/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * 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.
Vector listeners = new Vector();
+ /**
+ * register a listener for alignment sequence mouseover events
+ * @param svl
+ */
public void addStructureViewerListener(Object svl)
{
if (!listeners.contains(svl))
}
/**
- * create sequence structure mappings between each sequence and the given pdbFile (retrieved via the given protocol).
+ * 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
+ * @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,
AlignSeq maxAlignseq = null;
String maxChainId = " ";
PDBChain maxChain = null;
- boolean first=true;
+ boolean first = true;
for (int i = 0; i < pdb.chains.size(); i++)
{
- // TODO: re http://issues.jalview.org/browse/JAL-583 : this patch may need to be revoked
+ // TODO: re http://issues.jalview.org/browse/JAL-583 : this patch may
+ // need to be revoked
PDBChain chain = ((PDBChain) pdb.chains.elementAt(i));
- if (targetChain.length()>0 && !targetChain.equals(chain.id))
+ if (targetChain.length() > 0 && !targetChain.equals(chain.id))
{
continue; // don't try to map chains don't match.
}
// end of patch for limiting computed mappings
// 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);
+ 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;
+ first = false;
maxChain = chain;
max = as.maxscore;
maxAlignseq = as;
maxChainId = chain.id;
}
}
- if (maxChain==null)
+ if (maxChain == null)
{
continue;
}
maxChain.transferRESNUMFeatures(sequence[s], null);
- int[][] mapping = new int[sequence[s].getEnd() + 2][2];
+ // allocate enough slots to store the mapping from positions in
+ // sequence[s] to the associated chain
+ int[][] mapping = new int[maxChain.sequence.getEnd() + 2][2];
int resNum = -10000;
int index = 0;
pdbFile = "INLINE" + pdb.id;
mappings[mappings.length - 1] = new StructureMapping(sequence[s],
- pdbFile, pdb.id, maxChainId, mapping, mappingDetails
- .toString());
+ pdbFile, pdb.id, maxChainId, mapping,
+ mappingDetails.toString());
maxChain.transferResidueAnnotation(mappings[mappings.length - 1]);
}
// ///////
public void removeStructureViewerListener(Object svl, String[] pdbfiles)
{
listeners.removeElement(svl);
- if (pdbfiles==null)
+ if (pdbfiles == null)
{
return;
}
}
}
-
- if (pdbs.size()>0 && mappings != null)
+
+ if (pdbs.size() > 0 && mappings != null)
{
Vector tmp = new Vector();
for (int i = 0; i < mappings.length; i++)
{
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)
{
results = new SearchResults();
}
- int indexpos;
- for (int j = 0; j < mappings.length; j++)
+ if (mappings != null)
{
- if (mappings[j].pdbfile.equals(pdbfile)
- && mappings[j].pdbchain.equals(chain))
+ for (int j = 0; j < mappings.length; j++)
{
- indexpos = mappings[j].getSeqPos(pdbResNum);
- results.addResult(mappings[j].sequence, indexpos, indexpos);
- // construct highlighted sequence list
- if (seqmappings != null)
+ 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())
+ Enumeration e = seqmappings.elements();
+ while (e.hasMoreElements())
- {
- ((AlignedCodonFrame) e.nextElement()).markMappedRegion(
- mappings[j].sequence, indexpos, results);
+ {
+ ((AlignedCodonFrame) e.nextElement()).markMappedRegion(
+ mappings[j].sequence, indexpos, results);
+ }
+ }
}
+
}
}
}
* the sequence position (if -1, seq.findPosition is called to
* resolve the residue number)
*/
- public void mouseOverSequence(SequenceI seq, int indexpos, int index)
+ public void mouseOverSequence(SequenceI seq, int indexpos, int index,
+ VamsasSource source)
{
boolean hasSequenceListeners = handlingVamsasMo || seqmappings != null;
SearchResults results = null;
if (listeners.elementAt(i) instanceof StructureListener)
{
sl = (StructureListener) listeners.elementAt(i);
- if (mappings==null)
+ if (mappings == null)
{
continue;
}
// index);
// pass the mouse over and absolute position onto the
// VamsasListener(s)
- ((VamsasListener) listeners.elementAt(i))
- .mouseOver(seq, indexpos);
+ ((VamsasListener) listeners.elementAt(i)).mouseOver(seq,
+ indexpos, source);
}
}
}
* @param position
* in an alignment sequence
*/
- public void mouseOverVamsasSequence(SequenceI sequenceI, int position)
+ 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);
+ mouseOverSequence(sequenceI, position, -1, source);
}
handlingVamsasMo = false;
}
public StructureMapping[] getMapping(String pdbfile)
{
Vector tmp = new Vector();
- for (int i = 0; i < mappings.length; i++)
+ if (mappings != null)
{
- if (mappings[i].pdbfile.equals(pdbfile))
+ for (int i = 0; i < mappings.length; i++)
{
- tmp.addElement(mappings[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++)
{
git://source.jalview.org / jalview.git / blobdiff