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JAL-3858 minimum value for a range is used to shade ranges in PAE map
[jalview.git]
/
src
/
jalview
/
io
/
gff
/
Gff3Helper.java
diff --git
a/src/jalview/io/gff/Gff3Helper.java
b/src/jalview/io/gff/Gff3Helper.java
index
1ef8848
..
646900d
100644
(file)
--- a/
src/jalview/io/gff/Gff3Helper.java
+++ b/
src/jalview/io/gff/Gff3Helper.java
@@
-154,7
+154,7
@@
public class Gff3Helper extends GffHelperBase
*/
if ("-".equals(strand))
{
*/
if ("-".equals(strand))
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Skipping mapping from reverse complement as not yet supported");
return null;
}
"Skipping mapping from reverse complement as not yet supported");
return null;
}
@@
-162,7
+162,7
@@
public class Gff3Helper extends GffHelperBase
List<String> targets = attributes.get(TARGET);
if (targets == null)
{
List<String> targets = attributes.get(TARGET);
if (targets == null)
{
- System.err.println("'Target' missing in GFF");
+ jalview.bin.Console.errPrintln("'Target' missing in GFF");
return null;
}
return null;
}
@@
-178,7
+178,7
@@
public class Gff3Helper extends GffHelperBase
String[] tokens = target.split(" ");
if (tokens.length < 3)
{
String[] tokens = target.split(" ");
if (tokens.length < 3)
{
- System.err.println("Incomplete Target: " + target);
+ jalview.bin.Console.errPrintln("Incomplete Target: " + target);
continue;
}
continue;
}
@@
-225,7
+225,7
@@
public class Gff3Helper extends GffHelperBase
}
} catch (NumberFormatException nfe)
{
}
} catch (NumberFormatException nfe)
{
- System.err.println("Invalid start or end in Target " + target);
+ jalview.bin.Console.errPrintln("Invalid start or end in Target " + target);
}
}
}
}