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JAL-3829 JAL-3865 test structure chooser queries to mocked 3D Beacons FTS
[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
c7e1d7a
..
1ef8848
100644
(file)
--- a/
src/jalview/io/gff/Gff3Helper.java
+++ b/
src/jalview/io/gff/Gff3Helper.java
@@
-39,6
+39,8
@@
import java.util.Map;
*/
public class Gff3Helper extends GffHelperBase
{
*/
public class Gff3Helper extends GffHelperBase
{
+ public static final String ALLELES = "alleles";
+
protected static final String TARGET = "Target";
protected static final String ID = "ID";
protected static final String TARGET = "Target";
protected static final String ID = "ID";
@@
-348,15
+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
*/
@@
-399,7
+392,7
@@
public class Gff3Helper extends GffHelperBase
/*
* Ensembl returns dna variants as 'alleles'
*/
/*
* Ensembl returns dna variants as 'alleles'
*/
- desc = StringUtils.listToDelimitedString(attributes.get("alleles"),
+ desc = StringUtils.listToDelimitedString(attributes.get(ALLELES),
",");
}
",");
}
@@
-422,6
+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;
}
}