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JAL-3076 fetch Ensembl sequence as JSON instead of Fasta
[jalview.git]
/
src
/
jalview
/
ext
/
ensembl
/
EnsemblFeatures.java
diff --git
a/src/jalview/ext/ensembl/EnsemblFeatures.java
b/src/jalview/ext/ensembl/EnsemblFeatures.java
index
cb6f548
..
582eac6
100644
(file)
--- a/
src/jalview/ext/ensembl/EnsemblFeatures.java
+++ b/
src/jalview/ext/ensembl/EnsemblFeatures.java
@@
-22,9
+22,11
@@
package jalview.ext.ensembl;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
+import jalview.io.DataSourceType;
import jalview.io.FeaturesFile;
import jalview.io.FileParse;
import jalview.io.FeaturesFile;
import jalview.io.FileParse;
+import java.io.BufferedReader;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
@@
-84,12
+86,13
@@
class EnsemblFeatures extends EnsemblRestClient
// TODO: use a vararg String... for getSequenceRecords instead?
List<String> queries = new ArrayList<>();
queries.add(query);
// TODO: use a vararg String... for getSequenceRecords instead?
List<String> queries = new ArrayList<>();
queries.add(query);
- FileParse fp = getSequenceReader(queries);
- if (fp == null || !fp.isValid())
+ BufferedReader fp = getSequenceReader(queries);
+ if (fp == null)
{
return null;
}
{
return null;
}
- FeaturesFile fr = new FeaturesFile(fp);
+ FeaturesFile fr = new FeaturesFile(
+ new FileParse(fp, null, DataSourceType.URL));
return new Alignment(fr.getSeqsAsArray());
}
return new Alignment(fr.getSeqsAsArray());
}
@@
-140,13
+143,13
@@
class EnsemblFeatures extends EnsemblRestClient
* describes the required encoding of the response.
*/
@Override
* describes the required encoding of the response.
*/
@Override
- protected String getRequestMimeType(boolean multipleIds)
+ protected String getRequestMimeType()
{
return "text/x-gff3";
}
/**
{
return "text/x-gff3";
}
/**
- * Returns the MIME type for GFF3.
+ * Returns the MIME type for GFF3
*/
@Override
protected String getResponseMimeType()
*/
@Override
protected String getResponseMimeType()