Merge branch 'develop' into features/JAL-1705_ensembl

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

diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java
index 0e486ac..6d5f9fe 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()));
@@ -409,8 +409,7 @@ 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 +473,10 @@ 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 +505,8 @@ 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;