X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblSequenceFetcher.java;h=2008fb6aeebf58e5956623d0e0e60cc848f71da8;hb=7d602d0e4b439e56af3e4551ed71f181a8025534;hp=9a4952e9082d87642432f920f6c208752fd1bea9;hpb=e24933a537e0f640c75d4685c468615872bc77fc;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
index 9a4952e..2008fb6 100644
--- a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
+++ b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
@@ -1,6 +1,29 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.ext.ensembl;
 
+import jalview.analysis.AlignmentUtils;
+import jalview.bin.Cache;
 import jalview.datamodel.DBRefSource;
+import jalview.util.Platform;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;
 
 import com.stevesoft.pat.Regex;
@@ -12,13 +35,41 @@ import com.stevesoft.pat.Regex;
  */
 abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
 {
+  // domain properties lookup keys:
+  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_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
    * or ENSMUSP or similar for other species
    * or CCDSnnnnn.nn with at least 3 digits
    */
-  private static final Regex ACCESSION_REGEX = new Regex(
-          "(ENS([A-Z]{3}|)[GTEP]{1}[0-9]{11}$)" + "|" + "(CCDS[0-9.]{3,}$)");
+  private static final Regex ACCESSION_REGEX = Platform.newRegex(
+          "(ENS([A-Z]{3}|)[GTEP]{1}[0-9]{11}$)" + "|"
+                  + "(CCDS[0-9.]{3,}$)");
+
+  protected final String ensemblGenomesDomain;
+
+  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
@@ -31,17 +82,29 @@ abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
     constrained, regulatory
   }
 
-  @Override
-  public String getDbSource()
+  private String domain;
+
+  /**
+   * Constructor
+   */
+  public EnsemblSequenceFetcher()
   {
-    // NB ensure Uniprot xrefs are canonicalised from "Ensembl" to "ENSEMBL"
-    return DBRefSource.ENSEMBL; // "ENSEMBL"
+    /*
+     * 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).trim();
+    ensemblGenomesDomain = Cache.getDefault(ENSEMBL_GENOMES_BASEURL,
+            DEFAULT_ENSEMBL_GENOMES_BASEURL).trim();
+    domain = ensemblDomain;
   }
 
   @Override
-  public String getDbVersion()
+  public String getDbSource()
   {
-    return "0";
+    // NB ensure Uniprot xrefs are canonicalised from "Ensembl" to "ENSEMBL"
+    return DBRefSource.ENSEMBL;
   }
 
   @Override
@@ -90,4 +153,20 @@ abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
   {
     return true;
   }
+
+  /**
+   * Returns the domain name to query e.g. http://rest.ensembl.org or
+   * http://rest.ensemblgenomes.org
+   * 
+   * @return
+   */
+  protected String getDomain()
+  {
+    return domain;
+  }
+
+  protected void setDomain(String d)
+  {
+    domain = d == null ? null : d.trim();
+  }
 }