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Merge branch 'develop' into improvement/JAL-4124_dont_duplacate_PAE_data_acrossviews
[jalview.git]
/
src
/
jalview
/
io
/
gff
/
ExonerateHelper.java
diff --git
a/src/jalview/io/gff/ExonerateHelper.java
b/src/jalview/io/gff/ExonerateHelper.java
index
9ce4cc6
..
77b641a
100644
(file)
--- a/
src/jalview/io/gff/ExonerateHelper.java
+++ b/
src/jalview/io/gff/ExonerateHelper.java
@@
-90,7
+90,7
@@
public class ExonerateHelper extends Gff2Helper
relaxedIdMatching);
} catch (IOException ivfe)
{
relaxedIdMatching);
} catch (IOException ivfe)
{
- System.err.println(ivfe);
+ jalview.bin.Console.errPrintln(ivfe);
}
/*
}
/*
@@
-200,7
+200,7
@@
public class ExonerateHelper extends Gff2Helper
}
else if (!"+".equals(strand))
{
}
else if (!"+".equals(strand))
{
- System.err.println("Strand must be specified for alignment");
+ jalview.bin.Console.errPrintln("Strand must be specified for alignment");
return;
}
return;
}
@@
-239,7
+239,7
@@
public class ExonerateHelper extends Gff2Helper
String[] tokens = region.split(" ");
if (tokens.length != 3)
{
String[] tokens = region.split(" ");
if (tokens.length != 3)
{
- System.err.println("Malformed Align descriptor: " + region);
+ jalview.bin.Console.errPrintln("Malformed Align descriptor: " + region);
return null;
}
return null;
}
@@
-257,7
+257,7
@@
public class ExonerateHelper extends Gff2Helper
alignCount = Integer.parseInt(tokens[2]);
} catch (NumberFormatException nfe)
{
alignCount = Integer.parseInt(tokens[2]);
} catch (NumberFormatException nfe)
{
- System.err.println(nfe.toString());
+ jalview.bin.Console.errPrintln(nfe.toString());
return null;
}
return null;
}
@@
-351,7
+351,7
@@
public class ExonerateHelper extends Gff2Helper
return true;
}
}
return true;
}
}
- System.err.println("Sorry, I don't handle exonerate model " + model);
+ jalview.bin.Console.errPrintln("Sorry, I don't handle exonerate model " + model);
return false;
}
return false;
}