git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Merge branch 'patch/JAL-4062_sort_and_merge_contiguousregions' into develop
[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
a25a014
..
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);
}
}
}
}
@@
-350,15
+350,6
@@
public class Gff3Helper extends GffHelperBase
}
/**
}
/**
- * Return '=' as the name-value separator used in column 9 attributes.
- */
- @Override
- protected char getNameValueSeparator()
- {
- return '=';
- }
-
- /**
* Modifies the default SequenceFeature in order to set the Target sequence id
* as the description
*/
* Modifies the default SequenceFeature in order to set the Target sequence id
* as the description
*/
@@
-424,6
+415,11
@@
public class Gff3Helper extends GffHelperBase
desc = (String) sf.getValue(ID);
}
desc = (String) sf.getValue(ID);
}
+ /*
+ * and decode comma, equals, semi-colon as required by GFF3 spec
+ */
+ desc = StringUtils.urlDecode(desc, GFF_ENCODABLE);
+
return desc;
}
}
return desc;
}
}