X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblSequenceFetcher.java;h=21f9f7e01b87b878f805f38e6f3f93015986877e;hb=990ed4ffbaa7a95b2ebb6bf6ab0440310f6e83ab;hp=dd1739b418fe4e613445518bacdab8142054a80e;hpb=1c6ddae580d69eb0fa5b4291ba84fd6ba9b83621;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
index dd1739b..21f9f7e 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;
@@ -12,17 +35,34 @@ import com.stevesoft.pat.Regex;
  */
 abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
 {
-  /*
-   * 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}$)" + "|" + "(CCDS[0-9.]{3,}$)");
+  // 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;
+
+  private static Regex ACCESSION_REGEX;
+
+  protected final String ensemblGenomesDomain;
+
+  protected final String ensemblDomain;
+
+  protected static final String OBJECT_TYPE_TRANSLATION = "Translation";
 
-  protected static final String ENSEMBL_GENOMES_REST = "http://rest.ensemblgenomes.org";
+  protected static final String OBJECT_TYPE_TRANSCRIPT = "Transcript";
 
-  protected static final String ENSEMBL_REST = "http://rest.ensembl.org";
+  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
@@ -35,16 +75,28 @@ abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
     constrained, regulatory
   }
 
-  private String domain = ENSEMBL_REST;
+  private String domain;
+
+  /**
+   * Constructor
+   */
+  public EnsemblSequenceFetcher()
+  {
+    /*
+     * 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 getDbSource()
   {
     // NB ensure Uniprot xrefs are canonicalised from "Ensembl" to "ENSEMBL"
-    if (ENSEMBL_GENOMES_REST.equals(getDomain()))
-    {
-      return DBRefSource.ENSEMBLGENOMES;
-    }
     return DBRefSource.ENSEMBL;
   }
 
@@ -63,6 +115,17 @@ abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
   @Override
   public Regex getAccessionValidator()
   {
+    if (ACCESSION_REGEX == null)
+    {
+      /*
+       * accepts ENSG/T/E/P with 11 digits
+       * or ENSMUSP or similar for other species
+       * or CCDSnnnnn.nn with at least 3 digits
+       */
+      ACCESSION_REGEX = Platform
+              .newRegex("(ENS([A-Z]{3}|)[GTEP]{1}[0-9]{11}$)" + "|"
+                      + "(CCDS[0-9.]{3,}$)", null);
+    }
     return ACCESSION_REGEX;
   }
 
@@ -108,6 +171,6 @@ abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
 
   protected void setDomain(String d)
   {
-    domain = d;
+    domain = d == null ? null : d.trim();
   }
 }