X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblSequenceFetcher.java;h=7454eb627cff9b5bbb76910c3083b1a7e753840a;hb=dc39278fe37a89fd9c8e1155c2361e5a1fa3e513;hp=2f642b5dda146b3fec670591d8e853152e2a07e8;hpb=f87f3bc59e76f6112821e01ed88cf4c3ed853379;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
index 2f642b5..7454eb6 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;
@@ -34,12 +35,15 @@ import com.stevesoft.pat.Regex;
 abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
 {
   // domain properties lookup keys:
-  protected static final String ENSEMBL_DOMAIN = "ENSEMBL_DOMAIN";
-  protected static final String ENSEMBL_GENOMES_DOMAIN = "ENSEMBL_GENOMES_DOMAIN";
+  protected static final String ENSEMBL_BASEURL = "ENSEMBL_BASEURL";
+
+  protected static final String ENSEMBL_GENOMES_BASEURL = "ENSEMBL_GENOMES_BASEURL";
 
   // domain properties default values:
-  protected static final String DEFAULT_ENSEMBL_DOMAIN = "http://rest.ensembl.org";
-  protected static final String DEFAULT_ENSEMBL_GENOMES_DOMAIN = "http://rest.ensemblgenomes.org";
+  protected static final String DEFAULT_ENSEMBL_BASEURL = "https://rest.ensembl.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
@@ -54,6 +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
@@ -76,9 +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_DOMAIN, DEFAULT_ENSEMBL_DOMAIN);
-    ensemblGenomesDomain = Cache.getDefault(ENSEMBL_GENOMES_DOMAIN,
-            DEFAULT_ENSEMBL_GENOMES_DOMAIN);
+    ensemblDomain = Cache.getDefault(ENSEMBL_BASEURL,
+            DEFAULT_ENSEMBL_BASEURL).trim();
+    ensemblGenomesDomain = Cache.getDefault(ENSEMBL_GENOMES_BASEURL,
+            DEFAULT_ENSEMBL_GENOMES_BASEURL).trim();
     domain = ensemblDomain;
   }
 
@@ -86,10 +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;
   }
 
@@ -153,6 +166,6 @@ abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
 
   protected void setDomain(String d)
   {
-    domain = d;
+    domain = d == null ? null : d.trim();
   }
 }