/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
* Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* 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 .
*/
package jalview.structure;
import java.io.*;
import java.util.*;
import MCview.*;
import jalview.analysis.*;
import jalview.api.AlignmentViewPanel;
import jalview.api.StructureSelectionManagerProvider;
import jalview.datamodel.*;
public class StructureSelectionManager
{
static IdentityHashMap instances;
StructureMapping[] mappings;
/**
* 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();
}
StructureSelectionManager instance=instances.get(context);
if (instance==null)
{
instances.put(context, instance=new StructureSelectionManager());
}
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;
}
/**
* create sequence structure mappings between each sequence and the given
* pdbFile (retrieved via the given protocol).
*
* @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)
{
/*
* 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;
try
{
pdb = new MCview.PDBfile(pdbFile, protocol);
} 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 = ((PDBChain) 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],
((PDBChain) pdb.chains.elementAt(i)).sequence,
((PDBChain) 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)
{
public void print(String x)
{
mappingDetails.append(x);
}
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]);
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 (mappings == null)
{
mappings = new StructureMapping[1];
}
else
{
StructureMapping[] tmp = new StructureMapping[mappings.length + 1];
System.arraycopy(mappings, 0, tmp, 0, mappings.length);
mappings = tmp;
}
if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
pdbFile = "INLINE" + pdb.id;
mappings[mappings.length - 1] = new StructureMapping(sequence[s],
pdbFile, pdb.id, maxChainId, mapping,
mappingDetails.toString());
maxChain.transferResidueAnnotation(mappings[mappings.length - 1]);
}
// ///////
return pdb;
}
public void removeStructureViewerListener(Object svl, String[] pdbfiles)
{
listeners.removeElement(svl);
if (svl instanceof SequenceListener)
{
for (int i=0;i 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)
{
Enumeration e = seqmappings.elements();
while (e.hasMoreElements())
{
((AlignedCodonFrame) e.nextElement()).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);
}
}
}
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
* @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);
StructureListener sl;
int atomNo = 0;
for (int i = 0; i < listeners.size(); i++)
{
if (listeners.elementAt(i) instanceof StructureListener)
{
sl = (StructureListener) listeners.elementAt(i);
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);
}
}
}
}
else
{
if (relaySeqMappings && hasSequenceListeners
&& listeners.elementAt(i) instanceof SequenceListener)
{
// DEBUG
// System.err.println("relay Seq " + seq.getDisplayId(false) + " " +
// index);
if (results == null)
{
results = new SearchResults();
if (index >= seq.getStart() && index <= seq.getEnd())
{
// construct highlighted sequence list
if (seqmappings != null)
{
Enumeration e = seqmappings.elements();
while (e.hasMoreElements())
{
((AlignedCodonFrame) e.nextElement()).markMappedRegion(
seq, index, results);
}
}
// 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);
}
}
}
if (hasSequenceListeners)
{
((SequenceListener) listeners.elementAt(i))
.highlightSequence(results);
}
}
else if (listeners.elementAt(i) 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) listeners.elementAt(i)).mouseOver(seq,
indexpos, source);
}
}
}
}
/**
* 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 int[] seqmappingrefs = null; // refcount for seqmappings elements
private synchronized void modifySeqMappingList(boolean add,
AlignedCodonFrame[] codonFrames)
{
if (!add && (seqmappings == null || seqmappings.size() == 0))
return;
if (seqmappings == null)
seqmappings = new Vector();
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.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;
}
}
}
}
}
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 (mappingData!=null)
{
mappingData.clear();
mappingData=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)
{
StructureSelectionManager mnger=(instances.get(jalviewLite));
if (mnger!=null)
{
instances.remove(jalviewLite);
try {
mnger.finalize();
} catch (Throwable x){};
}
}
}