X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=b6bb70d198c455626cf6c438ee773796f9ba24cf;hb=a4ace9297e743fb504dffd43ebb11074db263e10;hp=e9053ed0d65b3c615fc490d813892d5aa012b8e4;hpb=4ff572f7cf17f5ca9c23f82bbe41005af8af55cc;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index e9053ed..b6bb70d 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -32,11 +32,13 @@ import jalview.datamodel.Annotation; 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; @@ -45,10 +47,8 @@ import java.util.Collections; 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; @@ -69,10 +69,16 @@ public class StructureSelectionManager private boolean addTempFacAnnot = false; + private IProgressIndicator progressIndicator; + + private SiftsClient siftsClient = null; + + private long progressSessionId; + /* * Set of any registered mappings between (dataset) sequences. */ - public Set seqmappings = new LinkedHashSet(); + private List seqmappings = new ArrayList(); private List commandListeners = new ArrayList(); @@ -373,9 +379,7 @@ public class StructureSelectionManager } } 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, @@ -482,63 +486,73 @@ public class StructureSelectionManager pdbFile = "INLINE" + pdb.id; } - ArrayList seqToStrucMapping = null; + ArrayList seqToStrucMapping = new ArrayList(); 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(); - 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 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) @@ -613,9 +627,7 @@ public class StructureSelectionManager StructureMapping nwMapping = new StructureMapping(seq, pdbFile, pdb.id, maxChainId, mapping, mappingDetails.toString()); maxChain.transferResidueAnnotation(nwMapping, sqmpping); - ArrayList mappings = new ArrayList(); - mappings.add(nwMapping); - return mappings; + return nwMapping; } public void removeStructureViewerListener(Object svl, String[] pdbfiles) @@ -756,19 +768,19 @@ public class StructureSelectionManager * 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++) { @@ -781,7 +793,7 @@ public class StructureSelectionManager } if (listener instanceof StructureListener) { - highlightStructure((StructureListener) listener, seq, index); + highlightStructure((StructureListener) listener, seq, seqPos); } else { @@ -795,12 +807,12 @@ public class StructureSelectionManager { 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()) @@ -818,7 +830,7 @@ public class StructureSelectionManager else if (listener instanceof SecondaryStructureListener) { ((SecondaryStructureListener) listener).mouseOverSequence(seq, - indexpos, index); + indexpos, seqPos); } } } @@ -826,14 +838,14 @@ public class StructureSelectionManager /** * 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)) { @@ -845,12 +857,15 @@ public class StructureSelectionManager { 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)); + } } } } @@ -1006,13 +1021,13 @@ public class StructureSelectionManager /** * Add each of the given codonFrames to the stored set, if not aready present. * - * @param set + * @param mappings */ - public void registerMappings(Set set) + public void registerMappings(List mappings) { - if (set != null) + if (mappings != null) { - for (AlignedCodonFrame acf : set) + for (AlignedCodonFrame acf : mappings) { registerMapping(acf); } @@ -1224,4 +1239,35 @@ public class StructureSelectionManager } 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 getSequenceMappings() + { + return seqmappings; + } + }