JAL-2189 source formatting

[jalview.git] / src / jalview / io / gff / Gff3Helper.java

diff --git a/src/jalview/io/gff/Gff3Helper.java b/src/jalview/io/gff/Gff3Helper.java
index 031900d..f517310 100644 (file)
--- a/src/jalview/io/gff/Gff3Helper.java
+++ b/src/jalview/io/gff/Gff3Helper.java
@@ -77,8 +77,8 @@ public class Gff3Helper extends GffHelperBase
       }
       else if (so.isA(soTerm, SequenceOntologyI.NUCLEOTIDE_MATCH))
       {
-        sf = processNucleotideMatch(attributes, seq, gff, align,
-                newseqs, relaxedIdMatching);
+        sf = processNucleotideMatch(attributes, seq, gff, align, newseqs,
+                relaxedIdMatching);
       }
       else
       {
@@ -92,7 +92,7 @@ public class Gff3Helper extends GffHelperBase
        */
       sf = buildSequenceFeature(gff, null);
     }
-  
+
     return sf;
   }
 
@@ -119,8 +119,7 @@ public class Gff3Helper extends GffHelperBase
   protected SequenceFeature processNucleotideMatch(
           Map<String, List<String>> attributes, SequenceI seq,
           String[] gffColumns, AlignmentI align, List<SequenceI> newseqs,
-          boolean relaxedIdMatching)
-          throws IOException
+          boolean relaxedIdMatching) throws IOException
   {
     String strand = gffColumns[STRAND_COL];
 
@@ -166,8 +165,8 @@ public class Gff3Helper extends GffHelperBase
        * (new or existing) virtual sequence in the newseqs list 
        */
       String targetId = findTargetId(tokens[0], attributes);
-      SequenceI mappedSequence1 = findSequence(targetId, align,
-      newseqs, relaxedIdMatching);
+      SequenceI mappedSequence1 = findSequence(targetId, align, newseqs,
+              relaxedIdMatching);
       SequenceI mappedSequence = mappedSequence1;
       if (mappedSequence == null)
       {
@@ -195,8 +194,7 @@ public class Gff3Helper extends GffHelperBase
         int fromStart = Integer.parseInt(gffColumns[START_COL]);
         int fromEnd = Integer.parseInt(gffColumns[END_COL]);
         MapList mapping = constructMappingFromAlign(fromStart, fromEnd,
-                toStart, toEnd,
-                MappingType.NucleotideToNucleotide);
+                toStart, toEnd, MappingType.NucleotideToNucleotide);
 
         if (mapping != null)
         {
@@ -280,8 +278,8 @@ public class Gff3Helper extends GffHelperBase
       for (String target : targets)
       {
 
-        SequenceI mappedSequence1 = findSequence(findTargetId(target, set), align,
-        newseqs, relaxedIdMatching);
+        SequenceI mappedSequence1 = findSequence(findTargetId(target, set),
+                align, newseqs, relaxedIdMatching);
         SequenceI mappedSequence = mappedSequence1;
         if (mappedSequence == null)
         {
@@ -379,8 +377,8 @@ public class Gff3Helper extends GffHelperBase
       /*
        * Ensembl returns dna variants as 'alleles'
        */
-      desc = StringUtils.listToDelimitedString(
-              attributes.get("alleles"), ",");
+      desc = StringUtils.listToDelimitedString(attributes.get("alleles"),
+              ",");
     }
 
     /*