import jalview.analysis.AlignSeq;
import jalview.api.StructureSelectionManagerProvider;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
import jalview.commands.OrderCommand;
* @return null or the structure data parsed as a pdb file
*/
synchronized public StructureFile setMapping(SequenceI[] sequence,
- String[] targetChains, String pdbFile, DataSourceType protocol,
+ String[] targetChains, String pdbFile, DataSourceType protocol,
IProgressIndicator progress)
{
return computeMapping(true, sequence, targetChains, pdbFile, protocol,
* mapping operation
* @return null or the structure data parsed as a pdb file
*/
- synchronized public StructureFile computeMapping(
- boolean forStructureView, SequenceI[] sequenceArray,
- String[] targetChainIds, String pdbFile, DataSourceType sourceType,
+ synchronized public StructureFile computeMapping(boolean forStructureView,
+ SequenceI[] sequenceArray, String[] targetChainIds,
+ String pdbFile, DataSourceType sourceType,
IProgressIndicator progress)
{
long progressSessionId = System.currentTimeMillis() * 3;
registerPDBFile(pdb.getId().trim(), pdbFile);
}
// if PDBId is unavailable then skip SIFTS mapping execution path
- // TODO: JAL-3868 need to know if structure is actually from
- // PDB (has valid PDB ID and has provenance suggesting it
+ // TODO: JAL-3868 need to know if structure is actually from
+ // PDB (has valid PDB ID and has provenance suggesting it
// actually came from PDB)
boolean isProtein = false;
- for (SequenceI s:sequenceArray) {
- if (s.isProtein()) {
+ for (SequenceI s : sequenceArray)
+ {
+ if (s.isProtein())
+ {
isProtein = true;
break;
}
}
- isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable() && !pdb.getId().startsWith("AF-") && isProtein;
+ isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable()
+ && !pdb.getId().startsWith("AF-") && isProtein;
} catch (Exception ex)
{
} catch (SiftsException e)
{
isMapUsingSIFTs = false;
- Cache.log.error("SIFTS mapping failed", e);
- Cache.log.error("Falling back on Needleman & Wunsch alignment");
+ Console.error("SIFTS mapping failed", e);
+ Console.error("Falling back on Needleman & Wunsch alignment");
siftsClient = null;
}
List<StructureMapping> seqToStrucMapping = new ArrayList<>();
if (isMapUsingSIFTs && seq.isProtein())
{
- if (progress!=null) {
- progress.setProgressBar(MessageManager
- .getString("status.obtaining_mapping_with_sifts"),
+ if (progress != null)
+ {
+ progress.setProgressBar(
+ MessageManager
+ .getString("status.obtaining_mapping_with_sifts"),
progressSessionId);
}
jalview.datamodel.Mapping sqmpping = maxAlignseq
pdb, maxChain, sqmpping, maxAlignseq, siftsClient);
seqToStrucMapping.add(siftsMapping);
maxChain.makeExactMapping(siftsMapping, seq);
- maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS",pdb.getId().toLowerCase(Locale.ROOT));
+ maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS",
+ pdb.getId().toLowerCase(Locale.ROOT));
maxChain.transferResidueAnnotation(siftsMapping, null);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
} catch (SiftsException e)
{
// fall back to NW alignment
- Cache.log.error(e.getMessage());
+ Console.error(e.getMessage());
StructureMapping nwMapping = getNWMappings(seq, pdbFile,
targetChainId, maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
maxChain.makeExactMapping(maxAlignseq, seq);
- maxChain.transferRESNUMFeatures(seq, "IEA:Jalview",pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is
- // this
- // "IEA:Jalview" ?
+ maxChain.transferRESNUMFeatures(seq, "IEA:Jalview",
+ pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is
+ // this
+ // "IEA:Jalview" ?
maxChain.transferResidueAnnotation(nwMapping, sqmpping);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
}
StructureMapping siftsMapping = null;
try
{
- siftsMapping = getStructureMapping(seq,
- pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq,
- siftsClient);
+ siftsMapping = getStructureMapping(seq, pdbFile, chain.id,
+ pdb, chain, sqmpping, maxAlignseq, siftsClient);
foundSiftsMappings.add(siftsMapping);
chain.makeExactMapping(siftsMapping, seq);
- chain.transferRESNUMFeatures(seq, "IEA: SIFTS",pdb.getId().toLowerCase(Locale.ROOT));// FIXME: is this
+ chain.transferRESNUMFeatures(seq, "IEA: SIFTS",
+ pdb.getId().toLowerCase(Locale.ROOT));// FIXME: is this
// "IEA:SIFTS" ?
chain.transferResidueAnnotation(siftsMapping, null);
} catch (SiftsException e)
{
System.err.println(e.getMessage());
- }
- catch (Exception e)
+ } catch (Exception e)
{
- System.err
- .println(
- "Unexpected exception during SIFTS mapping - falling back to NW for this sequence/structure pair");
+ System.err.println(
+ "Unexpected exception during SIFTS mapping - falling back to NW for this sequence/structure pair");
System.err.println(e.getMessage());
}
}
StructureMapping nwMapping = getNWMappings(seq, pdbFile,
maxChainId, maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
- maxChain.transferRESNUMFeatures(seq, null,pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is this
- // "IEA:Jalview" ?
+ maxChain.transferRESNUMFeatures(seq, null,
+ pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is this
+ // "IEA:Jalview" ?
maxChain.transferResidueAnnotation(nwMapping, sqmpping);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
}
{
if (progress != null)
{
- progress.setProgressBar(MessageManager
- .getString("status.obtaining_mapping_with_nw_alignment"),
+ progress.setProgressBar(
+ MessageManager.getString(
+ "status.obtaining_mapping_with_nw_alignment"),
progressSessionId);
}
StructureMapping nwMapping = getNWMappings(seq, pdbFile, maxChainId,
private StructureMapping getStructureMapping(SequenceI seq,
String pdbFile, String targetChainId, StructureFile pdb,
PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
- AlignSeq maxAlignseq, SiftsClient siftsClient) throws SiftsException
+ AlignSeq maxAlignseq, SiftsClient siftsClient)
+ throws SiftsException
{
StructureMapping curChainMapping = siftsClient
.getSiftsStructureMapping(seq, pdbFile, targetChainId);
maxChain.makeExactMapping(maxAlignseq, seq);
jalview.datamodel.Mapping sqmpping = maxAlignseq
.getMappingFromS1(false);
- maxChain.transferRESNUMFeatures(seq, null, pdb.getId().toLowerCase(Locale.ROOT));
+ maxChain.transferRESNUMFeatures(seq, null,
+ pdb.getId().toLowerCase(Locale.ROOT));
HashMap<Integer, int[]> mapping = new HashMap<>();
int resNum = -10000;
}
/**
+ * hack to highlight a range of positions at once on any structure views
+ *
+ * @param sequenceRef
+ * @param is
+ * - series of int start-end ranges as positions on sequenceRef
+ * @param i
+ * @param object
+ */
+ public void highlightPositionsOn(SequenceI sequenceRef, int[][] is,
+ Object source)
+ {
+ boolean hasSequenceListeners = handlingVamsasMo
+ || !seqmappings.isEmpty();
+ SearchResultsI results = null;
+ ArrayList<Integer> listOfPositions = new ArrayList<Integer>();
+ for (int[] s_e : is)
+ {
+ for (int p = s_e[0]; p <= s_e[1]; listOfPositions.add(p++))
+ ;
+ }
+ int seqpos[] = new int[listOfPositions.size()];
+ int i = 0;
+ for (Integer p : listOfPositions)
+ {
+ seqpos[i++] = p;
+ }
+
+ for (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, sequenceRef,
+ seqpos);
+ }
+
+ }
+ }
+
+ /**
* Propagate mouseover of a single position in a structure
*
* @param pdbResNum
git://source.jalview.org / jalview.git / blobdiff