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JAL-3076 fetch Ensembl sequence as JSON instead of Fasta
[jalview.git]
/
src
/
jalview
/
ext
/
ensembl
/
EnsemblXref.java
diff --git
a/src/jalview/ext/ensembl/EnsemblXref.java
b/src/jalview/ext/ensembl/EnsemblXref.java
index
c0b00b1
..
77768a6
100644
(file)
--- a/
src/jalview/ext/ensembl/EnsemblXref.java
+++ b/
src/jalview/ext/ensembl/EnsemblXref.java
@@
-88,18
+88,6
@@
class EnsemblXref extends EnsemblRestClient
return true;
}
return true;
}
- @Override
- protected String getRequestMimeType(boolean multipleIds)
- {
- return "application/json";
- }
-
- @Override
- protected String getResponseMimeType()
- {
- return "application/json";
- }
-
/**
* Calls the Ensembl xrefs REST endpoint and retrieves any cross-references
* ("primary_id") for the given identifier (Ensembl accession id) and database
/**
* Calls the Ensembl xrefs REST endpoint and retrieves any cross-references
* ("primary_id") for the given identifier (Ensembl accession id) and database
@@
-113,8
+101,8
@@
class EnsemblXref extends EnsemblRestClient
*/
public List<DBRefEntry> getCrossReferences(String identifier)
{
*/
public List<DBRefEntry> getCrossReferences(String identifier)
{
- List<DBRefEntry> result = new ArrayList<DBRefEntry>();
- List<String> ids = new ArrayList<String>();
+ List<DBRefEntry> result = new ArrayList<>();
+ List<String> ids = new ArrayList<>();
ids.add(identifier);
BufferedReader br = null;
ids.add(identifier);
BufferedReader br = null;
@@
-124,8
+112,11
@@
class EnsemblXref extends EnsemblRestClient
if (url != null)
{
br = getHttpResponse(url, ids);
if (url != null)
{
br = getHttpResponse(url, ids);
+ if (br != null)
+ {
+ result = parseResponse(br);
+ }
}
}
- return (parseResponse(br));
} catch (IOException e)
{
// ignore
} catch (IOException e)
{
// ignore
@@
-160,7
+151,7
@@
class EnsemblXref extends EnsemblRestClient
throws IOException
{
JSONParser jp = new JSONParser();
throws IOException
{
JSONParser jp = new JSONParser();
- List<DBRefEntry> result = new ArrayList<DBRefEntry>();
+ List<DBRefEntry> result = new ArrayList<>();
try
{
JSONArray responses = (JSONArray) jp.parse(br);
try
{
JSONArray responses = (JSONArray) jp.parse(br);
@@
-168,16
+159,13
@@
class EnsemblXref extends EnsemblRestClient
while (rvals.hasNext())
{
JSONObject val = (JSONObject) rvals.next();
while (rvals.hasNext())
{
JSONObject val = (JSONObject) rvals.next();
- String dbName = val.get("dbname").toString();
- if (dbName.equals(GO_GENE_ONTOLOGY))
- {
- continue;
- }
+ String db = val.get("dbname").toString();
String id = val.get("primary_id").toString();
String id = val.get("primary_id").toString();
- if (dbName != null && id != null)
+ if (db != null && id != null
+ && !GO_GENE_ONTOLOGY.equals(db))
{
{
- dbName = DBRefUtils.getCanonicalName(dbName);
- DBRefEntry dbref = new DBRefEntry(dbName, getXRefVersion(), id);
+ db = DBRefUtils.getCanonicalName(db);
+ DBRefEntry dbref = new DBRefEntry(db, getXRefVersion(), id);
result.add(dbref);
}
}
result.add(dbref);
}
}
@@
-211,7
+199,7
@@
class EnsemblXref extends EnsemblRestClient
protected URL getUrl(String identifier)
{
String url = getDomain() + "/xrefs/id/" + identifier
protected URL getUrl(String identifier)
{
String url = getDomain() + "/xrefs/id/" + identifier
- + "?content-type=application/json&all_levels=1";
+ + CONTENT_TYPE_JSON + "&all_levels=1";
try
{
return new URL(url);
try
{
return new URL(url);