Merge branch 'develop' into features/JAL-518_justify_seqs_in_region

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

diff --git a/src/jalview/io/FeaturesFile.java b/src/jalview/io/FeaturesFile.java
index 745bce3..38e27f9 100755 (executable)
--- a/src/jalview/io/FeaturesFile.java
+++ b/src/jalview/io/FeaturesFile.java
@@ -20,8 +20,6 @@
  */
 package jalview.io;
 
-import java.util.Locale;
-
 import java.awt.Color;
 import java.io.IOException;
 import java.util.ArrayList;
@@ -30,6 +28,7 @@ import java.util.Collections;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Map.Entry;
 import java.util.TreeMap;
@@ -313,7 +312,8 @@ 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;
@@ -355,8 +355,8 @@ 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",
-                tokens.length, line));
+        jalview.bin.Console.errPrintln(String.format(
+                "Invalid token count %d for %d", tokens.length, line));
       }
       else
       {
@@ -393,7 +393,7 @@ 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;
     }
@@ -416,13 +416,14 @@ 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;
     }
 
@@ -1010,7 +1011,8 @@ 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;
   }
 
@@ -1334,8 +1336,9 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
      */
     if (gffColumns.length < 5)
     {
-      System.err.println("Ignoring GFF feature line with too few columns ("
-              + gffColumns.length + ")");
+      jalview.bin.Console
+              .errPrintln("Ignoring GFF feature line with too few columns ("
+                      + gffColumns.length + ")");
       return null;
     }
 
@@ -1365,7 +1368,8 @@ 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;
       }
     }
@@ -1533,7 +1537,7 @@ public class FeaturesFile extends AlignFile implements FeaturesSourceI
     }
     else
     {
-      System.err.println("Ignoring unknown pragma: " + line);
+      jalview.bin.Console.errPrintln("Ignoring unknown pragma: " + line);
     }
   }
 }