import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JmolParser;
import jalview.gui.IProgressIndicator;
+import jalview.io.AppletFormatAdapter;
import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.util.MappingUtils;
}
else
{
- System.err.println("reportMapping: There are " + mappings.size()
- + " mappings.");
+ System.err.println(
+ "reportMapping: There are " + mappings.size() + " mappings.");
int i = 0;
for (StructureMapping sm : mappings)
{
{
if (instances != null)
{
- throw new Error(
- MessageManager
- .getString("error.implementation_error_structure_selection_manager_null"),
+ throw new Error(MessageManager.getString(
+ "error.implementation_error_structure_selection_manager_null"),
new NullPointerException(MessageManager
.getString("exception.ssm_context_is_null")));
}
* - one or more sequences to be mapped to pdbFile
* @param targetChainIds
* - optional chain specification for mapping each sequence to pdb
- * (may be nill, individual elements may be nill)
+ * (may be nill, individual elements may be nill) - JBPNote: JAL-2693
+ * - this should be List<List<String>>, empty lists indicate no
+ * predefined mappings
* @param pdbFile
* - structure data resource
* @param sourceType
boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
try
{
+ sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
pdb = new JmolParser(pdbFile, sourceType);
if (pdb.getId() != null && pdb.getId().trim().length() > 0
}
else if (seq.getName().indexOf("|") > -1)
{
- targetChainId = seq.getName().substring(
- seq.getName().lastIndexOf("|") + 1);
+ targetChainId = seq.getName()
+ .substring(seq.getName().lastIndexOf("|") + 1);
if (targetChainId.length() > 1)
{
if (targetChainId.trim().length() == 0)
String maxChainId = " ";
PDBChain maxChain = null;
boolean first = true;
+ List<PDBChain> maximalChain = new ArrayList<>();
+ List<AlignSeq> maximalAlignseqs = new ArrayList<>();
+ List<String> maximalChainIds = new ArrayList<>();
for (PDBChain chain : pdb.getChains())
{
if (targetChainId.length() > 0 && !targetChainId.equals(chain.id)
// as.calcScoreMatrix();
// as.traceAlignment();
- if (first || as.maxscore > max
- || (as.maxscore == max && chain.id.equals(targetChainId)))
+ if (targetChainId.length() > 0 && chain.id.equals(targetChainId))
{
- first = false;
+ // Don't care - just pick this chain as the mapping
maxChain = chain;
max = as.maxscore;
maxAlignseq = as;
maxChainId = chain.id;
+ // if targetChainId is specified then it is expected to be unique, so
+ // precisely one maximal chain will be added
+ maximalChainIds.add(chain.id);
+ maximalChain.add(chain);
+ maximalAlignseqs.add(as);
+ }
+ else
+ {
+ // select chains with maximal mappings to this sequence
+ if (first || as.maxscore > max)
+ {
+ // clear out old maximal mappings (if any)
+ max = as.maxscore;
+ maximalChain.clear();
+ maxChain = chain;
+ max = as.maxscore;
+ maxAlignseq = as;
+ maxChainId = chain.id;
+ first = false;
+ }
+ if (as.maxscore == max)
+ {
+ maximalChainIds.add(chain.id);
+ maximalChain.add(chain);
+ maximalAlignseqs.add(as);
+ }
}
}
if (maxChain == null)
pdbFile = "INLINE" + pdb.getId();
}
- List<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
+ List<StructureMapping> seqToStrucMapping = new ArrayList<>();
if (isMapUsingSIFTs && seq.isProtein())
{
setProgressBar(null);
// fall back to NW alignment
System.err.println(e.getMessage());
StructureMapping nwMapping = getNWMappings(seq, pdbFile,
- targetChainId, maxChain, pdb, maxAlignseq);
+ maximalChainIds, maximalChain, pdb, maximalAlignseqs)
+ .get(0);
seqToStrucMapping.add(nwMapping);
maxChain.makeExactMapping(maxAlignseq, seq);
maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
}
else
{
- List<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
+ List<StructureMapping> foundSiftsMappings = new ArrayList<>();
for (PDBChain chain : pdb.getChains())
{
try
else
{
StructureMapping nwMapping = getNWMappings(seq, pdbFile,
- maxChainId, maxChain, pdb, maxAlignseq);
+ maximalChainIds, maximalChain, pdb, maximalAlignseqs)
+ .get(0);
seqToStrucMapping.add(nwMapping);
maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
// "IEA:Jalview" ?
setProgressBar(null);
setProgressBar(MessageManager
.getString("status.obtaining_mapping_with_nw_alignment"));
- StructureMapping nwMapping = getNWMappings(seq, pdbFile,
- maxChainId, maxChain, pdb, maxAlignseq);
- seqToStrucMapping.add(nwMapping);
- ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
+ List<StructureMapping> nwMapping = getNWMappings(seq, pdbFile,
+ maximalChainIds, maximalChain, pdb, maximalAlignseqs);
+ seqToStrucMapping.addAll(nwMapping);
+ for (PDBChain mc : maximalChain)
+ {
+ ds.addPDBId(mc.sequence.getAllPDBEntries().get(0));
+ }
+ ;
}
return curChainMapping;
}
- private StructureMapping getNWMappings(SequenceI seq, String pdbFile,
- String maxChainId, PDBChain maxChain, StructureFile pdb,
- AlignSeq maxAlignseq)
+ private List<StructureMapping> getNWMappings(SequenceI seq,
+ String pdbFile,
+ List<String> maximalChainId, List<PDBChain> maximalChain,
+ StructureFile pdb, List<AlignSeq> maximalAlignseq)
{
+ List<StructureMapping> nwMappings = new ArrayList();
+ for (int ch = 0; ch < maximalChain.size(); ch++)
+ {
+ String maxChainId = maximalChainId.get(ch);
+ PDBChain maxChain = maximalChain.get(ch);
+ AlignSeq maxAlignseq = maximalAlignseq.get(ch);
final StringBuilder mappingDetails = new StringBuilder(128);
- mappingDetails.append(NEWLINE).append(
- "Sequence \u27f7 Structure mapping details");
+ mappingDetails.append(NEWLINE)
+ .append("Sequence \u27f7 Structure mapping details");
mappingDetails.append(NEWLINE);
mappingDetails
.append("Method: inferred with Needleman & Wunsch alignment");
.append(" ");
mappingDetails.append(String.valueOf(maxAlignseq.seq2end));
mappingDetails.append(NEWLINE).append("SEQ start/end ");
- mappingDetails.append(
- String.valueOf(maxAlignseq.seq1start + (seq.getStart() - 1)))
+ mappingDetails
+ .append(String
+ .valueOf(maxAlignseq.seq1start + (seq.getStart() - 1)))
.append(" ");
- mappingDetails.append(String.valueOf(maxAlignseq.seq1end
- + (seq.getStart() - 1)));
+ mappingDetails.append(
+ String.valueOf(maxAlignseq.seq1end + (seq.getStart() - 1)));
mappingDetails.append(NEWLINE);
maxChain.makeExactMapping(maxAlignseq, seq);
jalview.datamodel.Mapping sqmpping = maxAlignseq
insCode = tmp.insCode;
if (tmp.alignmentMapping >= -1)
{
- mapping.put(tmp.alignmentMapping + 1, new int[] { tmp.resNumber,
- tmp.atomIndex });
+ mapping.put(tmp.alignmentMapping + 1,
+ new int[]
+ { tmp.resNumber, tmp.atomIndex });
}
}
StructureMapping nwMapping = new StructureMapping(seq, pdbFile,
pdb.getId(), maxChainId, mapping, mappingDetails.toString());
maxChain.transferResidueAnnotation(nwMapping, sqmpping);
- return nwMapping;
+ nwMappings.add(nwMapping);
+ }
+ return nwMappings;
}
public void removeStructureViewerListener(Object svl, String[] pdbfiles)
* @param chain
* @param pdbfile
*/
- public void mouseOverStructure(int pdbResNum, String chain, String pdbfile)
+ public void mouseOverStructure(int pdbResNum, String chain,
+ String pdbfile)
{
AtomSpec atomSpec = new AtomSpec(pdbfile, chain, pdbResNum, 0);
List<AtomSpec> atoms = Collections.singletonList(atomSpec);
return;
}
- SearchResultsI results = findAlignmentPositionsForStructurePositions(atoms);
+ SearchResultsI results = findAlignmentPositionsForStructurePositions(
+ atoms);
for (Object li : listeners)
{
if (li instanceof SequenceListener)
List<AtomSpec> atoms = new ArrayList<AtomSpec>();
for (StructureMapping sm : mappings)
{
- if (sm.sequence == seq
- || sm.sequence == seq.getDatasetSequence()
+ if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence()
|| (sm.sequence.getDatasetSequence() != null && sm.sequence
.getDatasetSequence() == seq.getDatasetSequence()))
{
if (atomNo > 0)
{
- atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, sm
- .getPDBResNum(index), atomNo));
+ atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain,
+ sm.getPDBResNum(index), atomNo));
}
}
}
public synchronized void sendSelection(
jalview.datamodel.SequenceGroup selection,
- jalview.datamodel.ColumnSelection colsel, SelectionSource source)
+ jalview.datamodel.ColumnSelection colsel, HiddenColumns hidden,
+ SelectionSource source)
{
for (SelectionListener slis : sel_listeners)
{
if (slis != source)
{
- slis.selection(selection, colsel, source);
+ slis.selection(selection, colsel, hidden, source);
}
}
}
{
if (command instanceof EditCommand)
{
- return MappingUtils.mapEditCommand((EditCommand) command, undo,
- mapTo, gapChar, seqmappings);
+ return MappingUtils.mapEditCommand((EditCommand) command, undo, mapTo,
+ gapChar, seqmappings);
}
else if (command instanceof OrderCommand)
{
git://source.jalview.org / jalview.git / blobdiff