X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=b74f10110d10426061f66b36f6358e5c4b8c7098;hb=853624fb32058cccc544ae7d13af6ad4b0800b6c;hp=248cf29bd45a0cefb61d8a4c502eadc573029e0b;hpb=44cbaf5e4c094d90ef1294dd47c75a652e5f2509;p=jalview.git

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 248cf29..b74f101 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -29,8 +29,8 @@ 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 java.awt.Color;
 import java.util.List;
@@ -357,53 +357,53 @@ public class PDBChain
       else
       {
 
-      // Make a new Residue object with the new atoms vector
-      residues.addElement(new Residue(resAtoms, resNumber - 1, count));
+        // 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
+        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);
-      resFeatures.addElement(sf);
-      resAnnotation.addElement(new Annotation(tmpat.tfactor));
-      // Keep totting up the sequence
+                + ":" + tmpat.resNumIns + " " + pdbid + id, "", 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)
-      {
-        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)
         {
+          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++;
       }
     }
@@ -423,13 +423,13 @@ public class PDBChain
     // System.out.println("PDB Sequence is :\nSequence = " + seq);
     // System.out.println("No of residues = " + residues.size());
 
-    if (StructureViewSettings.isShowSeqFeatures())
+    if (StructureImportSettings.isShowSeqFeatures())
     {
-    for (i = 0, iSize = resFeatures.size(); i < iSize; i++)
-    {
-      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)
     {
@@ -582,12 +582,13 @@ 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