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

[jalview.git] / src / jalview / io / vcf / VCFLoader.java

diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java
index ea5b8e0..c3fbea8 100644 (file)
--- a/src/jalview/io/vcf/VCFLoader.java
+++ b/src/jalview/io/vcf/VCFLoader.java
@@ -278,7 +278,7 @@ public class VCFLoader
       initialise(vcfFile);
     } catch (IOException e)
     {
-      System.err.println("Error opening VCF file: " + e.getMessage());
+      jalview.bin.Console.errPrintln("Error opening VCF file: " + e.getMessage());
     }
 
     // map of species!chromosome!fromAssembly!toAssembly to {fromRange, toRange}
@@ -398,7 +398,7 @@ public class VCFLoader
       }
     } catch (Throwable e)
     {
-      System.err.println("Error processing VCF: " + e.getMessage());
+      jalview.bin.Console.errPrintln("Error processing VCF: " + e.getMessage());
       e.printStackTrace();
       if (gui != null)
       {
@@ -678,7 +678,7 @@ public class VCFLoader
         patterns.add(Pattern.compile(token.toUpperCase(Locale.ROOT)));
       } catch (PatternSyntaxException e)
       {
-        System.err.println("Invalid pattern ignored: " + token);
+        jalview.bin.Console.errPrintln("Invalid pattern ignored: " + token);
       }
     }
     return patterns;