JAL-674 formatting

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

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 0949e7f..8812dcc 100755 (executable)
--- a/src/MCview/PDBChain.java
+++ b/src/MCview/PDBChain.java
@@ -534,52 +534,55 @@ public class PDBChain
       }
       else
       {
-      if (sequence != null && sequence.getAnnotation() != null)
-      {
-        for (AlignmentAnnotation ana : sequence.getAnnotation())
+        if (sequence != null && sequence.getAnnotation() != null)
         {
-          List<AlignmentAnnotation> transfer = sq.getAlignmentAnnotations(
-                  ana.getCalcId(), ana.label);
-          if (transfer == null || transfer.size() == 0)
-          {
-            ana.liftOver(dsq, sqmpping);
-            // mapping.transfer(ana);
-          }
-          else
+          for (AlignmentAnnotation ana : sequence.getAnnotation())
           {
-            continue;
+            List<AlignmentAnnotation> transfer = sq
+                    .getAlignmentAnnotations(ana.getCalcId(), ana.label);
+            if (transfer == null || transfer.size() == 0)
+            {
+              ana.liftOver(dsq, sqmpping);
+              // mapping.transfer(ana);
+            }
+            else
+            {
+              continue;
+            }
           }
         }
       }
-      }
-      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));
-
     }
   }
 }