X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=8089fdfca8d7e5db83a7eae73537b2dd5a302248;hb=b40bbf24867e2f44c40e9af6cf43bdfee29c337c;hp=e4e619c577052c6a7a0803760c994c33af058f92;hpb=77ac7f545e96bd4bde47991f77291a71eb5b90e6;p=jalview.git diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java index e4e619c..8089fdf 100755 --- a/src/MCview/PDBChain.java +++ b/src/MCview/PDBChain.java @@ -30,6 +30,7 @@ import jalview.datamodel.SequenceI; import jalview.schemes.ColourSchemeI; import jalview.schemes.ResidueProperties; import jalview.structure.StructureMapping; +import jalview.structure.StructureViewSettings; import java.awt.Color; import java.util.List; @@ -147,6 +148,10 @@ public class PDBChain if (as.astr1.charAt(i) == as.astr2.charAt(i)) { + if (pdbpos >= residues.size()) + { + continue; + } Residue res = residues.elementAt(pdbpos); for (Atom atom : res.atoms) { @@ -335,6 +340,7 @@ 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) { SequenceFeature sf = new SequenceFeature("INSERTION", @@ -347,19 +353,32 @@ public class PDBChain else { + // 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("RES NUM", tmpat.resName + 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(); @@ -409,11 +428,15 @@ 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++) { sequence.addSequenceFeature(resFeatures.elementAt(i)); resFeatures.setElementAt(null, i); } + } if (visibleChainAnnotation) { Annotation[] annots = new Annotation[resAnnotation.size()];