X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblMap.java;h=f2ab1956a49712df9c162b4c3651c18b7d7f2e74;hb=2bb9cad4fa36d64cebbe09bc63732e8dbb4dcb32;hp=e9cc9e15fb11f4d7fe09b72714cba36e47c33815;hpb=17e4ea278bc9a5fb280db1252ce78b7a295215f5;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblMap.java b/src/jalview/ext/ensembl/EnsemblMap.java
index e9cc9e1..f2ab195 100644
--- a/src/jalview/ext/ensembl/EnsemblMap.java
+++ b/src/jalview/ext/ensembl/EnsemblMap.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.AlignmentI;
@@ -84,8 +104,8 @@ public class EnsemblMap extends EnsemblRestClient
    * @return
    * @throws MalformedURLException
    */
-  protected URL getAssemblyMapUrl(String species, String chromosome, String fromRef,
-          String toRef, int startPos, int endPos)
+  protected URL getAssemblyMapUrl(String species, String chromosome,
+          String fromRef, String toRef, int startPos, int endPos)
           throws MalformedURLException
   {
     /*
@@ -132,8 +152,8 @@ public class EnsemblMap extends EnsemblRestClient
     URL url = null;
     try
     {
-      url = getAssemblyMapUrl(species, chromosome, fromRef, toRef, queryRange[0],
-              queryRange[1]);
+      url = getAssemblyMapUrl(species, chromosome, fromRef, toRef,
+              queryRange[0], queryRange[1]);
       return (parseAssemblyMappingResponse(url));
     } catch (Throwable t)
     {
@@ -164,7 +184,8 @@ public class EnsemblMap extends EnsemblRestClient
 
     try
     {
-      Iterator<Object> rvals = (Iterator<Object>) getJSON(url, null, -1, MODE_ITERATOR, MAPPINGS);
+      Iterator<Object> rvals = (Iterator<Object>) getJSON(url, null, -1,
+              MODE_ITERATOR, MAPPINGS);
       if (rvals == null)
       {
         return null;
@@ -265,9 +286,9 @@ public class EnsemblMap extends EnsemblRestClient
   URL getIdMapUrl(String domain, String accession, int start, int end,
           String cdsOrCdna) throws MalformedURLException
   {
-    String url = String
-            .format("%s/map/%s/%s/%d..%d?include_original_region=1&content-type=application/json",
-                    domain, cdsOrCdna, accession, start, end);
+    String url = String.format(
+            "%s/map/%s/%s/%d..%d?include_original_region=1&content-type=application/json",
+            domain, cdsOrCdna, accession, start, end);
     return new URL(url);
   }
 
@@ -292,13 +313,13 @@ public class EnsemblMap extends EnsemblRestClient
    * @return
    */
   @SuppressWarnings("unchecked")
-GeneLociI parseIdMappingResponse(URL url, String accession,
-          String domain)
+  GeneLociI parseIdMappingResponse(URL url, String accession, String domain)
   {
 
     try
     {
-      Iterator<Object> rvals = (Iterator<Object>) getJSON(url, null, -1, MODE_ITERATOR, MAPPINGS);
+      Iterator<Object> rvals = (Iterator<Object>) getJSON(url, null, -1,
+              MODE_ITERATOR, MAPPINGS);
       if (rvals == null)
       {
         return null;
@@ -311,7 +332,8 @@ GeneLociI parseIdMappingResponse(URL url, String accession,
       while (rvals.hasNext())
       {
         Map<String, Object> val = (Map<String, Object>) rvals.next();
-        Map<String, Object> original = (Map<String, Object>) val.get("original");
+        Map<String, Object> original = (Map<String, Object>) val
+                .get("original");
         fromEnd = Integer.parseInt(original.get("end").toString());
 
         Map<String, Object> mapped = (Map<String, Object>) val.get(MAPPED);
@@ -320,16 +342,16 @@ GeneLociI parseIdMappingResponse(URL url, String accession,
         String ass = mapped.get("assembly_name").toString();
         if (assembly != null && !assembly.equals(ass))
         {
-          System.err
-                  .println("EnsemblMap found multiple assemblies - can't resolve");
+          System.err.println(
+                  "EnsemblMap found multiple assemblies - can't resolve");
           return null;
         }
         assembly = ass;
         String chr = mapped.get("seq_region_name").toString();
         if (chromosome != null && !chromosome.equals(chr))
         {
-          System.err
-                  .println("EnsemblMap found multiple chromosomes - can't resolve");
+          System.err.println(
+                  "EnsemblMap found multiple chromosomes - can't resolve");
           return null;
         }
         chromosome = chr;
@@ -352,8 +374,9 @@ GeneLociI parseIdMappingResponse(URL url, String accession,
               .getSpecies(accession);
       final String as = assembly;
       final String chr = chromosome;
-      List<int[]> fromRange = Collections.singletonList(new int[] { 1,
-          fromEnd });
+      List<int[]> fromRange = Collections
+              .singletonList(new int[]
+              { 1, fromEnd });
       Mapping mapping = new Mapping(new MapList(fromRange, regions, 1, 1));
       return new GeneLocus(species == null ? "" : species, as, chr,
               mapping);