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Merge branch 'features/JAL-3187_uitweaks' 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
594040a
..
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";
@@
-311,10
+313,9
@@
public class Gff3Helper extends GffHelperBase
* give the mapped sequence a copy of the sequence feature, with
* start/end range adjusted
*/
* give the mapped sequence a copy of the sequence feature, with
* start/end range adjusted
*/
- SequenceFeature sf2 = new SequenceFeature(sf);
- sf2.setBegin(1);
int sequenceFeatureLength = 1 + sf.getEnd() - sf.getBegin();
int sequenceFeatureLength = 1 + sf.getEnd() - sf.getBegin();
- sf2.setEnd(sequenceFeatureLength);
+ SequenceFeature sf2 = new SequenceFeature(sf, 1,
+ sequenceFeatureLength, sf.getFeatureGroup(), sf.getScore());
mappedSequence.addSequenceFeature(sf2);
/*
mappedSequence.addSequenceFeature(sf2);
/*
@@
-349,23
+350,16
@@
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
*/
@Override
protected SequenceFeature buildSequenceFeature(String[] gff,
* Modifies the default SequenceFeature in order to set the Target sequence id
* as the description
*/
@Override
protected SequenceFeature buildSequenceFeature(String[] gff,
+ int typeColumn, String group,
Map<String, List<String>> attributes)
{
Map<String, List<String>> attributes)
{
- SequenceFeature sf = super.buildSequenceFeature(gff, attributes);
+ SequenceFeature sf = super.buildSequenceFeature(gff, typeColumn, group,
+ attributes);
String desc = getDescription(sf, attributes);
if (desc != null)
{
String desc = getDescription(sf, attributes);
if (desc != null)
{
@@
-398,7
+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),
",");
}
",");
}
@@
-421,6
+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;
}
}