X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblSequenceFetcher.java;h=66b0e3bd49f8ab2570991c6a6036b09f56cc3669;hb=5d01a31888d046245981a4171850acd63a1f2862;hp=eb1d39969130ddbdcd6e23a4a926c12471183d5a;hpb=953a951c7e78cabc4b2db3981602f0a5b33423c9;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
index eb1d399..66b0e3b 100644
--- a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
+++ b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
@@ -20,6 +20,7 @@
  */
 package jalview.ext.ensembl;
 
+import jalview.analysis.AlignmentUtils;
 import jalview.bin.Cache;
 import jalview.datamodel.DBRefSource;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;
@@ -41,7 +42,8 @@ abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
   // domain properties default values:
   protected static final String DEFAULT_ENSEMBL_BASEURL = "https://rest.ensembl.org";
 
-  protected static final String DEFAULT_ENSEMBL_GENOMES_BASEURL = "https://rest.ensemblgenomes.org";
+  // ensemblgenomes REST service merged to ensembl 9th April 2019
+  protected static final String DEFAULT_ENSEMBL_GENOMES_BASEURL = DEFAULT_ENSEMBL_BASEURL;
 
   /*
    * accepts ENSG/T/E/P with 11 digits
@@ -56,6 +58,18 @@ abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
 
   protected final String ensemblDomain;
 
+  protected static final String OBJECT_TYPE_TRANSLATION = "Translation";
+
+  protected static final String OBJECT_TYPE_TRANSCRIPT = "Transcript";
+
+  protected static final String OBJECT_TYPE_GENE = "Gene";
+
+  protected static final String PARENT = "Parent";
+
+  protected static final String JSON_ID = AlignmentUtils.VARIANT_ID; // "id";
+
+  protected static final String OBJECT_TYPE = "object_type";
+
   /*
    * possible values for the 'feature' parameter of the /overlap REST service
    * @see http://rest.ensembl.org/documentation/info/overlap_id
@@ -78,10 +92,10 @@ abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
      * the default domain names may be overridden in .jalview_properties;
      * this allows an easy change from http to https in future if needed
      */
-    ensemblDomain = Cache.getDefault(ENSEMBL_BASEURL,
-            DEFAULT_ENSEMBL_BASEURL);
+    ensemblDomain = Cache
+            .getDefault(ENSEMBL_BASEURL, DEFAULT_ENSEMBL_BASEURL).trim();
     ensemblGenomesDomain = Cache.getDefault(ENSEMBL_GENOMES_BASEURL,
-            DEFAULT_ENSEMBL_GENOMES_BASEURL);
+            DEFAULT_ENSEMBL_GENOMES_BASEURL).trim();
     domain = ensemblDomain;
   }
 
@@ -89,10 +103,6 @@ abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
   public String getDbSource()
   {
     // NB ensure Uniprot xrefs are canonicalised from "Ensembl" to "ENSEMBL"
-    if (ensemblGenomesDomain.equals(getDomain()))
-    {
-      return DBRefSource.ENSEMBLGENOMES;
-    }
     return DBRefSource.ENSEMBL;
   }
 
@@ -156,6 +166,6 @@ abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
 
   protected void setDomain(String d)
   {
-    domain = d;
+    domain = d == null ? null : d.trim();
   }
 }