JAL-2050 make SequenceFeature.score final, adjust constructor calls

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

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 1f47014..ef86cfd 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -204,16 +204,16 @@ public class PDBChain
     }
     for (int i = 0; i < features.length; i++)
     {
-      if (features[i].getFeatureGroup() != null
-              && features[i].getFeatureGroup().equals(pdbid))
+      SequenceFeature feature = features[i];
+      if (feature.getFeatureGroup() != null
+              && feature.getFeatureGroup().equals(pdbid))
       {
-        int newBegin = 1 + residues.elementAt(features[i].getBegin()
-                - offset).atoms
+        int newBegin = 1 + residues.elementAt(feature.getBegin() - offset).atoms
                 .elementAt(0).alignmentMapping;
-        int newEnd = 1 + residues.elementAt(features[i].getEnd() - offset).atoms
+        int newEnd = 1 + residues.elementAt(feature.getEnd() - offset).atoms
                 .elementAt(0).alignmentMapping;
-        SequenceFeature tx = new SequenceFeature(features[i], newBegin,
-                newEnd, features[i].getFeatureGroup());
+        SequenceFeature tx = new SequenceFeature(feature, newBegin, newEnd,
+                feature.getFeatureGroup(), feature.getScore());
         tx.setStatus(status
                 + ((tx.getStatus() == null || tx.getStatus().length() == 0) ? ""
                         : ":" + tx.getStatus()));
@@ -355,25 +355,25 @@ public class PDBChain
               && !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
-        SequenceFeature sf = new SequenceFeature(RESNUM_FEATURE, tmpat.resName
-                + ":" + tmpat.resNumIns + " " + pdbid + id, "", offset
-                + count, offset + count, pdbid);
+        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