X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2FMCview%2FPDBChain.java;h=7fdf11bf8029a76467adf5760c57210e30500d22;hb=72cbe293bdfc802039f5be51d53351e97b89d28a;hp=6d5f9fe1d02bdc07d8b3ed50c809ad78babd08d0;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 6d5f9fe..7fdf11b 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -147,6 +147,10 @@ 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)
         {
@@ -252,7 +256,7 @@ public class PDBChain
      * If > 99% 'P', flag as nucleotide; note the count doesn't include the last
      * residue
      */
-    if (residues.size() > 0 && (numNa / (residues.size() - 1) > 0.99))
+    if (residues.size() > 1 && (numNa / (residues.size() - 1) > 0.99))
     {
       isNa = true;
     }
@@ -295,11 +299,15 @@ public class PDBChain
     Vector<Annotation> resAnnotation = new Vector<Annotation>();
     int i, iSize = atoms.size() - 1;
     int resNumber = -1;
+    char insCode = ' ';
     for (i = 0; i <= iSize; i++)
     {
       Atom tmp = atoms.elementAt(i);
       resNumber = tmp.resNumber;
+      insCode = tmp.insCode;
+
       int res = resNumber;
+      char ins = insCode;
 
       if (i == 0)
       {
@@ -309,7 +317,7 @@ public class PDBChain
       Vector<Atom> resAtoms = new Vector<Atom>();
       // Add atoms to a vector while the residue number
       // remains the same as the first atom's resNumber (res)
-      while ((resNumber == res) && (i < atoms.size()))
+      while ((resNumber == res) && (ins == insCode) && (i < atoms.size()))
       {
         resAtoms.add(atoms.elementAt(i));
         i++;
@@ -317,6 +325,7 @@ public class PDBChain
         if (i < atoms.size())
         {
           resNumber = atoms.elementAt(i).resNumber;
+          insCode = atoms.elementAt(i).insCode;
         }
         else
         {
@@ -327,13 +336,28 @@ public class PDBChain
       // We need this to keep in step with the outer for i = loop
       i--;
 
+      // Add inserted residues as features to the base residue
+      Atom currAtom = resAtoms.get(0);
+      if (currAtom.insCode != ' '
+              && 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");
+        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
-      SequenceFeature sf = new SequenceFeature("RESNUM", tmpat.resName
+        SequenceFeature sf = new SequenceFeature("RESNUM", tmpat.resName
               + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset
               + count, offset + count, pdbid);
       // MCview.PDBChain.PDBFILEFEATURE);
@@ -371,7 +395,8 @@ public class PDBChain
         }
         seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]);
       }
-      count++;
+        count++;
+      }
     }
 
     if (id.length() < 1)