X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=b973f45f869a381d6e052ea355a51482c77977a4;hb=6efcc6b872e24abc34363d37577eac99a8756614;hp=428cf6d06eb38d3108ceff4f36bc4eade9339fa2;hpb=bdf1428136ce701e58a90f346973dbdf9d42b316;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 428cf6d..b973f45 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -29,12 +29,14 @@ import jalview.datamodel.AlignedCodonFrame; 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; @@ -159,8 +161,8 @@ public class StructureSelectionManager } 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) { @@ -212,9 +214,8 @@ public class StructureSelectionManager { 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"))); } @@ -339,7 +340,9 @@ public class StructureSelectionManager * - 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>, empty lists indicate no + * predefined mappings * @param pdbFile * - structure data resource * @param sourceType @@ -384,6 +387,7 @@ public class StructureSelectionManager boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts(); try { + sourceType = AppletFormatAdapter.checkProtocol(pdbFile); pdb = new JmolParser(pdbFile, sourceType); if (pdb.getId() != null && pdb.getId().trim().length() > 0 @@ -430,8 +434,8 @@ public class StructureSelectionManager } 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) @@ -454,7 +458,7 @@ public class StructureSelectionManager * Attempt pairwise alignment of the sequence with each chain in the PDB, * and remember the highest scoring chain */ - int max = -10; + float max = -10; AlignSeq maxAlignseq = null; String maxChainId = " "; PDBChain maxChain = null; @@ -574,8 +578,8 @@ public class StructureSelectionManager setProgressBar(null); setProgressBar(MessageManager .getString("status.obtaining_mapping_with_nw_alignment")); - StructureMapping nwMapping = getNWMappings(seq, pdbFile, - maxChainId, maxChain, pdb, maxAlignseq); + StructureMapping nwMapping = getNWMappings(seq, pdbFile, maxChainId, + maxChain, pdb, maxAlignseq); seqToStrucMapping.add(nwMapping); ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); @@ -589,11 +593,9 @@ public class StructureSelectionManager return pdb; } - private boolean isCIFFile(String filename) + public void addStructureMapping(StructureMapping sm) { - String fileExt = filename.substring(filename.lastIndexOf(".") + 1, - filename.length()); - return "cif".equalsIgnoreCase(fileExt); + mappings.add(sm); } /** @@ -636,8 +638,8 @@ public class StructureSelectionManager AlignSeq maxAlignseq) { 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"); @@ -669,11 +671,12 @@ public class StructureSelectionManager .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 @@ -695,8 +698,9 @@ public class StructureSelectionManager 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 }); } } @@ -741,7 +745,7 @@ public class StructureSelectionManager if (listeners.elementAt(i) instanceof StructureListener) { sl = (StructureListener) listeners.elementAt(i); - for (String pdbfile : sl.getPdbFile()) + for (String pdbfile : sl.getStructureFiles()) { pdbs.remove(pdbfile); } @@ -774,7 +778,8 @@ public class StructureSelectionManager * @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 atoms = Collections.singletonList(atomSpec); @@ -806,7 +811,8 @@ public class StructureSelectionManager return; } - SearchResultsI results = findAlignmentPositionsForStructurePositions(atoms); + SearchResultsI results = findAlignmentPositionsForStructurePositions( + atoms); for (Object li : listeners) { if (li instanceof SequenceListener) @@ -949,8 +955,7 @@ public class StructureSelectionManager List atoms = new ArrayList(); 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())) { @@ -960,8 +965,8 @@ public class StructureSelectionManager 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)); } } } @@ -1203,13 +1208,14 @@ public class StructureSelectionManager 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); } } } @@ -1326,8 +1332,8 @@ public class StructureSelectionManager { 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) {