Merge remote-tracking branch 'origin/releases/Release_2_10_2b1_Branch'

[jalview.git] / src / jalview / analysis / Dna.java

diff --git a/src/jalview/analysis/Dna.java b/src/jalview/analysis/Dna.java
index 799a8ed..0128624 100644 (file)
--- a/src/jalview/analysis/Dna.java
+++ b/src/jalview/analysis/Dna.java
@@ -120,7 +120,8 @@ public class Dna
    * @param ac2
    * @return
    */
-  public static final int compareCodonPos(AlignedCodon ac1, AlignedCodon ac2)
+  public static final int compareCodonPos(AlignedCodon ac1,
+          AlignedCodon ac2)
   {
     return comparator.compare(ac1, ac2);
     // return jalview_2_8_2compare(ac1, ac2);
@@ -134,7 +135,8 @@ public class Dna
    * @param ac2
    * @return
    */
-  private static int jalview_2_8_2compare(AlignedCodon ac1, AlignedCodon ac2)
+  private static int jalview_2_8_2compare(AlignedCodon ac1,
+          AlignedCodon ac2)
   {
     if (ac1 == null || ac2 == null || (ac1.equals(ac2)))
     {
@@ -435,7 +437,8 @@ public class Dna
         /*
          * Filled up a reading frame...
          */
-        AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1], cdp[2]);
+        AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1],
+                cdp[2]);
         String aa = ResidueProperties.codonTranslate(new String(codon));
         rf = 0;
         final String gapString = String.valueOf(gapChar);
@@ -444,10 +447,11 @@ public class Dna
           aa = gapString;
           if (skipint == null)
           {
-            skipint = new int[] { alignedCodon.pos1, alignedCodon.pos3 /*
-                                                                        * cdp[0],
-                                                                        * cdp[2]
-                                                                        */};
+            skipint = new int[] { alignedCodon.pos1,
+                alignedCodon.pos3 /*
+                                   * cdp[0],
+                                   * cdp[2]
+                                   */ };
           }
           skipint[1] = alignedCodon.pos3; // cdp[2];
         }
@@ -502,8 +506,8 @@ public class Dna
                       }
                       if (vc + 2 < t.length)
                       {
-                        System.arraycopy(scontigs, vc + 2, t, vc, t.length
-                                - vc + 2);
+                        System.arraycopy(scontigs, vc + 2, t, vc,
+                                t.length - vc + 2);
                       }
                       scontigs = t;
                     }
@@ -596,9 +600,9 @@ public class Dna
         }
         else if (!alignedCodons[aspos].equals(alignedCodon))
         {
-          throw new IllegalStateException("Tried to coalign "
-                  + alignedCodons[aspos].toString() + " with "
-                  + alignedCodon.toString());
+          throw new IllegalStateException(
+                  "Tried to coalign " + alignedCodons[aspos].toString()
+                          + " with " + alignedCodon.toString());
         }
         if (aspos >= aaWidth)
         {
@@ -790,8 +794,8 @@ public class Dna
     {
       for (SequenceFeature sf : sfs)
       {
-        fgstate = (featureGroups == null) ? null : featureGroups
-                .get(sf.featureGroup);
+        fgstate = (featureGroups == null) ? null
+                : featureGroups.get(sf.featureGroup);
         if ((featureTypes == null || featureTypes.containsKey(sf.getType()))
                 && (fgstate == null || fgstate.booleanValue()))
         {