From: Jim Procter <jprocter@dundee.ac.uk>
Date: Wed, 26 Nov 2014 14:40:16 +0000 (+0000)
Subject: JAL-674 disable addition of PDBRESNUM annotation line
X-Git-Tag: Jalview_2_9~121^2~7^2~5
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f3f0f55e4e5a03b448a39f6bab2722698136f0f8;p=jalview.git

JAL-674 disable addition of PDBRESNUM annotation line
---

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 0949e7f..408108b 100755
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -552,34 +552,37 @@ public class PDBChain
         }
       }
       }
-      float min = -1, max = 0;
-      Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
-      for (int i = sq.getStart(), j = sq.getEnd(), k = 0; i <= j; i++, k++)
+      if (false)
       {
-        int prn = mapping.getPDBResNum(k + 1);
-
-        an[k] = new Annotation(prn);
-        if (min == -1)
+        // Useful for debugging mappings - adds annotation for mapped position
+        float min = -1, max = 0;
+        Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
+        for (int i = sq.getStart(), j = sq.getEnd(), k = 0; i <= j; i++, k++)
         {
-          min = k;
-          max = k;
-        }
-        else
-        {
-          if (min > k)
+          int prn = mapping.getPDBResNum(k + 1);
+
+          an[k] = new Annotation(prn);
+          if (min == -1)
           {
             min = k;
+            max = k;
           }
-          else if (max < k)
+          else
           {
-            max = k;
+            if (min > k)
+            {
+              min = k;
+            }
+            else if (max < k)
+            {
+              max = k;
+            }
           }
         }
+        sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
+                "PDB Residue Numbering for " + this.pdbid + ":" + this.id,
+                an, min, max, AlignmentAnnotation.LINE_GRAPH));
       }
-      sq.addAlignmentAnnotation(new AlignmentAnnotation("PDB.RESNUM",
-              "PDB Residue Numbering for " + this.pdbid + ":" + this.id,
-              an, min, max, AlignmentAnnotation.LINE_GRAPH));
-
     }
   }
 }