Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

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

diff --git a/src/jalview/io/gff/ExonerateHelper.java b/src/jalview/io/gff/ExonerateHelper.java
index 9ce4cc6..77b641a 100644 (file)
--- a/src/jalview/io/gff/ExonerateHelper.java
+++ b/src/jalview/io/gff/ExonerateHelper.java
@@ -90,7 +90,7 @@ public class ExonerateHelper extends Gff2Helper
               relaxedIdMatching);
     } catch (IOException ivfe)
     {
-      System.err.println(ivfe);
+      jalview.bin.Console.errPrintln(ivfe);
     }
 
     /*
@@ -200,7 +200,7 @@ 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;
     }
 
@@ -239,7 +239,7 @@ 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;
     }
 
@@ -257,7 +257,7 @@ 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;
     }
 
@@ -351,7 +351,7 @@ 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;
   }