X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2FMCview%2FPDBChain.java;h=f4bd31c13774b3e59b3128100383ea04265fc5fe;hb=refs%2Fheads%2Fportforward%2FJAL-2675_2102b1to2103;hp=91526e19e24233f02943c90fd78f8a8f59a95b97;hpb=43ee8686fab13cd6952335ade1382adf3226f7a1;p=jalview.git diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java index 91526e1..f4bd31c 100755 --- a/src/MCview/PDBChain.java +++ b/src/MCview/PDBChain.java @@ -29,8 +29,9 @@ import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.schemes.ColourSchemeI; import jalview.schemes.ResidueProperties; +import jalview.structure.StructureImportSettings; import jalview.structure.StructureMapping; -import jalview.structure.StructureViewSettings; +import jalview.util.Comparison; import java.awt.Color; import java.util.List; @@ -38,10 +39,7 @@ import java.util.Vector; public class PDBChain { - /** - * SequenceFeature group for PDB File features added to sequences - */ - private static final String PDBFILEFEATURE = "PDBFile"; + public static final String RESNUM_FEATURE = "RESNUM"; private static final String IEASTATUS = "IEA:jalview"; @@ -80,10 +78,10 @@ public class PDBChain public String pdbid = ""; - public PDBChain(String pdbid, String id) + public PDBChain(String thePdbid, String theId) { - this.pdbid = pdbid.toLowerCase(); - this.id = id; + this.pdbid = thePdbid == null ? thePdbid : thePdbid.toLowerCase(); + this.id = theId; } /** @@ -146,8 +144,14 @@ public class PDBChain pdbpos++; } - if (as.astr1.charAt(i) == as.astr2.charAt(i)) + boolean sameResidue = Comparison.isSameResidue(as.astr1.charAt(i), + as.astr2.charAt(i), false); + if (sameResidue) { + if (pdbpos >= residues.size()) + { + continue; + } Residue res = residues.elementAt(pdbpos); for (Atom atom : res.atoms) { @@ -158,15 +162,14 @@ public class PDBChain } /** - * copy over the RESNUM seqfeatures from the internal chain sequence to the + * 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; @@ -175,10 +178,11 @@ 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 @@ -188,18 +192,22 @@ public class PDBChain { status = PDBChain.IEASTATUS; } - SequenceFeature[] features = sequence.getSequenceFeatures(); - for (int i = 0; i < features.length; i++) + + List features = sequence.getSequenceFeatures(); + for (SequenceFeature feature : features) { - if (features[i].getFeatureGroup().equals(pdbid)) + if (feature.getFeatureGroup() != null + && feature.getFeatureGroup().equals(pdbid)) { - SequenceFeature tx = new SequenceFeature(features[i]); - tx.setBegin(1 + residues.elementAt(tx.getBegin() - offset).atoms - .elementAt(0).alignmentMapping); - tx.setEnd(1 + residues.elementAt(tx.getEnd() - offset).atoms - .elementAt(0).alignmentMapping); + int newBegin = 1 + residues.elementAt(feature.getBegin() - offset).atoms + .elementAt(0).alignmentMapping; + int newEnd = 1 + residues.elementAt(feature.getEnd() - offset).atoms + .elementAt(0).alignmentMapping; + 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) { @@ -207,7 +215,6 @@ public class PDBChain } } } - return features; } /** @@ -335,77 +342,68 @@ 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 + 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 - // boolean baseDetected = false; - // for (Atom resAtom : resAtoms) - // { - // if (resAtom.insCode == ' ') - // { - // baseDetected = true; - // } - // } - // if (!baseDetected) - // { - // continue; - // } - // 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", tmpat.resName - + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset - + count, offset + count, pdbid); - // MCview.PDBChain.PDBFILEFEATURE); - resFeatures.addElement(sf); - resAnnotation.addElement(new Annotation(tmpat.tfactor)); - // Keep totting up the sequence - - 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']; - if (tmpat.name.equalsIgnoreCase("CA") - || ResidueProperties.nucleotideIndex[nucname - .charAt((deoxyn ? 1 : 0))] == -1) + if ((symbol = ResidueProperties.getAA3Hash() + .get(tmpat.resName)) == null) { - seq.append("X"); - // System.err.println("PDBReader:Null aa3Hash for " + - // tmpat.resName); + 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']; + if (tmpat.name.equalsIgnoreCase("CA") + || ResidueProperties.nucleotideIndex[nucname + .charAt((deoxyn ? 1 : 0))] == -1) + { + char r = ResidueProperties.getSingleCharacterCode( + ResidueProperties.getCanonicalAminoAcid(tmpat.resName)); + seq.append(r == '0' ? 'X' : r); + // System.err.println("PDBReader:Null aa3Hash for " + + // tmpat.resName); + } + else + { + // nucleotide flag + nucleotide = true; + seq.append(nucname.charAt((deoxyn ? 1 : 0))); + } } else { - // nucleotide flag - nucleotide = true; - seq.append(nucname.charAt((deoxyn ? 1 : 0))); - } - } - else - { - if (nucleotide) - { - System.err - .println("Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!"); + if (nucleotide) + { + System.err.println( + "Warning: mixed nucleotide and amino acid chain.. its gonna do bad things to you!"); + } + seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]); } - seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]); - } count++; } } @@ -425,13 +423,13 @@ public class PDBChain // System.out.println("PDB Sequence is :\nSequence = " + seq); // System.out.println("No of residues = " + residues.size()); - if (StructureViewSettings.isShowSeqFeatures()) - { - for (i = 0, iSize = resFeatures.size(); i < iSize; i++) + if (StructureImportSettings.isShowSeqFeatures()) { - sequence.addSequenceFeature(resFeatures.elementAt(i)); - resFeatures.setElementAt(null, i); - } + for (i = 0, iSize = resFeatures.size(); i < iSize; i++) + { + sequence.addSequenceFeature(resFeatures.elementAt(i)); + resFeatures.setElementAt(null, i); + } } if (visibleChainAnnotation) { @@ -514,10 +512,12 @@ public class PDBChain try { index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue(); - b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0)); + 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)); + b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0), 0, + null, null, 0f); } catch (Exception e) { @@ -563,8 +563,8 @@ 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); @@ -584,12 +584,13 @@ public class PDBChain { for (AlignmentAnnotation ana : sequence.getAnnotation()) { - List transfer = sq + List transfer = dsq .getAlignmentAnnotations(ana.getCalcId(), ana.label); if (transfer == null || transfer.size() == 0) { ana = new AlignmentAnnotation(ana); ana.liftOver(dsq, sqmpping); + dsq.addAlignmentAnnotation(ana); // mapping.transfer(ana); } else @@ -604,7 +605,8 @@ 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);