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

[jalview.git] / src / jalview / io / FeaturesFile.java

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 6332561..a704f24 100755 (executable)
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -312,7 +312,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
       // should report somewhere useful for UI if necessary
       warningMessage = ((warningMessage == null) ? "" : warningMessage)
               + "Parsing error at\n" + line;
-      System.out.println("Error parsing feature file: " + ex + "\n" + line);
+      jalview.bin.Console.outPrintln("Error parsing feature file: " + ex + "\n" + line);
       ex.printStackTrace(System.err);
       resetMatcher();
       return false;
@@ -354,7 +354,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
       String[] tokens = line.split(TAB_REGEX);
       if (tokens.length != 2)
       {
-        System.err.println(String.format("Invalid token count %d for %d",
+        jalview.bin.Console.errPrintln(String.format("Invalid token count %d for %d",
                 tokens.length, line));
       }
       else
@@ -392,7 +392,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
      */
     if (gffColumns.length < 6)
     {
-      System.err.println("Ignoring feature line '" + line
+      jalview.bin.Console.errPrintln("Ignoring feature line '" + line
               + "' with too few columns (" + gffColumns.length + ")");
       return false;
     }
@@ -415,13 +415,13 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
         seq = alignment.getSequenceAt(idx);
       } catch (NumberFormatException ex)
       {
-        System.err.println("Invalid sequence index: " + seqIndex);
+        jalview.bin.Console.errPrintln("Invalid sequence index: " + seqIndex);
       }
     }
 
     if (seq == null)
     {
-      System.out.println("Sequence not found: " + line);
+      jalview.bin.Console.outPrintln("Sequence not found: " + line);
       return false;
     }
 
@@ -1009,7 +1009,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
   @Override
   public String print(SequenceI[] sqs, boolean jvsuffix)
   {
-    System.out.println("Use printGffFormat() or printJalviewFormat()");
+    jalview.bin.Console.outPrintln("Use printGffFormat() or printJalviewFormat()");
     return null;
   }
 
@@ -1333,7 +1333,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
      */
     if (gffColumns.length < 5)
     {
-      System.err.println("Ignoring GFF feature line with too few columns ("
+      jalview.bin.Console.errPrintln("Ignoring GFF feature line with too few columns ("
               + gffColumns.length + ")");
       return null;
     }
@@ -1364,7 +1364,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
         }
       } catch (IOException e)
       {
-        System.err.println("GFF parsing failed with: " + e.getMessage());
+        jalview.bin.Console.errPrintln("GFF parsing failed with: " + e.getMessage());
         return null;
       }
     }
@@ -1532,7 +1532,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
     }
     else
     {
-      System.err.println("Ignoring unknown pragma: " + line);
+      jalview.bin.Console.errPrintln("Ignoring unknown pragma: " + line);
     }
   }
 }