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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
82e5313
..
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";
@@
-152,8
+154,8
@@
public class Gff3Helper extends GffHelperBase
*/
if ("-".equals(strand))
{
*/
if ("-".equals(strand))
{
- System.err
- .println("Skipping mapping from reverse complement as not yet supported");
+ System.err.println(
+ "Skipping mapping from reverse complement as not yet supported");
return null;
}
return null;
}
@@
-244,7
+246,8
@@
public class Gff3Helper extends GffHelperBase
* @return
*/
@SuppressWarnings("unused")
* @return
*/
@SuppressWarnings("unused")
- protected String findTargetId(String target, Map<String, List<String>> set)
+ protected String findTargetId(String target,
+ Map<String, List<String>> set)
{
return target;
}
{
return target;
}
@@
-275,8
+278,8
@@
public class Gff3Helper extends GffHelperBase
* @throws IOException
*/
protected SequenceFeature processProteinMatch(
* @throws IOException
*/
protected SequenceFeature processProteinMatch(
- Map<String, List<String>> set, SequenceI seq,
- String[] gffColumns, AlignmentI align, List<SequenceI> newseqs,
+ Map<String, List<String>> set, SequenceI seq, String[] gffColumns,
+ AlignmentI align, List<SequenceI> newseqs,
boolean relaxedIdMatching)
{
// This is currently tailored to InterProScan GFF output:
boolean relaxedIdMatching)
{
// This is currently tailored to InterProScan GFF output:
@@
-310,10
+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);
/*
@@
-321,8
+323,8
@@
public class Gff3Helper extends GffHelperBase
* renamed with its qualified accession id; renaming has to wait until
* all sequence reference resolution is complete
*/
* renamed with its qualified accession id; renaming has to wait until
* all sequence reference resolution is complete
*/
- String accessionId = StringUtils.listToDelimitedString(
- set.get(NAME), ",");
+ String accessionId = StringUtils
+ .listToDelimitedString(set.get(NAME), ",");
if (accessionId.length() > 0)
{
String database = sf.getType(); // TODO InterProScan only??
if (accessionId.length() > 0)
{
String database = sf.getType(); // TODO InterProScan only??
@@
-348,23
+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)
{
@@
-397,7
+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),
",");
}
",");
}
@@
-420,6
+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;
}
}