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Merge branch 'bug/JAL-3120restoreFeatureColour' into merge/JAL-3120
[jalview.git]
/
src
/
jalview
/
ext
/
ensembl
/
EnsemblSeqProxy.java
diff --git
a/src/jalview/ext/ensembl/EnsemblSeqProxy.java
b/src/jalview/ext/ensembl/EnsemblSeqProxy.java
index
7b448fd
..
5dc701d
100644
(file)
--- a/
src/jalview/ext/ensembl/EnsemblSeqProxy.java
+++ b/
src/jalview/ext/ensembl/EnsemblSeqProxy.java
@@
-62,8
+62,6
@@
import org.json.simple.parser.ParseException;
*/
public abstract class EnsemblSeqProxy extends EnsemblRestClient
{
*/
public abstract class EnsemblSeqProxy extends EnsemblRestClient
{
- protected static final String NAME = "Name";
-
protected static final String DESCRIPTION = "description";
/*
protected static final String DESCRIPTION = "description";
/*
@@
-867,9
+865,8
@@
public abstract class EnsemblSeqProxy extends EnsemblRestClient
protected boolean featureMayBelong(SequenceFeature sf, String identifier)
{
String parent = (String) sf.getValue(PARENT);
protected boolean featureMayBelong(SequenceFeature sf, String identifier)
{
String parent = (String) sf.getValue(PARENT);
- // using contains to allow for prefix "gene:", "transcript:" etc
if (parent != null
if (parent != null
- && !parent.toUpperCase().contains(identifier.toUpperCase()))
+ && !parent.equalsIgnoreCase(identifier))
{
// this genomic feature belongs to a different transcript
return false;
{
// this genomic feature belongs to a different transcript
return false;
@@
-877,6
+874,9
@@
public abstract class EnsemblSeqProxy extends EnsemblRestClient
return true;
}
return true;
}
+ /**
+ * Answers a short description of the sequence fetcher
+ */
@Override
public String getDescription()
{
@Override
public String getDescription()
{
@@
-915,10
+915,14
@@
public abstract class EnsemblSeqProxy extends EnsemblRestClient
/**
* Answers true if the feature type is either 'NMD_transcript_variant' or
/**
* Answers true if the feature type is either 'NMD_transcript_variant' or
- * 'transcript' or one of its sub-types in the Sequence Ontology. This is
- * needed because NMD_transcript_variant behaves like 'transcript' in Ensembl
+ * 'transcript' (or one of its sub-types in the Sequence Ontology). This is
+ * because NMD_transcript_variant behaves like 'transcript' in Ensembl
* although strictly speaking it is not (it is a sub-type of
* sequence_variant).
* although strictly speaking it is not (it is a sub-type of
* sequence_variant).
+ * <p>
+ * (This test was needed when fetching transcript features as GFF. As we are
+ * now fetching as JSON, all features have type 'transcript' so the check for
+ * NMD_transcript_variant is redundant. Left in for any future case arising.)
*
* @param featureType
* @return
*
* @param featureType
* @return