X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=24320b54276f0f29539677311bd6a85a6914c0ff;hb=refs%2Fheads%2Ffeatures%2Fr2_11_2_alphafold%2FJAL-2349_JAL-3855;hp=6319338e4cb80b67d2e21e1dbb05fcc63e4ea3b9;hpb=7720585dc8cc56cdad2486b330ed37ddd0133531;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 6319338..24320b5 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -28,12 +28,13 @@ import java.util.Enumeration; import java.util.HashMap; import java.util.IdentityHashMap; import java.util.List; +import java.util.Locale; import java.util.Map; import java.util.Vector; 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; @@ -41,6 +42,7 @@ import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; +import jalview.datamodel.ContiguousI; import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; import jalview.datamodel.SearchResults; @@ -320,7 +322,7 @@ public class StructureSelectionManager * @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, @@ -377,9 +379,9 @@ public class StructureSelectionManager * 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; @@ -410,7 +412,20 @@ public class StructureSelectionManager registerPDBFile(pdb.getId().trim(), pdbFile); } // if PDBId is unavailable then skip SIFTS mapping execution path - isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable(); + // 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()) + { + isProtein = true; + break; + } + } + isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable() + && !pdb.getId().startsWith("AF-") && isProtein; } catch (Exception ex) { @@ -430,7 +445,8 @@ public class StructureSelectionManager } catch (SiftsException e) { isMapUsingSIFTs = false; - e.printStackTrace(); + Console.error("SIFTS mapping failed", e); + Console.error("Falling back on Needleman & Wunsch alignment"); siftsClient = null; } @@ -521,9 +537,11 @@ public class StructureSelectionManager List 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 @@ -537,21 +555,23 @@ public class StructureSelectionManager pdb, maxChain, sqmpping, maxAlignseq, siftsClient); seqToStrucMapping.add(siftsMapping); maxChain.makeExactMapping(siftsMapping, seq); - maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS"); + 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"); // 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)); } @@ -564,23 +584,21 @@ public class StructureSelectionManager 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");// 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()); } } @@ -594,8 +612,9 @@ public class StructureSelectionManager StructureMapping nwMapping = getNWMappings(seq, pdbFile, maxChainId, maxChain, pdb, maxAlignseq); seqToStrucMapping.add(nwMapping); - maxChain.transferRESNUMFeatures(seq, null); // 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)); } @@ -605,8 +624,9 @@ public class StructureSelectionManager { 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, @@ -696,7 +716,8 @@ public class StructureSelectionManager 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); @@ -762,7 +783,8 @@ public class StructureSelectionManager maxChain.makeExactMapping(maxAlignseq, seq); jalview.datamodel.Mapping sqmpping = maxAlignseq .getMappingFromS1(false); - maxChain.transferRESNUMFeatures(seq, null); + maxChain.transferRESNUMFeatures(seq, null, + pdb.getId().toLowerCase(Locale.ROOT)); HashMap mapping = new HashMap<>(); int resNum = -10000; @@ -853,6 +875,52 @@ public class StructureSelectionManager } /** + * 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 listOfPositions = new ArrayList(); + 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 @@ -1062,6 +1130,62 @@ public class StructureSelectionManager sl.highlightAtoms(atoms); } + public void highlightStructureRegionsFor(StructureListener sl, + SequenceI[] seqs, int... columns) + { + List to_highlight = new ArrayList(); + for (SequenceI seq : seqs) + { + if (sl.isListeningFor(seq)) + { + to_highlight.add(seq); + } + } + if (to_highlight.size() == 0) + { + return; + } + List atoms = new ArrayList<>(); + for (SequenceI seq : to_highlight) + { + int atomNo; + for (StructureMapping sm : mappings) + { + if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence() + || (sm.sequence.getDatasetSequence() != null && sm.sequence + .getDatasetSequence() == seq.getDatasetSequence())) + { + + for (int i = 0; i < columns.length; i += 2) + { + ContiguousI positions = seq.findPositions(columns[i] + 1, + columns[i + 1] + 1); + if (positions == null) + { + continue; + } + for (int index = positions.getBegin(); index <= positions + .getEnd(); index++) + { + + atomNo = sm.getAtomNum(index); + + if (atomNo > 0) + { + atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, + sm.getPDBResNum(index), atomNo)); + } + } + } + } + } + if (atoms.size() > 0) + { + sl.highlightAtoms(atoms); + } + } + } + /** * true if a mouse over event from an external (ie Vamsas) source is being * handled @@ -1440,4 +1564,34 @@ public class StructureSelectionManager return seqmappings; } + /** + * quick and dirty route to just highlight all structure positions for a range + * of columns + * + * @param sequencesArray + * @param is + * start-end columns on sequencesArray + * @param source + * origin parent AlignmentPanel + */ + public void highlightPositionsOnMany(SequenceI[] sequencesArray, int[] is, + Object source) + { + for (int 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) + { + highlightStructureRegionsFor((StructureListener) listener, + sequencesArray, is); + } + } + } + }