X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fmc_view%2FPDBChain.java;h=6d02630f118091f70858ccbfee74b61ae503a965;hb=a67002917b669aaff650904ec4353f8c70866cc8;hp=60c289e91ff89f6841d26e127032bc2613f9ed75;hpb=d46c8cbd1a5282ede9a0a94471f23ca002cf7df6;p=jalview.git diff --git a/src/mc_view/PDBChain.java b/src/mc_view/PDBChain.java index 60c289e..6d02630 100755 --- a/src/mc_view/PDBChain.java +++ b/src/mc_view/PDBChain.java @@ -20,23 +20,26 @@ */ package mc_view; +import java.awt.Color; +import java.util.List; +import java.util.Locale; +import java.util.Vector; + import jalview.analysis.AlignSeq; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.Annotation; +import jalview.datamodel.ContactMatrixI; import jalview.datamodel.Mapping; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.datamodel.annotations.AnnotationRowBuilder; import jalview.schemes.ColourSchemeI; import jalview.schemes.ResidueProperties; import jalview.structure.StructureImportSettings; import jalview.structure.StructureMapping; import jalview.util.Comparison; -import java.awt.Color; -import java.util.List; -import java.util.Vector; - public class PDBChain { public static final String RESNUM_FEATURE = "RESNUM"; @@ -78,11 +81,31 @@ public class PDBChain public String pdbid = ""; - public PDBChain(String thePdbid, String theId, boolean isAlphaFoldModel) + AnnotationRowBuilder tfacTemplate = new AnnotationRowBuilder( + "Temperature Factor"); + + public PDBChain(String thePdbid, String theId, + AnnotationRowBuilder template) { - this.pdbid = thePdbid == null ? thePdbid : thePdbid.toLowerCase(); + this(thePdbid, theId); + if (template != null) + { + tfacTemplate = template; + } + } + + /** + * import chain data assuming Temperature Factor is in the Temperature Factor + * column + * + * @param thePdbid + * @param theId + */ + public PDBChain(String thePdbid, String theId) + { + this.pdbid = thePdbid == null ? thePdbid + : thePdbid.toLowerCase(Locale.ROOT); this.id = theId; - this.alphaFoldModel = isAlphaFoldModel; } /** @@ -92,8 +115,6 @@ public class PDBChain public Mapping shadowMap; - private boolean alphaFoldModel; - public void setNewlineString(String nl) { newline = nl; @@ -196,8 +217,8 @@ public class PDBChain } char seqchar = ds.getCharAt(seqpos - ds.getStart()); - boolean sameResidue = Comparison.isSameResidue( - seqchar, strchar, false); + boolean sameResidue = Comparison.isSameResidue(seqchar, strchar, + false); if (sameResidue) { for (Atom atom : res.atoms) @@ -215,10 +236,18 @@ public class PDBChain * @param seq * @param status * The Status of the transferred annotation + * + * @param altPDBID + * the group id for the features on the destination sequence (e.g. + * the official accession ID) */ - public void transferRESNUMFeatures(SequenceI seq, - String status) + public void transferRESNUMFeatures(SequenceI seq, String status, + String altPDBID) { + if (altPDBID == null) + { + altPDBID = pdbid; + } SequenceI sq = seq; while (sq != null && sq.getDatasetSequence() != null) { @@ -246,12 +275,13 @@ public class PDBChain if (feature.getFeatureGroup() != null && feature.getFeatureGroup().equals(pdbid)) { - int newBegin = 1 + residues.elementAt(feature.getBegin() - 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()); + altPDBID, feature.getScore()); tx.setStatus(status + ((tx.getStatus() == null || tx.getStatus().length() == 0) ? "" @@ -396,8 +426,8 @@ public class PDBChain { String desc = currAtom.resName + ":" + currAtom.resNumIns + " " + pdbid + id; - SequenceFeature sf = new SequenceFeature("INSERTION", desc, offset - + count - 1, offset + count - 1, "PDB_INS"); + SequenceFeature sf = new SequenceFeature("INSERTION", desc, + offset + count - 1, offset + count - 1, "PDB_INS"); resFeatures.addElement(sf); residues.lastElement().atoms.addAll(resAtoms); } @@ -409,8 +439,8 @@ public class PDBChain 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; + String desc = tmpat.resName + ":" + tmpat.resNumIns + " " + pdbid + + id; SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE, desc, offset + count, offset + count, pdbid); resFeatures.addElement(sf); @@ -489,28 +519,31 @@ public class PDBChain for (int i = 0; i < iSize; i++) { annots[i] = resAnnotation.elementAt(i); + tfacTemplate.processAnnotation(annots[i]); max = Math.max(max, annots[i].value); min = Math.min(min, annots[i].value); resAnnotation.setElementAt(null, i); } - String tfacName = "Temperature Factor"; - if (isAlphaFoldModel()) + if (tfacTemplate.isHasMinMax()) { - tfacName = "Alphafold Reliability"; + max = tfacTemplate.getMax(); + min = tfacTemplate.getMin(); } + AlignmentAnnotation tfactorann = new AlignmentAnnotation( - tfacName, tfacName + " for " + pdbid + id, + tfacTemplate.getName(), + (tfacTemplate.isHasDescription() + ? tfacTemplate.getDescription() + : tfacTemplate.getName()) + " for " + pdbid + id, annots, min, max, AlignmentAnnotation.LINE_GRAPH); + tfactorann.setTFType(tfacTemplate.getTFType()); + tfactorann.setCalcId(getClass().getName()); + tfactorann.setSequenceRef(sequence); sequence.addAlignmentAnnotation(tfactorann); } } - private boolean isAlphaFoldModel() - { - return alphaFoldModel; - } - /** * Colour start/end of bonds by charge *