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Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges
[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
ab35829
..
bc94619
100644
(file)
--- a/
src/jalview/ext/ensembl/EnsemblFeatures.java
+++ b/
src/jalview/ext/ensembl/EnsemblFeatures.java
@@
-89,12
+89,12
@@
class EnsemblFeatures extends EnsemblRestClient
public AlignmentI getSequenceRecords(String query) throws IOException
{
// TODO: use a vararg String... for getSequenceRecords instead?
public AlignmentI getSequenceRecords(String query) throws IOException
{
// TODO: use a vararg String... for getSequenceRecords instead?
-
+
List<String> queries = new ArrayList<>();
queries.add(query);
SequenceI seq = parseFeaturesJson(queries);
if (seq == null)
List<String> queries = new ArrayList<>();
queries.add(query);
SequenceI seq = parseFeaturesJson(queries);
if (seq == null)
- return null;
+ return null;
return new Alignment(new SequenceI[] { seq });
}
return new Alignment(new SequenceI[] { seq });
}
@@
-112,13
+112,14
@@
class EnsemblFeatures extends EnsemblRestClient
SequenceI seq = new Sequence("Dummy", "");
try
{
SequenceI seq = new Sequence("Dummy", "");
try
{
- Iterator<Object> rvals = (Iterator<Object>) getJSON(null, queries, -1, MODE_ITERATOR, null);
+ Iterator<Object> rvals = (Iterator<Object>) getJSON(null, queries, -1,
+ MODE_ITERATOR, null);
if (rvals == null)
{
if (rvals == null)
{
- return null;
+ return null;
}
while (rvals.hasNext())
}
while (rvals.hasNext())
- {
+ {
try
{
Map<String, Object> obj = (Map<String, Object>) rvals.next();
try
{
Map<String, Object> obj = (Map<String, Object>) rvals.next();
@@
-130,9
+131,8
@@
class EnsemblFeatures extends EnsemblRestClient
Object phase = obj.get("phase");
String alleles = JSONUtils
.arrayToStringList((List<Object>) obj.get("alleles"));
Object phase = obj.get("phase");
String alleles = JSONUtils
.arrayToStringList((List<Object>) obj.get("alleles"));
- String clinSig = JSONUtils
- .arrayToStringList(
- (List<Object>) obj.get("clinical_significance"));
+ String clinSig = JSONUtils.arrayToStringList(
+ (List<Object>) obj.get("clinical_significance"));
/*
* convert 'variation' to 'sequence_variant', and 'cds' to 'CDS'
/*
* convert 'variation' to 'sequence_variant', and 'cds' to 'CDS'
@@
-164,7
+164,7
@@
class EnsemblFeatures extends EnsemblRestClient
sf.setValue("clinical_significance", clinSig);
seq.addSequenceFeature(sf);
sf.setValue("clinical_significance", clinSig);
seq.addSequenceFeature(sf);
-
+
} catch (Throwable t)
{
// ignore - keep trying other features
} catch (Throwable t)
{
// ignore - keep trying other features
@@
-172,7
+172,7
@@
class EnsemblFeatures extends EnsemblRestClient
}
} catch (ParseException | IOException e)
{
}
} catch (ParseException | IOException e)
{
- e.printStackTrace();
+ e.printStackTrace();
// ignore
}
// ignore
}
@@
-216,8
+216,8
@@
class EnsemblFeatures extends EnsemblRestClient
* @param obj
* @param key
*/
* @param obj
* @param key
*/
- protected void setFeatureAttribute(SequenceFeature sf, Map<String, Object> obj,
- String key)
+ protected void setFeatureAttribute(SequenceFeature sf,
+ Map<String, Object> obj, String key)
{
Object object = obj.get(key);
if (object != null)
{
Object object = obj.get(key);
if (object != null)