JAL-3438 spotless for 2.11.2.0

[jalview.git] / src / jalview / ext / ensembl / EnsemblSequenceFetcher.java

diff --git a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
index 0aaaf93..66b0e3b 100644 (file)
--- 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
@@ -64,7 +66,7 @@ abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
 
   protected static final String PARENT = "Parent";
 
-  protected static final String ID = "id";
+  protected static final String JSON_ID = AlignmentUtils.VARIANT_ID; // "id";
 
   protected static final String OBJECT_TYPE = "object_type";
 
@@ -90,10 +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;
   }
 
@@ -101,10 +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;
   }
 
@@ -168,6 +166,6 @@ abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
 
   protected void setDomain(String d)
   {
-    domain = d;
+    domain = d == null ? null : d.trim();
   }
 }