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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)
{
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}
}
// map of species!chromosome!fromAssembly!toAssembly to {fromRange, toRange}
@@
-398,7
+398,7
@@
public class VCFLoader
}
} catch (Throwable e)
{
}
} 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)
{
e.printStackTrace();
if (gui != null)
{
@@
-678,7
+678,7
@@
public class VCFLoader
patterns.add(Pattern.compile(token.toUpperCase(Locale.ROOT)));
} catch (PatternSyntaxException e)
{
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;
}
}
return patterns;