JAL-1793 update spike build to latest incl stop and synonymous variants on peptides

[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 dd1739b..cfb3c6d 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
+++ b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
@@ -1,3 +1,23 @@
+/*
+ * 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.datamodel.DBRefSource;
@@ -18,12 +38,25 @@ abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
    * 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}$)" + "|" + "(CCDS[0-9.]{3,}$)");
+          "(ENS([A-Z]{3}|)[GTEP]{1}[0-9]{11}$)" + "|"
+                  + "(CCDS[0-9.]{3,}$)");
 
   protected static final String ENSEMBL_GENOMES_REST = "http://rest.ensemblgenomes.org";
 
   protected static final String ENSEMBL_REST = "http://rest.ensembl.org";
 
+  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 = "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