X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fensembl%2FEnsemblMap.java;h=f2ab1956a49712df9c162b4c3651c18b7d7f2e74;hb=1114062d7c3034db3387f46a860c0e334206ce49;hp=f01bd4f6b56ed7640f9e027503ff886d2918320a;hpb=f59dd9efbb3dfc313ab0b0507832e21cd0076fe1;p=jalview.git

diff --git a/src/jalview/ext/ensembl/EnsemblMap.java b/src/jalview/ext/ensembl/EnsemblMap.java
index f01bd4f..f2ab195 100644
--- a/src/jalview/ext/ensembl/EnsemblMap.java
+++ b/src/jalview/ext/ensembl/EnsemblMap.java
@@ -1,11 +1,32 @@
+/*
+ * 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;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.GeneLociI;
+import jalview.datamodel.GeneLocus;
+import jalview.datamodel.Mapping;
 import jalview.util.MapList;
 
-import java.io.BufferedReader;
 import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URL;
@@ -13,12 +34,22 @@ import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Iterator;
 import java.util.List;
+import java.util.Map;
 
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
 import org.json.simple.parser.ParseException;
 
+/**
+ * A client for the Ensembl REST service /map endpoint, to convert from
+ * coordinates of one genome assembly to another.
+ * <p>
+ * Note that species and assembly identifiers passed to this class must be valid
+ * in Ensembl. They are not case sensitive.
+ * 
+ * @author gmcarstairs
+ * @see https://rest.ensembl.org/documentation/info/assembly_map
+ * @see https://rest.ensembl.org/info/assembly/human?content-type=text/xml
+ * @see https://rest.ensembl.org/info/species?content-type=text/xml
+ */
 public class EnsemblMap extends EnsemblRestClient
 {
   private static final String MAPPED = "mapped";
@@ -73,8 +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
   {
     /*
@@ -119,30 +150,15 @@ public class EnsemblMap extends EnsemblRestClient
           String fromRef, String toRef, int[] queryRange)
   {
     URL url = null;
-    BufferedReader br = null;
-
     try
     {
-      url = getAssemblyMapUrl(species, chromosome, fromRef, toRef, queryRange[0],
-              queryRange[1]);
-      br = getHttpResponse(url, null);
-      return (parseAssemblyMappingResponse(br));
+      url = getAssemblyMapUrl(species, chromosome, fromRef, toRef,
+              queryRange[0], queryRange[1]);
+      return (parseAssemblyMappingResponse(url));
     } catch (Throwable t)
     {
       System.out.println("Error calling " + url + ": " + t.getMessage());
       return null;
-    } finally
-    {
-      if (br != null)
-      {
-        try
-        {
-          br.close();
-        } catch (IOException e)
-        {
-          // ignore
-        }
-      }
     }
   }
 
@@ -161,22 +177,24 @@ public class EnsemblMap extends EnsemblRestClient
    * @param br
    * @return
    */
-  protected int[] parseAssemblyMappingResponse(BufferedReader br)
+  @SuppressWarnings("unchecked")
+  protected int[] parseAssemblyMappingResponse(URL url)
   {
     int[] result = null;
-    JSONParser jp = new JSONParser();
 
     try
     {
-      JSONObject parsed = (JSONObject) jp.parse(br);
-      JSONArray mappings = (JSONArray) parsed.get(MAPPINGS);
-
-      Iterator rvals = mappings.iterator();
+      Iterator<Object> rvals = (Iterator<Object>) getJSON(url, null, -1,
+              MODE_ITERATOR, MAPPINGS);
+      if (rvals == null)
+      {
+        return null;
+      }
       while (rvals.hasNext())
       {
         // todo check for "mapped"
-        JSONObject val = (JSONObject) rvals.next();
-        JSONObject mapped = (JSONObject) val.get(MAPPED);
+        Map<String, Object> val = (Map<String, Object>) rvals.next();
+        Map<String, Object> mapped = (Map<String, Object>) val.get(MAPPED);
         int start = Integer.parseInt(mapped.get("start").toString());
         int end = Integer.parseInt(mapped.get("end").toString());
         String strand = mapped.get("strand").toString();
@@ -236,37 +254,19 @@ public class EnsemblMap extends EnsemblRestClient
           int end, String cdsOrCdna)
   {
     URL url = null;
-    BufferedReader br = null;
-
     try
     {
       String domain = new EnsemblInfo().getDomain(division);
       if (domain != null)
       {
         url = getIdMapUrl(domain, accession, start, end, cdsOrCdna);
-        br = getHttpResponse(url, null);
-        if (br != null)
-        {
-          return (parseIdMappingResponse(br, accession, domain));
-        }
+        return (parseIdMappingResponse(url, accession, domain));
       }
       return null;
     } catch (Throwable t)
     {
       System.out.println("Error calling " + url + ": " + t.getMessage());
       return null;
-    } finally
-    {
-      if (br != null)
-      {
-        try
-        {
-          br.close();
-        } catch (IOException e)
-        {
-          // ignore
-        }
-      }
     }
   }
 
@@ -286,9 +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);
   }
 
@@ -312,17 +312,18 @@ public class EnsemblMap extends EnsemblRestClient
    * @param domain
    * @return
    */
-  GeneLociI parseIdMappingResponse(BufferedReader br, String accession,
-          String domain)
+  @SuppressWarnings("unchecked")
+  GeneLociI parseIdMappingResponse(URL url, String accession, String domain)
   {
-    JSONParser jp = new JSONParser();
 
     try
     {
-      JSONObject parsed = (JSONObject) jp.parse(br);
-      JSONArray mappings = (JSONArray) parsed.get(MAPPINGS);
-
-      Iterator rvals = mappings.iterator();
+      Iterator<Object> rvals = (Iterator<Object>) getJSON(url, null, -1,
+              MODE_ITERATOR, MAPPINGS);
+      if (rvals == null)
+      {
+        return null;
+      }
       String assembly = null;
       String chromosome = null;
       int fromEnd = 0;
@@ -330,26 +331,27 @@ public class EnsemblMap extends EnsemblRestClient
 
       while (rvals.hasNext())
       {
-        JSONObject val = (JSONObject) rvals.next();
-        JSONObject original = (JSONObject) val.get("original");
+        Map<String, Object> val = (Map<String, Object>) rvals.next();
+        Map<String, Object> original = (Map<String, Object>) val
+                .get("original");
         fromEnd = Integer.parseInt(original.get("end").toString());
 
-        JSONObject mapped = (JSONObject) val.get(MAPPED);
+        Map<String, Object> mapped = (Map<String, Object>) val.get(MAPPED);
         int start = Integer.parseInt(mapped.get("start").toString());
         int end = Integer.parseInt(mapped.get("end").toString());
         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;
@@ -372,36 +374,12 @@ public class EnsemblMap extends EnsemblRestClient
               .getSpecies(accession);
       final String as = assembly;
       final String chr = chromosome;
-      List<int[]> fromRange = Collections.singletonList(new int[] { 1,
-          fromEnd });
-      final MapList map = new MapList(fromRange, regions, 1, 1);
-      return new GeneLociI()
-      {
-
-        @Override
-        public String getSpeciesId()
-        {
-          return species == null ? "" : species;
-        }
-
-        @Override
-        public String getAssemblyId()
-        {
-          return as;
-        }
-
-        @Override
-        public String getChromosomeId()
-        {
-          return chr;
-        }
-
-        @Override
-        public MapList getMap()
-        {
-          return map;
-        }
-      };
+      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);
     } catch (IOException | ParseException | NumberFormatException e)
     {
       // ignore