X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fgff%2FGff3Helper.java;h=646900d5c1d88e49372dae8dd5244c673bbeb21d;hb=cd669a0e8c7b91b379bca8fe6e702cf0fcbd1ce0;hp=a25a0141482317eae632b79764ac7996c4c49cc6;hpb=55eef00ac2435b5cc0ee64b92ad87a915375a709;p=jalview.git

diff --git a/src/jalview/io/gff/Gff3Helper.java b/src/jalview/io/gff/Gff3Helper.java
index a25a014..646900d 100644
--- a/src/jalview/io/gff/Gff3Helper.java
+++ b/src/jalview/io/gff/Gff3Helper.java
@@ -154,7 +154,7 @@ public class Gff3Helper extends GffHelperBase
      */
     if ("-".equals(strand))
     {
-      System.err.println(
+      jalview.bin.Console.errPrintln(
               "Skipping mapping from reverse complement as not yet supported");
       return null;
     }
@@ -162,7 +162,7 @@ public class Gff3Helper extends GffHelperBase
     List<String> targets = attributes.get(TARGET);
     if (targets == null)
     {
-      System.err.println("'Target' missing in GFF");
+      jalview.bin.Console.errPrintln("'Target' missing in GFF");
       return null;
     }
 
@@ -178,7 +178,7 @@ public class Gff3Helper extends GffHelperBase
       String[] tokens = target.split(" ");
       if (tokens.length < 3)
       {
-        System.err.println("Incomplete Target: " + target);
+        jalview.bin.Console.errPrintln("Incomplete Target: " + target);
         continue;
       }
 
@@ -225,7 +225,7 @@ public class Gff3Helper extends GffHelperBase
         }
       } catch (NumberFormatException nfe)
       {
-        System.err.println("Invalid start or end in Target " + target);
+        jalview.bin.Console.errPrintln("Invalid start or end in Target " + target);
       }
     }
 
@@ -350,15 +350,6 @@ public class Gff3Helper extends GffHelperBase
   }
 
   /**
-   * Return '=' as the name-value separator used in column 9 attributes.
-   */
-  @Override
-  protected char getNameValueSeparator()
-  {
-    return '=';
-  }
-
-  /**
    * Modifies the default SequenceFeature in order to set the Target sequence id
    * as the description
    */
@@ -424,6 +415,11 @@ public class Gff3Helper extends GffHelperBase
       desc = (String) sf.getValue(ID);
     }
 
+    /*
+     * and decode comma, equals, semi-colon as required by GFF3 spec
+     */
+    desc = StringUtils.urlDecode(desc, GFF_ENCODABLE);
+
     return desc;
   }
 }