X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructures%2Fmodels%2FAAStructureBindingModel.java;h=b844b5213ec9113cb7ed9195b28037e318a9fdbf;hb=2373f90e6077de127c55ec6cb7671d8ba2436684;hp=12be239e85811c86f3ac277af618d5d04a301986;hpb=c66902a9536b10a5477b58aaf7c2d75772890a5d;p=jalview.git diff --git a/src/jalview/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java index 12be239..b844b52 100644 --- a/src/jalview/structures/models/AAStructureBindingModel.java +++ b/src/jalview/structures/models/AAStructureBindingModel.java @@ -1,17 +1,22 @@ package jalview.structures.models; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; + import jalview.api.StructureSelectionManagerProvider; +import jalview.datamodel.AlignmentI; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; +import jalview.structure.AtomSpec; import jalview.structure.StructureListener; +import jalview.structure.StructureMapping; import jalview.structure.StructureSelectionManager; +import jalview.util.Comparison; import jalview.util.MessageManager; -import java.awt.event.ComponentEvent; -import java.util.ArrayList; -import java.util.List; - /** + * * A base class to hold common function for protein structure model binding. * Initial version created by refactoring JMol and Chimera binding models, but * other structure viewers could in principle be accommodated in future. @@ -45,6 +50,39 @@ public abstract class AAStructureBindingModel extends protected boolean colourBySequence = true; + private boolean nucleotide; + + private boolean finishedInit = false; + + /** + * Data bean class to simplify parameterisation in superposeStructures + */ + protected class SuperposeData + { + /** + * Constructor with alignment width argument + * + * @param width + */ + public SuperposeData(int width) + { + pdbResNo = new int[width]; + } + + public String filename; + + public String pdbId; + + public String chain = ""; + + public boolean isRna; + + /* + * The pdb residue number (if any) mapped to each column of the alignment + */ + public int[] pdbResNo; + } + /** * Constructor * @@ -73,6 +111,7 @@ public abstract class AAStructureBindingModel extends { this.ssm = ssm; this.sequence = sequenceIs; + this.nucleotide = Comparison.isNucleotide(sequenceIs); this.chains = chains; this.pdbEntry = pdbentry; this.protocol = protocol; @@ -99,6 +138,27 @@ public abstract class AAStructureBindingModel extends } /** + * Answers true if this binding includes the given PDB id, else false + * + * @param pdbId + * @return + */ + public boolean hasPdbId(String pdbId) + { + if (pdbEntry != null) + { + for (PDBEntry pdb : pdbEntry) + { + if (pdb.getId().equals(pdbId)) + { + return true; + } + } + } + return false; + } + + /** * Returns the number of modelled PDB file entries. * * @return @@ -342,4 +402,237 @@ public abstract class AAStructureBindingModel extends addSequenceAndChain(pe, seq, null); } + /** + * add the given sequences to the mapping scope for the given pdb file handle + * + * @param pdbFile + * - pdbFile identifier + * @param seq + * - set of sequences it can be mapped to + */ + public void addSequenceForStructFile(String pdbFile, SequenceI[] seq) + { + for (int pe = 0; pe < getPdbCount(); pe++) + { + if (getPdbEntry(pe).getFile().equals(pdbFile)) + { + addSequence(pe, seq); + } + } + } + + @Override + public abstract void highlightAtoms(List atoms); + + protected boolean isNucleotide() + { + return this.nucleotide; + } + + /** + * Returns a readable description of all mappings for the wrapped pdbfile to + * any mapped sequences + * + * @param pdbfile + * @param seqs + * @return + */ + public String printMappings() + { + if (pdbEntry == null) + { + return ""; + } + StringBuilder sb = new StringBuilder(128); + for (int pdbe = 0; pdbe < getPdbCount(); pdbe++) + { + String pdbfile = getPdbEntry(pdbe).getFile(); + List seqs = Arrays.asList(getSequence()[pdbe]); + sb.append(getSsm().printMappings(pdbfile, seqs)); + } + return sb.toString(); + } + + /** + * Returns the mapped structure position for a given aligned column of a given + * sequence, or -1 if the column is gapped, beyond the end of the sequence, or + * not mapped to structure. + * + * @param seq + * @param alignedPos + * @param mapping + * @return + */ + protected int getMappedPosition(SequenceI seq, int alignedPos, + StructureMapping mapping) + { + if (alignedPos >= seq.getLength()) + { + return -1; + } + + if (Comparison.isGap(seq.getCharAt(alignedPos))) + { + return -1; + } + int seqPos = seq.findPosition(alignedPos); + int pos = mapping.getPDBResNum(seqPos); + return pos; + } + + /** + * Helper method to identify residues that can participate in a structure + * superposition command. For each structure, identify a sequence in the + * alignment which is mapped to the structure. Identify non-gapped columns in + * the sequence which have a mapping to a residue in the structure. Returns + * the index of the first structure that has a mapping to the alignment. + * + * @param alignment + * the sequence alignment which is the basis of structure + * superposition + * @param matched + * an array of booleans, indexed by alignment column, where true + * indicates that every structure has a mapped residue present in the + * column (so the column can participate in structure alignment) + * @param structures + * an array of data beans corresponding to pdb file index + * @return + */ + protected int findSuperposableResidues(AlignmentI alignment, + boolean[] matched, SuperposeData[] structures) + { + int refStructure = -1; + String[] files = getPdbFile(); + for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + { + StructureMapping[] mappings = getSsm().getMapping(files[pdbfnum]); + int lastPos = -1; + + /* + * Find the first mapped sequence (if any) for this PDB entry which is in + * the alignment + */ + final int seqCountForPdbFile = getSequence()[pdbfnum].length; + for (int s = 0; s < seqCountForPdbFile; s++) + { + for (StructureMapping mapping : mappings) + { + final SequenceI theSequence = getSequence()[pdbfnum][s]; + if (mapping.getSequence() == theSequence + && alignment.findIndex(theSequence) > -1) + { + if (refStructure < 0) + { + refStructure = pdbfnum; + } + for (int r = 0; r < matched.length; r++) + { + if (!matched[r]) + { + continue; + } + int pos = getMappedPosition(theSequence, r, mapping); + if (pos < 1 || pos == lastPos) + { + matched[r] = false; + continue; + } + lastPos = pos; + structures[pdbfnum].pdbResNo[r] = pos; + } + String chain = mapping.getChain(); + if (chain != null && chain.trim().length() > 0) + { + structures[pdbfnum].chain = chain; + } + structures[pdbfnum].pdbId = mapping.getPdbId(); + structures[pdbfnum].isRna = theSequence.getRNA() != null; + // move on to next pdb file + s = seqCountForPdbFile; + break; + } + } + } + } + return refStructure; + } + + /** + * Returns true if the structure viewer has loaded all of the files of + * interest (identified by the file mapping having been set up), or false if + * any are still not loaded after a timeout interval. + * + * @param files + */ + protected boolean waitForFileLoad(String[] files) + { + /* + * give up after 10 secs plus 1 sec per file + */ + long starttime = System.currentTimeMillis(); + long endTime = 10000 + 1000 * files.length + starttime; + String notLoaded = null; + + boolean waiting = true; + while (waiting && System.currentTimeMillis() < endTime) + { + waiting = false; + for (String file : files) + { + notLoaded = file; + try + { + StructureMapping[] sm = getSsm().getMapping(file); + if (sm == null || sm.length == 0) + { + waiting = true; + } + } catch (Throwable x) + { + waiting = true; + } + } + } + + if (waiting) + { + System.err + .println("Timed out waiting for structure viewer to load file " + + notLoaded); + return false; + } + return true; + } + + @Override + public boolean isListeningFor(SequenceI seq) + { + if (sequence != null) + { + for (SequenceI[] seqs : sequence) + { + if (seqs != null) + { + for (SequenceI s : seqs) + { + if (s == seq) + { + return true; + } + } + } + } + } + return false; + } + + public boolean isFinishedInit() + { + return finishedInit; + } + + public void setFinishedInit(boolean fi) + { + this.finishedInit = fi; + } } \ No newline at end of file