X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fgff%2FExonerateHelper.java;h=1ee99c0ecd0c125480922e8c6a5fbe36ef95251e;hb=853624fb32058cccc544ae7d13af6ad4b0800b6c;hp=e37386177be417510aaae8d2982140258ae3c720;hpb=8f920d337154e092f5f9056ffde3cdf2735eca43;p=jalview.git

diff --git a/src/jalview/io/gff/ExonerateHelper.java b/src/jalview/io/gff/ExonerateHelper.java
index e373861..1ee99c0 100644
--- a/src/jalview/io/gff/ExonerateHelper.java
+++ b/src/jalview/io/gff/ExonerateHelper.java
@@ -41,7 +41,7 @@ public class ExonerateHelper extends Gff2Helper
    * 
    * @param seq
    *          the sequence with which this feature is associated
-   * @param sf
+   * @param gffColumns
    *          the sequence feature with ATTRIBUTES property containing any
    *          additional attributes
    * @param align
@@ -64,8 +64,8 @@ public class ExonerateHelper extends Gff2Helper
 
     try
     {
-      processGffSimilarity(set, seq, gffColumns,
-              align, newseqs, relaxedIdMatching);
+      processGffSimilarity(set, seq, gffColumns, align, newseqs,
+              relaxedIdMatching);
     } catch (IOException ivfe)
     {
       System.err.println(ivfe);
@@ -98,8 +98,7 @@ public class ExonerateHelper extends Gff2Helper
    *          if true allow fuzzy search for a matching target sequence
    * @throws IOException
    */
-  protected void processGffSimilarity(
-          Map<String, List<String>> set,
+  protected void processGffSimilarity(Map<String, List<String>> set,
           SequenceI seq, String[] gff, AlignmentI align,
           List<SequenceI> newseqs, boolean relaxedIdMatching)
           throws IOException
@@ -167,7 +166,7 @@ public class ExonerateHelper extends Gff2Helper
             mapToSequence);
 
     /*
-     * exonerate GFF has the strand of the target in column 7 rather
+     * exonerate GFF has the strand of the target in column 7
      * (differs from GFF3 which has it in the Target descriptor)
      */
     String strand = gff[STRAND_COL];
@@ -228,15 +227,17 @@ public class ExonerateHelper extends Gff2Helper
     int alignFromStart;
     int alignToStart;
     int alignCount;
-    try {
+    try
+    {
       alignFromStart = Integer.parseInt(tokens[0]);
       alignToStart = Integer.parseInt(tokens[1]);
       alignCount = Integer.parseInt(tokens[2]);
-    } catch (NumberFormatException nfe) {
+    } catch (NumberFormatException nfe)
+    {
       System.err.println(nfe.toString());
       return null;
     }
-    
+
     int fromStart;
     int fromEnd;
     int toStart;
@@ -290,10 +291,8 @@ public class ExonerateHelper extends Gff2Helper
     {
       result = MappingType.PeptideToNucleotide;
     }
-    else if (model.contains(CODING2CODING)
-            || model.contains(CODING2GENOME)
-            || model.contains(CDNA2GENOME)
-            || model.contains(GENOME2GENOME))
+    else if (model.contains(CODING2CODING) || model.contains(CODING2GENOME)
+            || model.contains(CDNA2GENOME) || model.contains(GENOME2GENOME))
     {
       result = MappingType.NucleotideToNucleotide;
     }
@@ -304,7 +303,7 @@ public class ExonerateHelper extends Gff2Helper
    * Tests whether the GFF data looks like it was generated by exonerate, and is
    * a format we are willing to handle
    * 
-   * @param sf
+   * @param columns
    * @return
    */
   public static boolean recognises(String[] columns)
@@ -323,10 +322,8 @@ public class ExonerateHelper extends Gff2Helper
     {
       String mdl = model.toLowerCase();
       if (mdl.contains(PROTEIN2DNA) || mdl.contains(PROTEIN2GENOME)
-              || mdl.contains(CODING2CODING)
-              || mdl.contains(CODING2GENOME)
-              || mdl.contains(CDNA2GENOME)
-              || mdl.contains(GENOME2GENOME))
+              || mdl.contains(CODING2CODING) || mdl.contains(CODING2GENOME)
+              || mdl.contains(CDNA2GENOME) || mdl.contains(GENOME2GENOME))
       {
         return true;
       }