X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=904a8601f18865002dc0a43cc4870b80475fe1bb;hb=refs%2Fheads%2Freleases%2FRelease_2_11_Branch;hp=1f4701477e1f4f7849ccda827b9a823929bf873e;hpb=4816a1eeeec4c5b9ff845a711b2e10d621aed6e8;p=jalview.git diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java index 1f47014..904a860 100755 --- a/src/MCview/PDBChain.java +++ b/src/MCview/PDBChain.java @@ -41,20 +41,15 @@ public class PDBChain { public static final String RESNUM_FEATURE = "RESNUM"; - /** - * SequenceFeature group for PDB File features added to sequences - */ - private static final String PDBFILEFEATURE = "PDBFile"; - private static final String IEASTATUS = "IEA:jalview"; public String id; - public Vector bonds = new Vector(); + public Vector bonds = new Vector<>(); - public Vector atoms = new Vector(); + public Vector atoms = new Vector<>(); - public Vector residues = new Vector(); + public Vector residues = new Vector<>(); public int offset; @@ -83,10 +78,10 @@ public class PDBChain public String pdbid = ""; - public PDBChain(String pdbid, String id) + public PDBChain(String thePdbid, String theId) { - this.pdbid = pdbid == null ? pdbid : pdbid.toLowerCase(); - this.id = id; + this.pdbid = thePdbid == null ? thePdbid : thePdbid.toLowerCase(); + this.id = theId; } /** @@ -167,15 +162,58 @@ public class PDBChain } /** - * copy over the RESNUM seqfeatures from the internal chain sequence to the + * Annotate the residues with their corresponding positions in s1 using the + * alignment in as NOTE: This clears all atom.alignmentMapping values on the + * structure. + * + * @param as + * @param s1 + */ + public void makeExactMapping(StructureMapping mapping, SequenceI s1) + { + // first clear out any old alignmentMapping values: + for (Atom atom : atoms) + { + atom.alignmentMapping = -1; + } + SequenceI ds = s1; + while (ds.getDatasetSequence() != null) + { + ds = ds.getDatasetSequence(); + } + int pdboffset = 0; + for (Residue res : residues) + { + // res.number isn't set correctly for discontinuous/mismapped residues + int seqpos = mapping.getSeqPos(res.atoms.get(0).resNumber); + char strchar = sequence.getCharAt(pdboffset++); + if (seqpos == StructureMapping.UNASSIGNED_VALUE) + { + continue; + } + char seqchar = ds.getCharAt(seqpos - ds.getStart()); + + boolean sameResidue = Comparison.isSameResidue( + seqchar, strchar, false); + if (sameResidue) + { + for (Atom atom : res.atoms) + { + atom.alignmentMapping = seqpos - 1; + } + } + } + } + + /** + * Copies over the RESNUM seqfeatures from the internal chain sequence to the * mapped sequence * * @param seq * @param status * The Status of the transferred annotation - * @return the features added to sq (or its dataset) */ - public SequenceFeature[] transferRESNUMFeatures(SequenceI seq, + public void transferRESNUMFeatures(SequenceI seq, String status) { SequenceI sq = seq; @@ -184,10 +222,11 @@ public class PDBChain sq = sq.getDatasetSequence(); if (sq == sequence) { - return null; + return; } } - /** + + /* * Remove any existing features for this chain if they exist ? * SequenceFeature[] seqsfeatures=seq.getSequenceFeatures(); int * totfeat=seqsfeatures.length; // Remove any features for this exact chain @@ -197,25 +236,22 @@ public class PDBChain { status = PDBChain.IEASTATUS; } - SequenceFeature[] features = sequence.getSequenceFeatures(); - if (features == null) - { - return null; - } - for (int i = 0; i < features.length; i++) + + List features = sequence.getSequenceFeatures(); + for (SequenceFeature feature : features) { - if (features[i].getFeatureGroup() != null - && features[i].getFeatureGroup().equals(pdbid)) + if (feature.getFeatureGroup() != null + && feature.getFeatureGroup().equals(pdbid)) { - int newBegin = 1 + residues.elementAt(features[i].getBegin() - - offset).atoms + int newBegin = 1 + residues.elementAt(feature.getBegin() - offset).atoms .elementAt(0).alignmentMapping; - int newEnd = 1 + residues.elementAt(features[i].getEnd() - offset).atoms + int newEnd = 1 + residues.elementAt(feature.getEnd() - offset).atoms .elementAt(0).alignmentMapping; - SequenceFeature tx = new SequenceFeature(features[i], newBegin, - newEnd, features[i].getFeatureGroup()); + SequenceFeature tx = new SequenceFeature(feature, newBegin, newEnd, + feature.getFeatureGroup(), feature.getScore()); tx.setStatus(status - + ((tx.getStatus() == null || tx.getStatus().length() == 0) ? "" + + ((tx.getStatus() == null || tx.getStatus().length() == 0) + ? "" : ":" + tx.getStatus())); if (tx.begin != 0 && tx.end != 0) { @@ -223,7 +259,6 @@ public class PDBChain } } } - return features; } /** @@ -308,12 +343,13 @@ public class PDBChain boolean deoxyn = false; boolean nucleotide = false; StringBuilder seq = new StringBuilder(256); - Vector resFeatures = new Vector(); - Vector resAnnotation = new Vector(); - int i, iSize = atoms.size() - 1; + Vector resFeatures = new Vector<>(); + Vector resAnnotation = new Vector<>(); + int iSize = atoms.size() - 1; int resNumber = -1; char insCode = ' '; - for (i = 0; i <= iSize; i++) + + for (int i = 0; i <= iSize; i++) { Atom tmp = atoms.elementAt(i); resNumber = tmp.resNumber; @@ -327,7 +363,7 @@ public class PDBChain offset = resNumber; } - Vector resAtoms = new Vector(); + Vector resAtoms = new Vector<>(); // Add atoms to a vector while the residue number // remains the same as the first atom's resNumber (res) while ((resNumber == res) && (ins == insCode) && (i < atoms.size())) @@ -351,47 +387,48 @@ public class PDBChain // Add inserted residues as features to the base residue Atom currAtom = resAtoms.get(0); - if (currAtom.insCode != ' ' - && !residues.isEmpty() - && residues.lastElement().atoms.get(0).resNumber == currAtom.resNumber) + if (currAtom.insCode != ' ' && !residues.isEmpty() + && residues.lastElement().atoms + .get(0).resNumber == currAtom.resNumber) { - SequenceFeature sf = new SequenceFeature("INSERTION", - currAtom.resName + ":" + currAtom.resNumIns + " " + pdbid - + id, "", offset + count - 1, offset + count - 1, - "PDB_INS"); + String desc = currAtom.resName + ":" + currAtom.resNumIns + " " + + pdbid + id; + SequenceFeature sf = new SequenceFeature("INSERTION", desc, offset + + count - 1, offset + count - 1, "PDB_INS"); resFeatures.addElement(sf); residues.lastElement().atoms.addAll(resAtoms); } else { - // Make a new Residue object with the new atoms vector residues.addElement(new Residue(resAtoms, resNumber - 1, count)); Residue tmpres = residues.lastElement(); Atom tmpat = tmpres.atoms.get(0); // Make A new SequenceFeature for the current residue numbering - SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE, tmpat.resName - + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset - + count, offset + count, pdbid); + String desc = tmpat.resName + + ":" + tmpat.resNumIns + " " + pdbid + id; + SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE, desc, + offset + count, offset + count, pdbid); resFeatures.addElement(sf); resAnnotation.addElement(new Annotation(tmpat.tfactor)); // Keep totting up the sequence - if ((symbol = ResidueProperties.getAA3Hash().get(tmpat.resName)) == null) + if ((symbol = ResidueProperties.getAA3Hash() + .get(tmpat.resName)) == null) { String nucname = tmpat.resName.trim(); // use the aaIndex rather than call 'toLower' - which would take a bit // more time. deoxyn = nucname.length() == 2 - && ResidueProperties.aaIndex[nucname.charAt(0)] == ResidueProperties.aaIndex['D']; + && ResidueProperties.aaIndex[nucname + .charAt(0)] == ResidueProperties.aaIndex['D']; if (tmpat.name.equalsIgnoreCase("CA") || ResidueProperties.nucleotideIndex[nucname .charAt((deoxyn ? 1 : 0))] == -1) { - char r = ResidueProperties - .getSingleCharacterCode(ResidueProperties - .getCanonicalAminoAcid(tmpat.resName)); + char r = ResidueProperties.getSingleCharacterCode( + ResidueProperties.getCanonicalAminoAcid(tmpat.resName)); seq.append(r == '0' ? 'X' : r); // System.err.println("PDBReader:Null aa3Hash for " + // tmpat.resName); @@ -407,8 +444,8 @@ public class PDBChain { if (nucleotide) { - System.err - .println("Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!"); + System.err.println( + "Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!"); } seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]); } @@ -433,7 +470,8 @@ public class PDBChain if (StructureImportSettings.isShowSeqFeatures()) { - for (i = 0, iSize = resFeatures.size(); i < iSize; i++) + iSize = resFeatures.size(); + for (int i = 0; i < iSize; i++) { sequence.addSequenceFeature(resFeatures.elementAt(i)); resFeatures.setElementAt(null, i); @@ -442,20 +480,20 @@ public class PDBChain if (visibleChainAnnotation) { Annotation[] annots = new Annotation[resAnnotation.size()]; - float max = 0; - for (i = 0, iSize = annots.length; i < iSize; i++) + float max = 0f; + float min = 0f; + iSize = annots.length; + for (int i = 0; i < iSize; i++) { annots[i] = resAnnotation.elementAt(i); - if (annots[i].value > max) - { - max = annots[i].value; - } + max = Math.max(max, annots[i].value); + min = Math.min(min, annots[i].value); resAnnotation.setElementAt(null, i); } AlignmentAnnotation tfactorann = new AlignmentAnnotation( "Temperature Factor", "Temperature Factor for " + pdbid + id, - annots, 0, max, AlignmentAnnotation.LINE_GRAPH); + annots, min, max, AlignmentAnnotation.LINE_GRAPH); tfactorann.setSequenceRef(sequence); sequence.addAlignmentAnnotation(tfactorann); } @@ -520,8 +558,8 @@ public class PDBChain try { index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue(); - b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0), - 0, null, null, 0f); + b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0), 0, + null, null, 0f); index = ResidueProperties.aa3Hash.get(b.at2.resName).intValue(); b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0), 0, @@ -558,6 +596,12 @@ public class PDBChain { SequenceI sq = mapping.getSequence(); SequenceI dsq = sq; + if (sqmpping == null) + { + // SIFTS mappings are recorded in the StructureMapping object... + + sqmpping = mapping.getSeqToPdbMapping(); + } if (sq != null) { while (dsq.getDatasetSequence() != null) @@ -571,8 +615,8 @@ public class PDBChain for (AlignmentAnnotation ana : shadow.getAnnotation()) { - List transfer = sq.getAlignmentAnnotations( - ana.getCalcId(), ana.label); + List transfer = sq + .getAlignmentAnnotations(ana.getCalcId(), ana.label); if (transfer == null || transfer.size() == 0) { ana = new AlignmentAnnotation(ana); @@ -613,7 +657,8 @@ public class PDBChain // Useful for debugging mappings - adds annotation for mapped position float min = -1, max = 0; Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1]; - for (int i = sq.getStart(), j = sq.getEnd(), k = 0; i <= j; i++, k++) + for (int i = sq.getStart(), j = sq + .getEnd(), k = 0; i <= j; i++, k++) { int prn = mapping.getPDBResNum(k + 1);