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 7774dac..ef86cfd 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -31,6 +31,7 @@ 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;
@@ -38,6 +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
    */
@@ -146,7 +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())
         {
@@ -199,14 +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))
       {
-        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()));
@@ -348,25 +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", 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
@@ -513,10 +520,12 @@ 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)
       {