X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=8285d883acb2b7cb67c997a7bfbb11d1bdb9791b;hb=ffa5c07d90b4a933762a5d9faa0578c11693d63a;hp=7fdf11bf8029a76467adf5760c57210e30500d22;hpb=81764c0a4a0a1807ac2a1cab2e4d99d588d09669;p=jalview.git

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 7fdf11b..8285d88 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -29,7 +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.util.Comparison;
 
 import java.awt.Color;
 import java.util.List;
@@ -37,6 +39,8 @@ import java.util.Vector;
 
 public class PDBChain
 {
+  public static final String RESNUM_FEATURE = "RESNUM";
+
   /**
    * SequenceFeature group for PDB File features added to sequences
    */
@@ -81,7 +85,7 @@ public class PDBChain
 
   public PDBChain(String pdbid, String id)
   {
-    this.pdbid = pdbid.toLowerCase();
+    this.pdbid = pdbid == null ? pdbid : pdbid.toLowerCase();
     this.id = id;
   }
 
@@ -145,7 +149,9 @@ 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())
         {
@@ -161,15 +167,14 @@ 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;
@@ -178,10 +183,11 @@ 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
@@ -191,16 +197,19 @@ public class PDBChain
     {
       status = PDBChain.IEASTATUS;
     }
-    SequenceFeature[] features = sequence.getSequenceFeatures();
-    for (int i = 0; i < features.length; i++)
+
+    List<SequenceFeature> 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()));
@@ -210,7 +219,6 @@ public class PDBChain
         }
       }
     }
-    return features;
   }
 
   /**
@@ -339,62 +347,66 @@ 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",
-                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
 
-      // 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++;
       }
     }
@@ -413,10 +425,14 @@ public class PDBChain
 
     // System.out.println("PDB Sequence is :\nSequence = " + seq);
     // System.out.println("No of residues = " + residues.size());
-    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)
     {
@@ -499,10 +515,12 @@ 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)
       {
@@ -569,12 +587,13 @@ public class PDBChain
         {
           for (AlignmentAnnotation ana : sequence.getAnnotation())
           {
-            List<AlignmentAnnotation> transfer = sq
+            List<AlignmentAnnotation> 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