (nullProvider == null)
{
if (instances != null)
{
throw new Error(MessageManager.getString("error.implementation_error_structure_selection_manager_null"),
new NullPointerException(MessageManager.getString("exception.ssm_context_is_null")));
}
else
{
nullProvider = new StructureSelectionManager();
}
return nullProvider;
}
}
if (instances == null)
{
instances = new java.util.IdentityHashMap();
}
StructureSelectionManager instance = instances.get(context);
if (instance == null)
{
if (nullProvider != null)
{
instance = nullProvider;
}
else
{
instance = new StructureSelectionManager();
}
instances.put(context, instance);
}
return instance;
}
/**
* flag controlling whether SeqMappings are relayed from received sequence
* mouse over events to other sequences
*/
boolean relaySeqMappings = true;
/**
* Enable or disable relay of seqMapping events to other sequences. You might
* want to do this if there are many sequence mappings and the host computer
* is slow
*
* @param relay
*/
public void setRelaySeqMappings(boolean relay)
{
relaySeqMappings = relay;
}
/**
* get the state of the relay seqMappings flag.
*
* @return true if sequence mouse overs are being relayed to other mapped
* sequences
*/
public boolean isRelaySeqMappingsEnabled()
{
return relaySeqMappings;
}
Vector listeners = new Vector();
/**
* register a listener for alignment sequence mouseover events
*
* @param svl
*/
public void addStructureViewerListener(Object svl)
{
if (!listeners.contains(svl))
{
listeners.addElement(svl);
}
}
public String alreadyMappedToFile(String pdbid)
{
if (mappings != null)
{
for (int i = 0; i < mappings.length; i++)
{
if (mappings[i].getPdbId().equals(pdbid))
{
return mappings[i].pdbfile;
}
}
}
return null;
}
/**
* Import structure data and register a structure mapping for broadcasting
* colouring, mouseovers and selection events (convenience wrapper).
*
* @param sequence
* - one or more sequences to be mapped to pdbFile
* @param targetChains
* - optional chain specification for mapping each sequence to pdb
* (may be nill, individual elements may be nill)
* @param pdbFile
* - structure data resource
* @param protocol
* - how to resolve data from resource
* @return null or the structure data parsed as a pdb file
*/
synchronized public MCview.PDBfile setMapping(SequenceI[] sequence,
String[] targetChains, String pdbFile, String protocol)
{
return setMapping(true, sequence, targetChains, pdbFile, protocol);
}
/**
* create sequence structure mappings between each sequence and the given
* pdbFile (retrieved via the given protocol).
*
* @param forStructureView
* when true, record the mapping for use in mouseOvers
*
* @param sequence
* - one or more sequences to be mapped to pdbFile
* @param targetChains
* - optional chain specification for mapping each sequence to pdb
* (may be nill, individual elements may be nill)
* @param pdbFile
* - structure data resource
* @param protocol
* - how to resolve data from resource
* @return null or the structure data parsed as a pdb file
*/
synchronized public MCview.PDBfile setMapping(boolean forStructureView,
SequenceI[] sequence,
String[] targetChains, String pdbFile, String protocol)
{
/*
* There will be better ways of doing this in the future, for now we'll use
* the tried and tested MCview pdb mapping
*/
MCview.PDBfile pdb = null;
boolean parseSecStr = processSecondaryStructure;
if (isPDBFileRegistered(pdbFile))
{
for (SequenceI sq : sequence)
{
SequenceI ds = sq;
while (ds.getDatasetSequence() != null)
{
ds = ds.getDatasetSequence();
}
;
if (ds.getAnnotation() != null)
{
for (AlignmentAnnotation ala : ds.getAnnotation())
{
// false if any annotation present from this structure
// JBPNote this fails for jmol/chimera view because the *file* is
// passed, not the structure data ID -
if (MCview.PDBfile.isCalcIdForFile(ala,
findIdForPDBFile(pdbFile)))
{
parseSecStr = false;
}
}
}
}
}
try
{
pdb = new MCview.PDBfile(addTempFacAnnot, parseSecStr,
secStructServices, pdbFile, protocol);
if (pdb.id != null && pdb.id.trim().length() > 0
&& AppletFormatAdapter.FILE.equals(protocol))
{
registerPDBFile(pdb.id.trim(), pdbFile);
}
} catch (Exception ex)
{
ex.printStackTrace();
return null;
}
String targetChain;
for (int s = 0; s < sequence.length; s++)
{
boolean infChain = true;
if (targetChains != null && targetChains[s] != null)
{
infChain = false;
targetChain = targetChains[s];
}
else if (sequence[s].getName().indexOf("|") > -1)
{
targetChain = sequence[s].getName().substring(
sequence[s].getName().lastIndexOf("|") + 1);
if (targetChain.length() > 1)
{
if (targetChain.trim().length() == 0)
{
targetChain = " ";
}
else
{
// not a valid chain identifier
targetChain = "";
}
}
}
else
{
targetChain = "";
}
int max = -10;
AlignSeq maxAlignseq = null;
String maxChainId = " ";
PDBChain maxChain = null;
boolean first = true;
for (int i = 0; i < pdb.chains.size(); i++)
{
PDBChain chain = (pdb.chains.elementAt(i));
if (targetChain.length() > 0 && !targetChain.equals(chain.id)
&& !infChain)
{
continue; // don't try to map chains don't match.
}
// TODO: correctly determine sequence type for mixed na/peptide
// structures
AlignSeq as = new AlignSeq(sequence[s],
pdb.chains.elementAt(i).sequence,
pdb.chains.elementAt(i).isNa ? AlignSeq.DNA
: AlignSeq.PEP);
as.calcScoreMatrix();
as.traceAlignment();
if (first || as.maxscore > max
|| (as.maxscore == max && chain.id.equals(targetChain)))
{
first = false;
maxChain = chain;
max = as.maxscore;
maxAlignseq = as;
maxChainId = chain.id;
}
}
if (maxChain == null)
{
continue;
}
final StringBuffer mappingDetails = new StringBuffer();
mappingDetails.append("\n\nPDB Sequence is :\nSequence = "
+ maxChain.sequence.getSequenceAsString());
mappingDetails.append("\nNo of residues = "
+ maxChain.residues.size() + "\n\n");
PrintStream ps = new PrintStream(System.out)
{
@Override
public void print(String x)
{
mappingDetails.append(x);
}
@Override
public void println()
{
mappingDetails.append("\n");
}
};
maxAlignseq.printAlignment(ps);
mappingDetails.append("\nPDB start/end " + maxAlignseq.seq2start
+ " " + maxAlignseq.seq2end);
mappingDetails.append("\nSEQ start/end "
+ (maxAlignseq.seq1start + sequence[s].getStart() - 1) + " "
+ (maxAlignseq.seq1end + sequence[s].getEnd() - 1));
maxChain.makeExactMapping(maxAlignseq, sequence[s]);
jalview.datamodel.Mapping sqmpping = maxAlignseq
.getMappingFromS1(false);
jalview.datamodel.Mapping omap = new jalview.datamodel.Mapping(
sqmpping.getMap().getInverse());
maxChain.transferRESNUMFeatures(sequence[s], null);
// allocate enough slots to store the mapping from positions in
// sequence[s] to the associated chain
int[][] mapping = new int[sequence[s].findPosition(sequence[s]
.getLength()) + 2][2];
int resNum = -10000;
int index = 0;
do
{
Atom tmp = (Atom) maxChain.atoms.elementAt(index);
if (resNum != tmp.resNumber && tmp.alignmentMapping != -1)
{
resNum = tmp.resNumber;
mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber;
mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex;
}
index++;
} while (index < maxChain.atoms.size());
if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
{
pdbFile = "INLINE" + pdb.id;
}
StructureMapping newMapping = new StructureMapping(sequence[s],
pdbFile, pdb.id, maxChainId, mapping,
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;
}
maxChain.transferResidueAnnotation(newMapping, sqmpping);
}
// ///////
return pdb;
}
public void removeStructureViewerListener(Object svl, String[] pdbfiles)
{
listeners.removeElement(svl);
if (svl instanceof SequenceListener)
{
for (int i = 0; i < listeners.size(); i++)
{
if (listeners.elementAt(i) instanceof StructureListener)
{
((StructureListener) listeners.elementAt(i))
.releaseReferences(svl);
}
}
}
if (pdbfiles == null)
{
return;
}
String[] handlepdbs;
Vector pdbs = new Vector();
for (int i = 0; i < pdbfiles.length; pdbs.addElement(pdbfiles[i++]))
{
;
}
StructureListener sl;
for (int i = 0; i < listeners.size(); i++)
{
if (listeners.elementAt(i) instanceof StructureListener)
{
sl = (StructureListener) listeners.elementAt(i);
handlepdbs = sl.getPdbFile();
for (int j = 0; j < handlepdbs.length; j++)
{
if (pdbs.contains(handlepdbs[j]))
{
pdbs.removeElement(handlepdbs[j]);
}
}
}
}
if (pdbs.size() > 0 && mappings != null)
{
Vector tmp = new Vector();
for (int i = 0; i < mappings.length; i++)
{
if (!pdbs.contains(mappings[i].pdbfile))
{
tmp.addElement(mappings[i]);
}
}
mappings = new StructureMapping[tmp.size()];
tmp.copyInto(mappings);
}
}
public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)
{
if (listeners == null)
{
// old or prematurely sent event
return;
}
boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
SearchResults results = null;
SequenceI lastseq = null;
int lastipos = -1, indexpos;
for (int i = 0; i < listeners.size(); i++)
{
if (listeners.elementAt(i) instanceof SequenceListener)
{
if (results == null)
{
results = new SearchResults();
}
if (mappings != null)
{
for (int j = 0; j < mappings.length; j++)
{
if (mappings[j].pdbfile.equals(pdbfile)
&& mappings[j].pdbchain.equals(chain))
{
indexpos = mappings[j].getSeqPos(pdbResNum);
if (lastipos != indexpos && lastseq != mappings[j].sequence)
{
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);
}
}
}
}
}
}
}
}
if (results != null)
{
for (int i = 0; i < listeners.size(); i++)
{
Object li = listeners.elementAt(i);
if (li instanceof SequenceListener)
{
((SequenceListener) li).highlightSequence(results);
}
}
}
}
/**
* highlight regions associated with a position (indexpos) in seq
*
* @param seq
* the sequence that the mouse over occurred on
* @param indexpos
* the absolute position being mouseovered in seq (0 to seq.length())
* @param index
* the sequence position (if -1, seq.findPosition is called to
* resolve the residue number)
*/
public void mouseOverSequence(SequenceI seq, int indexpos, int index,
VamsasSource source)
{
boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
SearchResults results = null;
if (index == -1)
{
index = seq.findPosition(indexpos);
}
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)
{
highlightStructure((StructureListener) listener, seq, index);
}
else
{
if (listener instanceof SequenceListener)
{
final SequenceListener seqListener = (SequenceListener) listener;
if (hasSequenceListeners
&& seqListener.getVamsasSource() != source)
{
if (relaySeqMappings)
{
if (results == null)
{
results = buildSearchResults(seq, index);
}
seqListener.highlightSequence(results);
}
}
}
else if (listener instanceof VamsasListener && !handlingVamsasMo)
{
((VamsasListener) listener).mouseOverSequence(seq, indexpos,
source);
}
else if (listener instanceof SecondaryStructureListener)
{
((SecondaryStructureListener) listener).mouseOverSequence(seq,
indexpos);
}
}
}
}
/**
* 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.
*
* @param sl
* @param seq
* @param index
*/
protected void highlightStructure(StructureListener sl, SequenceI seq,
int index)
{
int atomNo;
if (mappings != null)
{
List atoms = new ArrayList();
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)
{
atoms.add(new AtomSpec(mappings[j].pdbfile,
mappings[j].pdbchain, mappings[j].getPDBResNum(index),
atomNo));
}
}
}
sl.highlightAtoms(atoms);
}
}
/**
* true if a mouse over event from an external (ie Vamsas) source is being
* handled
*/
boolean handlingVamsasMo = false;
long lastmsg = 0;
/**
* as mouseOverSequence but only route event to SequenceListeners
*
* @param sequenceI
* @param position
* in an alignment sequence
*/
public void mouseOverVamsasSequence(SequenceI sequenceI, int position,
VamsasSource source)
{
handlingVamsasMo = true;
long msg = sequenceI.hashCode() * (1 + position);
if (lastmsg != msg)
{
lastmsg = msg;
mouseOverSequence(sequenceI, position, -1, source);
}
handlingVamsasMo = false;
}
public Annotation[] colourSequenceFromStructure(SequenceI seq,
String pdbid)
{
return null;
// THIS WILL NOT BE AVAILABLE IN JALVIEW 2.3,
// UNTIL THE COLOUR BY ANNOTATION IS REWORKED
/*
* Annotation [] annotations = new Annotation[seq.getLength()];
*
* StructureListener sl; int atomNo = 0; for (int i = 0; i <
* listeners.size(); i++) { if (listeners.elementAt(i) instanceof
* StructureListener) { sl = (StructureListener) listeners.elementAt(i);
*
* for (int j = 0; j < mappings.length; j++) {
*
* if (mappings[j].sequence == seq && mappings[j].getPdbId().equals(pdbid)
* && mappings[j].pdbfile.equals(sl.getPdbFile())) {
* System.out.println(pdbid+" "+mappings[j].getPdbId() +"
* "+mappings[j].pdbfile);
*
* java.awt.Color col; for(int index=0; index 0) { col = sl.getColour(atomNo,
* mappings[j].getPDBResNum(index), mappings[j].pdbchain,
* mappings[j].pdbfile); }
*
* annotations[index] = new Annotation("X",null,' ',0,col); } return
* annotations; } } } }
*
* return annotations;
*/
}
public void structureSelectionChanged()
{
}
public void sequenceSelectionChanged()
{
}
public void sequenceColoursChanged(Object source)
{
StructureListener sl;
for (int i = 0; i < listeners.size(); i++)
{
if (listeners.elementAt(i) instanceof StructureListener)
{
sl = (StructureListener) listeners.elementAt(i);
sl.updateColours(source);
}
}
}
public StructureMapping[] getMapping(String pdbfile)
{
Vector tmp = new Vector();
if (mappings != null)
{
for (int i = 0; i < mappings.length; i++)
{
if (mappings[i].pdbfile.equals(pdbfile))
{
tmp.addElement(mappings[i]);
}
}
}
StructureMapping[] ret = new StructureMapping[tmp.size()];
for (int i = 0; i < tmp.size(); i++)
{
ret[i] = (StructureMapping) tmp.elementAt(i);
}
return ret;
}
public String printMapping(String pdbfile)
{
StringBuffer sb = new StringBuffer();
for (int i = 0; i < mappings.length; i++)
{
if (mappings[i].pdbfile.equals(pdbfile))
{
sb.append(mappings[i].mappingDetails);
}
}
return sb.toString();
}
private synchronized void modifySeqMappingList(boolean add,
AlignedCodonFrame[] codonFrames)
{
if (!add && (seqmappings == null || seqmappings.size() == 0))
{
return;
}
if (seqmappings == null)
{
seqmappings = new ArrayList();
}
if (codonFrames != null && codonFrames.length > 0)
{
for (int cf = 0; cf < codonFrames.length; cf++)
{
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.add(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;
}
}
}
}
}
public void removeMappings(AlignedCodonFrame[] codonFrames)
{
modifySeqMappingList(false, codonFrames);
}
public void addMappings(AlignedCodonFrame[] codonFrames)
{
modifySeqMappingList(true, codonFrames);
}
Vector sel_listeners = new Vector();
public void addSelectionListener(SelectionListener selecter)
{
if (!sel_listeners.contains(selecter))
{
sel_listeners.addElement(selecter);
}
}
public void removeSelectionListener(SelectionListener toremove)
{
if (sel_listeners.contains(toremove))
{
sel_listeners.removeElement(toremove);
}
}
public synchronized void sendSelection(
jalview.datamodel.SequenceGroup selection,
jalview.datamodel.ColumnSelection colsel, SelectionSource source)
{
if (sel_listeners != null && sel_listeners.size() > 0)
{
Enumeration listeners = sel_listeners.elements();
while (listeners.hasMoreElements())
{
SelectionListener slis = ((SelectionListener) listeners
.nextElement());
if (slis != source)
{
slis.selection(selection, colsel, source);
}
;
}
}
}
Vector view_listeners = new Vector();
public synchronized void sendViewPosition(
jalview.api.AlignmentViewPanel source, int startRes, int endRes,
int startSeq, int endSeq)
{
if (view_listeners != null && view_listeners.size() > 0)
{
Enumeration listeners = view_listeners
.elements();
while (listeners.hasMoreElements())
{
AlignmentViewPanelListener slis = listeners.nextElement();
if (slis != source)
{
slis.viewPosition(startRes, endRes, startSeq, endSeq, 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
*
* @param jalviewLite
*/
public static void release(StructureSelectionManagerProvider jalviewLite)
{
// synchronized (instances)
{
if (instances == null)
{
return;
}
StructureSelectionManager mnger = (instances.get(jalviewLite));
if (mnger != null)
{
instances.remove(jalviewLite);
try
{
mnger.finalize();
} catch (Throwable x)
{
}
;
}
}
}
public void registerPDBEntry(PDBEntry pdbentry)
{
if (pdbentry.getFile() != null
&& pdbentry.getFile().trim().length() > 0)
{
registerPDBFile(pdbentry.getId(), pdbentry.getFile());
}
}
public void addCommandListener(CommandListener cl)
{
if (!commandListeners.contains(cl))
{
commandListeners.add(cl);
}
}
public boolean hasCommandListener(CommandListener cl)
{
return this.commandListeners.contains(cl);
}
public boolean removeEditListener(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)
{
if (listener.getVamsasSource() != source)
{
listener.mirrorCommand(command, undo, this);
}
}
}
/**
* Returns a new EditCommand representing the given command as mapped to the
* given sequences. If there is no mapping, returns an empty EditCommand.
*
* @param command
* @param undo
* @param targetSeqs
* @param gapChar
* @return
*/
public EditCommand mapEditCommand(EditCommand command, boolean undo,
final List targetSeqs, 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 targetCopies = new HashMap();
for (SequenceI seq : targetSeqs)
{
SequenceI ds = seq.getDatasetSequence();
if (ds != null)
{
final Sequence copy = new Sequence("", new String(seq.getSequence()));
copy.setDatasetSequence(ds);
targetCopies.put(ds, copy);
}
}
/*
* Compute 'source' sequences as they were before applying edits:
*/
Map originalSequences = command.priorState(undo);
EditCommand result = new EditCommand();
Iterator edits = command.getEditIterator(!undo);
while (edits.hasNext())
{
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 result;
}
}