JAL-1818 reimplemented sequence and annotation processing for JmolParser and further...

[jalview.git] / src / MCview / PDBChain.java

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 0e486ac..f4263b1 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -20,10 +20,6 @@
  */
 package MCview;
 
-import java.awt.Color;
-import java.util.List;
-import java.util.Vector;
-
 import jalview.analysis.AlignSeq;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
@@ -35,6 +31,10 @@ import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ResidueProperties;
 import jalview.structure.StructureMapping;
 
+import java.awt.Color;
+import java.util.List;
+import java.util.Vector;
+
 public class PDBChain
 {
   /**
@@ -193,10 +193,10 @@ public class PDBChain
       if (features[i].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);
+        tx.setBegin(1 + residues.elementAt(tx.getBegin() - offset).atoms
+                .elementAt(0).alignmentMapping);
+        tx.setEnd(1 + residues.elementAt(tx.getEnd() - offset).atoms
+                .elementAt(0).alignmentMapping);
         tx.setStatus(status
                 + ((tx.getStatus() == null || tx.getStatus().length() == 0) ? ""
                         : ":" + tx.getStatus()));
@@ -252,7 +252,7 @@ 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 +295,15 @@ 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 +313,7 @@ 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 +321,7 @@ public class PDBChain
         if (i < atoms.size())
         {
           resNumber = atoms.elementAt(i).resNumber;
+          insCode = atoms.elementAt(i).insCode;
         }
         else
         {
@@ -327,19 +332,48 @@ 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.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");
+        resFeatures.addElement(sf);
+        residues.lastElement().atoms.addAll(resAtoms);
+      }
+      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("RESNUM", 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();
@@ -371,7 +405,8 @@ public class PDBChain
         }
         seq.append(ResidueProperties.aa[((Integer) symbol).intValue()]);
       }
-      count++;
+        count++;
+      }
     }
 
     if (id.length() < 1)
@@ -409,8 +444,7 @@ public class PDBChain
 
       AlignmentAnnotation tfactorann = new AlignmentAnnotation(
               "Temperature Factor", "Temperature Factor for " + pdbid + id,
-              annots, 0, max,
-              AlignmentAnnotation.LINE_GRAPH);
+              annots, 0, max, AlignmentAnnotation.LINE_GRAPH);
       tfactorann.setSequenceRef(sequence);
       sequence.addAlignmentAnnotation(tfactorann);
     }
@@ -474,12 +508,10 @@ public class PDBChain
     {
       try
       {
-        index = ResidueProperties.aa3Hash.get(b.at1.resName)
-                .intValue();
+        index = ResidueProperties.aa3Hash.get(b.at1.resName).intValue();
         b.startCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
 
-        index = ResidueProperties.aa3Hash.get(b.at2.resName)
-                .intValue();
+        index = ResidueProperties.aa3Hash.get(b.at2.resName).intValue();
         b.endCol = cs.findColour(ResidueProperties.aa[index].charAt(0));
 
       } catch (Exception e)
@@ -508,8 +540,8 @@ public class PDBChain
    * @param sqmpping
    *          - mapping between destination sequence and local chain
    */
-  public void transferResidueAnnotation(
-          StructureMapping mapping, jalview.datamodel.Mapping sqmpping)
+  public void transferResidueAnnotation(StructureMapping mapping,
+          jalview.datamodel.Mapping sqmpping)
   {
     SequenceI sq = mapping.getSequence();
     SequenceI dsq = sq;