import jalview.datamodel.PDBEntry;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SequenceI;
+import jalview.gui.IProgressIndicator;
import jalview.io.AppletFormatAdapter;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
import jalview.ws.sifts.SiftsClient;
import jalview.ws.sifts.SiftsException;
+import jalview.ws.sifts.SiftsSettings;
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.Enumeration;
import java.util.HashMap;
import java.util.IdentityHashMap;
-import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
-import java.util.Set;
import java.util.Vector;
import MCview.Atom;
private boolean addTempFacAnnot = false;
+ private IProgressIndicator progressIndicator;
+
+ private SiftsClient siftsClient = null;
+
+ private long progressSessionId;
+
/*
* Set of any registered mappings between (dataset) sequences.
*/
- public Set<AlignedCodonFrame> seqmappings = new LinkedHashSet<AlignedCodonFrame>();
+ private List<AlignedCodonFrame> seqmappings = new ArrayList<AlignedCodonFrame>();
private List<CommandListener> commandListeners = new ArrayList<CommandListener>();
}
}
PDBfile pdb = null;
- boolean isMapUsingSIFTs = Boolean.valueOf(jalview.bin.Cache.getDefault(
- "MAP_WITH_SIFTS", "false"));
- SiftsClient siftsClient = null;
+ boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
try
{
pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
pdbFile = "INLINE" + pdb.id;
}
- ArrayList<StructureMapping> seqToStrucMapping = null;
+ ArrayList<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
if (isMapUsingSIFTs)
{
- try
+ setProgressBar(null);
+ setProgressBar("Obtaining mapping with SIFTS");
+ jalview.datamodel.Mapping sqmpping = maxAlignseq
+ .getMappingFromS1(false);
+ if (targetChainId != null && !targetChainId.trim().isEmpty())
+ {
+ StructureMapping mapping = getStructureMapping(seq, pdbFile,
+ targetChainId, pdb, maxChain, sqmpping, maxAlignseq);
+ seqToStrucMapping.add(mapping);
+ }
+ else
{
- jalview.datamodel.Mapping sqmpping = maxAlignseq
- .getMappingFromS1(false);
- seqToStrucMapping = new ArrayList<StructureMapping>();
- if (targetChainId != null && !targetChainId.trim().isEmpty())
+ for (PDBChain chain : pdb.chains)
{
- StructureMapping curChainMapping = siftsClient
- .getSiftsStructureMapping(seq, pdbFile, targetChainId);
- seqToStrucMapping.add(curChainMapping);
- maxChainId = targetChainId;
- PDBChain chain = pdb.findChain(targetChainId);
- if (chain != null)
- {
- chain.transferResidueAnnotation(curChainMapping, sqmpping);
- }
+ StructureMapping mapping = getStructureMapping(seq, pdbFile,
+ chain.id, pdb, chain, sqmpping, maxAlignseq);
+ seqToStrucMapping.add(mapping);
}
- else
- {
- for (PDBChain chain : pdb.chains)
- {
- StructureMapping curChainMapping = siftsClient
- .getSiftsStructureMapping(seq, pdbFile, chain.id);
- seqToStrucMapping.add(curChainMapping);
- maxChainId = chain.id;
- chain.transferResidueAnnotation(curChainMapping, sqmpping);
- }
- }
- } catch (SiftsException e)
- {
- e.printStackTrace();
- System.err
- .println(">>>>>>> SIFTs mapping could not be obtained... Now mapping with NW alignment");
- seqToStrucMapping = getNWMappings(seq, pdbFile, maxChainId,
- maxChain, pdb, maxAlignseq);
}
}
else
{
- seqToStrucMapping = getNWMappings(seq, pdbFile,
- maxChainId, maxChain, pdb,
- maxAlignseq);
+ setProgressBar(null);
+ setProgressBar("Obtaining mapping with NW alignment");
+ seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
+ maxChain, pdb, maxAlignseq));
}
if (forStructureView)
{
- // mappings.add(seqToStrucMapping);
mappings.addAll(seqToStrucMapping);
}
}
return pdb;
}
- private ArrayList<StructureMapping> getNWMappings(SequenceI seq,
+ private StructureMapping getStructureMapping(SequenceI seq,
+ String pdbFile, String targetChainId, PDBfile pdb,
+ PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
+ AlignSeq maxAlignseq)
+ {
+ String maxChainId = targetChainId;
+ try
+ {
+ StructureMapping curChainMapping = siftsClient
+ .getSiftsStructureMapping(seq, pdbFile, targetChainId);
+ PDBChain chain = pdb.findChain(targetChainId);
+ if (chain != null)
+ {
+ chain.transferResidueAnnotation(curChainMapping, sqmpping);
+ }
+ return curChainMapping;
+ } catch (SiftsException e)
+ {
+ System.err.println(e.getMessage());
+ System.err.println(">>> Now switching mapping with NW alignment...");
+ setProgressBar(null);
+ setProgressBar(">>> Now switching mapping with NW alignment...");
+ return getNWMappings(seq, pdbFile, maxChainId, maxChain, pdb,
+ maxAlignseq);
+ }
+ }
+
+ private StructureMapping getNWMappings(SequenceI seq,
String pdbFile,
String maxChainId, PDBChain maxChain, PDBfile pdb,
AlignSeq maxAlignseq)
StructureMapping nwMapping = new StructureMapping(seq, pdbFile,
pdb.id, maxChainId, mapping, mappingDetails.toString());
maxChain.transferResidueAnnotation(nwMapping, sqmpping);
- ArrayList<StructureMapping> mappings = new ArrayList<StructureMapping>();
- mappings.add(nwMapping);
- return mappings;
+ return nwMapping;
}
public void removeStructureViewerListener(Object svl, String[] pdbfiles)
* the sequence that the mouse over occurred on
* @param indexpos
* the absolute position being mouseovered in seq (0 to seq.length())
- * @param index
+ * @param seqPos
* 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 seqPos,
VamsasSource source)
{
boolean hasSequenceListeners = handlingVamsasMo
|| !seqmappings.isEmpty();
SearchResults results = null;
- if (index == -1)
+ if (seqPos == -1)
{
- index = seq.findPosition(indexpos);
+ seqPos = seq.findPosition(indexpos);
}
for (int i = 0; i < listeners.size(); i++)
{
}
if (listener instanceof StructureListener)
{
- highlightStructure((StructureListener) listener, seq, index);
+ highlightStructure((StructureListener) listener, seq, seqPos);
}
else
{
{
if (results == null)
{
- results = MappingUtils.buildSearchResults(seq, index,
+ results = MappingUtils.buildSearchResults(seq, seqPos,
seqmappings);
}
if (handlingVamsasMo)
{
- results.addResult(seq, index, index);
+ results.addResult(seq, seqPos, seqPos);
}
if (!results.isEmpty())
else if (listener instanceof SecondaryStructureListener)
{
((SecondaryStructureListener) listener).mouseOverSequence(seq,
- indexpos, index);
+ indexpos, seqPos);
}
}
}
/**
* Send suitable messages to a StructureListener to highlight atoms
- * corresponding to the given sequence position.
+ * corresponding to the given sequence position(s)
*
* @param sl
* @param seq
- * @param index
+ * @param positions
*/
- protected void highlightStructure(StructureListener sl, SequenceI seq,
- int index)
+ public void highlightStructure(StructureListener sl, SequenceI seq,
+ int... positions)
{
if (!sl.isListeningFor(seq))
{
{
if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence())
{
- atomNo = sm.getAtomNum(index);
-
- if (atomNo > 0)
+ for (int index : positions)
{
- atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, sm
- .getPDBResNum(index), atomNo));
+ atomNo = sm.getAtomNum(index);
+
+ if (atomNo > 0)
+ {
+ atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, sm
+ .getPDBResNum(index), atomNo));
+ }
}
}
}
/**
* Add each of the given codonFrames to the stored set, if not aready present.
*
- * @param set
+ * @param mappings
*/
- public void registerMappings(Set<AlignedCodonFrame> set)
+ public void registerMappings(List<AlignedCodonFrame> mappings)
{
- if (set != null)
+ if (mappings != null)
{
- for (AlignedCodonFrame acf : set)
+ for (AlignedCodonFrame acf : mappings)
{
registerMapping(acf);
}
}
return null;
}
+
+ public IProgressIndicator getProgressIndicator()
+ {
+ return progressIndicator;
+ }
+
+ public void setProgressIndicator(IProgressIndicator progressIndicator)
+ {
+ this.progressIndicator = progressIndicator;
+ }
+
+ public long getProgressSessionId()
+ {
+ return progressSessionId;
+ }
+
+ public void setProgressSessionId(long progressSessionId)
+ {
+ this.progressSessionId = progressSessionId;
+ }
+
+ public void setProgressBar(String message)
+ {
+ progressIndicator.setProgressBar(message, progressSessionId);
+ }
+
+ public List<AlignedCodonFrame> getSequenceMappings()
+ {
+ return seqmappings;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff