Merge branch 'Release_2_9_0b1_Branch'

[jalview.git] / src / jalview / datamodel / xdb / embl / EmblEntry.java

diff --git a/src/jalview/datamodel/xdb/embl/EmblEntry.java b/src/jalview/datamodel/xdb/embl/EmblEntry.java
index 9c9447e..27aee24 100644 (file)
--- a/src/jalview/datamodel/xdb/embl/EmblEntry.java
+++ b/src/jalview/datamodel/xdb/embl/EmblEntry.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -408,9 +408,9 @@ public class EmblEntry
       dna.addDBRef(retrievedref);
       // add map to indicate the sequence is a valid coordinate frame for the
       // dbref
-      retrievedref.setMap(new Mapping(null, new int[]
-      { 1, dna.getLength() }, new int[]
-      { 1, dna.getLength() }, 1, 1));
+      retrievedref.setMap(new Mapping(null,
+              new int[] { 1, dna.getLength() }, new int[] { 1,
+                  dna.getLength() }, 1, 1));
       // TODO: transform EMBL Database refs to canonical form
       if (dbRefs != null)
       {
@@ -422,7 +422,7 @@ public class EmblEntry
     }
     try
     {
-      for (EmblFeature feature: features)
+      for (EmblFeature feature : features)
       {
         if (!noNa)
         {
@@ -599,19 +599,18 @@ public class EmblEntry
                   .println("Not allowing for additional stop codon at end of cDNA fragment... !");
           // this might occur for CDS sequences where no features are
           // marked.
-          exon = new int[]
-          { dna.getStart() + (prstart - 1), dna.getEnd() };
-          map = new jalview.datamodel.Mapping(product, exon, new int[]
-          { 1, prseq.length() }, 3, 1);
+          exon = new int[] { dna.getStart() + (prstart - 1), dna.getEnd() };
+          map = new jalview.datamodel.Mapping(product, exon, new int[] { 1,
+              prseq.length() }, 3, 1);
         }
         if ((prseq.length() + 1) * 3 == (1 - prstart + dna.getSequence().length))
         {
           System.err
                   .println("Allowing for additional stop codon at end of cDNA fragment... will probably cause an error in VAMSAs!");
-          exon = new int[]
-          { dna.getStart() + (prstart - 1), dna.getEnd() - 3 };
-          map = new jalview.datamodel.Mapping(product, exon, new int[]
-          { 1, prseq.length() }, 3, 1);
+          exon = new int[] { dna.getStart() + (prstart - 1),
+              dna.getEnd() - 3 };
+          map = new jalview.datamodel.Mapping(product, exon, new int[] { 1,
+              prseq.length() }, 3, 1);
         }
       }
       else
@@ -632,8 +631,8 @@ public class EmblEntry
           // final product length trunctation check
 
           map = new jalview.datamodel.Mapping(product,
-                  adjustForProteinLength(prseq.length(), exon), new int[]
-                  { 1, prseq.length() }, 3, 1);
+                  adjustForProteinLength(prseq.length(), exon), new int[] {
+                      1, prseq.length() }, 3, 1);
           // reconstruct the EMBLCDS entry
           // TODO: this is only necessary when there codon annotation is
           // complete (I think JBPNote)
@@ -641,9 +640,9 @@ public class EmblEntry
           pcdnaref.setAccessionId(prid);
           pcdnaref.setSource(DBRefSource.EMBLCDS);
           pcdnaref.setVersion(getVersion()); // same as parent EMBL version.
-          jalview.util.MapList mp = new jalview.util.MapList(new int[]
-          { 1, prseq.length() }, new int[]
-          { 1 + (prstart - 1), (prstart - 1) + 3 * prseq.length() }, 1, 3);
+          jalview.util.MapList mp = new jalview.util.MapList(new int[] { 1,
+              prseq.length() }, new int[] { 1 + (prstart - 1),
+              (prstart - 1) + 3 * prseq.length() }, 1, 3);
           // { 1 + (prstart - 1) * 3,
           // 1 + (prstart - 1) * 3 + prseq.length() * 3 - 1 }, new int[]
           // { 1prstart, prstart + prseq.length() - 1 }, 3, 1);