X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fgff%2FExonerateHelper.java;h=f522ac4796aedf246869ee1f87fc786d3aee5273;hb=faf491e024f9835435f5dd6c20a033250dd9297d;hp=eb74eea9dae6638668390dab363289483bd5e3df;hpb=604cbee405a837565ba1a74aa9bddd62aed685ab;p=jalview.git

diff --git a/src/jalview/io/gff/ExonerateHelper.java b/src/jalview/io/gff/ExonerateHelper.java
index eb74eea..f522ac4 100644
--- a/src/jalview/io/gff/ExonerateHelper.java
+++ b/src/jalview/io/gff/ExonerateHelper.java
@@ -20,6 +20,8 @@
  */
 package jalview.io.gff;
 
+import java.util.Locale;
+
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.MappingType;
@@ -88,7 +90,7 @@ public class ExonerateHelper extends Gff2Helper
               relaxedIdMatching);
     } catch (IOException ivfe)
     {
-      System.err.println(ivfe);
+      jalview.bin.Console.errPrintln(ivfe);
     }
 
     /*
@@ -165,7 +167,8 @@ public class ExonerateHelper extends Gff2Helper
     SequenceI mapFromSequence = seq;
     SequenceI mapToSequence = mappedSequence;
     if ((type == MappingType.NucleotideToPeptide && featureIsOnTarget)
-            || (type == MappingType.PeptideToNucleotide && !featureIsOnTarget))
+            || (type == MappingType.PeptideToNucleotide
+                    && !featureIsOnTarget))
     {
       mapFromSequence = mappedSequence;
       mapToSequence = seq;
@@ -197,7 +200,8 @@ public class ExonerateHelper extends Gff2Helper
     }
     else if (!"+".equals(strand))
     {
-      System.err.println("Strand must be specified for alignment");
+      jalview.bin.Console
+              .errPrintln("Strand must be specified for alignment");
       return;
     }
 
@@ -236,7 +240,8 @@ public class ExonerateHelper extends Gff2Helper
     String[] tokens = region.split(" ");
     if (tokens.length != 3)
     {
-      System.err.println("Malformed Align descriptor: " + region);
+      jalview.bin.Console
+              .errPrintln("Malformed Align descriptor: " + region);
       return null;
     }
 
@@ -254,7 +259,7 @@ public class ExonerateHelper extends Gff2Helper
       alignCount = Integer.parseInt(tokens[2]);
     } catch (NumberFormatException nfe)
     {
-      System.err.println(nfe.toString());
+      jalview.bin.Console.errPrintln(nfe.toString());
       return null;
     }
 
@@ -267,8 +272,8 @@ public class ExonerateHelper extends Gff2Helper
     {
       fromStart = alignToStart;
       toStart = alignFromStart;
-      toEnd = forwardStrand ? toStart + alignCount - 1 : toStart
-              - (alignCount - 1);
+      toEnd = forwardStrand ? toStart + alignCount - 1
+              : toStart - (alignCount - 1);
       int toLength = Math.abs(toEnd - toStart) + 1;
       int fromLength = toLength * type.getFromRatio() / type.getToRatio();
       fromEnd = fromStart + fromLength - 1;
@@ -340,7 +345,7 @@ public class ExonerateHelper extends Gff2Helper
     // e.g. exonerate:protein2genome:local
     if (model != null)
     {
-      String mdl = model.toLowerCase();
+      String mdl = model.toLowerCase(Locale.ROOT);
       if (mdl.contains(PROTEIN2DNA) || mdl.contains(PROTEIN2GENOME)
               || mdl.contains(CODING2CODING) || mdl.contains(CODING2GENOME)
               || mdl.contains(CDNA2GENOME) || mdl.contains(GENOME2GENOME))
@@ -348,16 +353,21 @@ public class ExonerateHelper extends Gff2Helper
         return true;
       }
     }
-    System.err.println("Sorry, I don't handle exonerate model " + model);
+    jalview.bin.Console
+            .errPrintln("Sorry, I don't handle exonerate model " + model);
     return false;
   }
 
+  /**
+   * An override to set feature group to "exonerate" instead of the default GFF
+   * source value (column 2)
+   */
   @Override
   protected SequenceFeature buildSequenceFeature(String[] gff,
           Map<String, List<String>> set)
   {
-    SequenceFeature sf = super.buildSequenceFeature(gff, set);
-    sf.setFeatureGroup("exonerate");
+    SequenceFeature sf = super.buildSequenceFeature(gff, TYPE_COL,
+            "exonerate", set);
 
     return sf;
   }