JAL-3725 helper methods for computing mapped feature range overlap

[jalview.git] / src / jalview / urls / IdentifiersUrlProvider.java

diff --git a/src/jalview/urls/IdentifiersUrlProvider.java b/src/jalview/urls/IdentifiersUrlProvider.java
index 98a5ee4..0988e7d 100644 (file)
--- a/src/jalview/urls/IdentifiersUrlProvider.java
+++ b/src/jalview/urls/IdentifiersUrlProvider.java
@@ -35,7 +35,6 @@ import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
 import java.util.StringTokenizer;
-import java.util.Vector;
 
 import org.json.simple.JSONArray;
 import org.json.simple.JSONObject;
@@ -53,6 +52,10 @@ import org.json.simple.parser.ParseException;
 public class IdentifiersUrlProvider extends UrlProviderImpl
 {
 
+  private static final String LOCAL_KEY = "Local";
+
+  private static final String ID_ORG_KEY = "identifiers.org";
+
   // map of string ids to urls
   private HashMap<String, UrlLink> urls;
 
@@ -73,8 +76,7 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
    *          name of identifiers.org download file
    * @return hashmap of identifiers.org data, keyed by MIRIAM id
    */
-  private HashMap<String, UrlLink> readIdentifiers(
-          String idFileName)
+  private HashMap<String, UrlLink> readIdentifiers(String idFileName)
   {
     JSONParser parser = new JSONParser();
 
@@ -84,8 +86,24 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
     try
     {
       FileReader reader = new FileReader(idFileName);
+      String key = "";
+      JSONObject obj = (JSONObject) parser.parse(reader);
+      if (obj.containsKey(ID_ORG_KEY))
+      {
+        key = ID_ORG_KEY;
+      }
+      else if (obj.containsKey(LOCAL_KEY))
+      {
+        key = LOCAL_KEY;
+      }
+      else
+      {
+        System.out.println(
+                "Unexpected key returned from identifiers jalview service");
+        return idData;
+      }
 
-      JSONArray jsonarray = (JSONArray) parser.parse(reader);
+      JSONArray jsonarray = (JSONArray) obj.get(key);
 
       // loop over each entry in JSON array and build HashMap entry
       for (int i = 0; i < jsonarray.size(); i++)
@@ -94,18 +112,22 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
 
         String url = (String) item.get("url") + "/" + DELIM + DB_ACCESSION
                 + DELIM;
-        UrlLink link = new UrlLink((String) item.get("name") + SEP + url);
+        UrlLink link = new UrlLink((String) item.get("name"), url,
+                (String) item.get("prefix"));
         idData.put((String) item.get("id"), link);
       }
     } catch (FileNotFoundException e)
     {
       e.printStackTrace();
+      idData.clear();
     } catch (IOException e)
     {
       e.printStackTrace();
+      idData.clear();
     } catch (ParseException e)
     {
       e.printStackTrace();
+      idData.clear();
     }
     return idData;
   }
@@ -128,19 +150,19 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
     }
 
     // reset defaultUrl in case it is no longer selected
-    setDefaultUrl(defaultUrl);
+    setPrimaryUrl(primaryUrl);
   }
 
   @Override
-  public boolean setDefaultUrl(String id)
+  public boolean setPrimaryUrl(String id)
   {
-    if (id == null)
+    if (urls.containsKey(id))
     {
-      defaultUrl = null;
+      primaryUrl = id;
     }
-    if (urls.containsKey(id))
+    else
     {
-      defaultUrl = id;
+      primaryUrl = null;
     }
 
     return urls.containsKey(id);
@@ -169,12 +191,12 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
   }
 
   @Override
-  public Vector<String> getLinksForMenu()
+  public List<String> getLinksForMenu()
   {
-    Vector<String> links = new Vector<String>();
+    List<String> links = new ArrayList<String>();
     for (String key : selectedUrls)
     {
-      links.add(urls.get(key).toString());
+      links.add(urls.get(key).toStringWithTarget());
     }
     return links;
   }
@@ -205,9 +227,9 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
           {
             selectedUrls.add(link.getId());
           }
-          if (link.getIsDefault())
+          if (link.getIsPrimary())
           {
-            setDefaultUrl(link.getId());
+            setPrimaryUrl(link.getId());
           }
         }
       }
@@ -215,26 +237,32 @@ public class IdentifiersUrlProvider extends UrlProviderImpl
   }
 
   @Override
-  public String getDefaultUrl(String seqid)
+  public String getPrimaryUrl(String seqid)
   {
-    return super.getDefaultUrl(seqid, urls);
+    return super.getPrimaryUrl(seqid, urls);
   }
 
   @Override
-  public String getDefaultUrlId()
+  public String getPrimaryUrlId()
   {
-    return defaultUrl;
+    return primaryUrl;
   }
 
   @Override
-  public String getDefaultTarget(String seqid)
+  public String getPrimaryTarget(String seqid)
   {
     return null;
   }
 
   @Override
-  public String chooseDefaultUrl()
+  public String choosePrimaryUrl()
   {
     return null;
   }
+
+  @Override
+  public boolean contains(String id)
+  {
+    return (urls.containsKey(id));
+  }
 }