JAL-975 JAL-974 JAL-976 always adjust height after new annotation added

[jalview.git] / src / jalview / ws / seqfetcher / ASequenceFetcher.java

diff --git a/src/jalview/ws/seqfetcher/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
index c63e148..09a7a95 100644 (file)
--- a/src/jalview/ws/seqfetcher/ASequenceFetcher.java
+++ b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
@@ -23,11 +23,13 @@ import jalview.datamodel.SequenceI;
 import jalview.util.DBRefUtils;\r
 \r
 import java.util.ArrayList;\r
+import java.util.Collection;\r
 import java.util.Enumeration;\r
 import java.util.HashSet;\r
 import java.util.Hashtable;\r
 import java.util.Iterator;\r
 import java.util.List;\r
+import java.util.Map;\r
 import java.util.Stack;\r
 import java.util.Vector;\r
 \r
@@ -37,7 +39,7 @@ public class ASequenceFetcher
   /**\r
    * set of databases we can retrieve entries from\r
    */\r
-  protected Hashtable<String, List<DbSourceProxy>> FETCHABLEDBS;\r
+  protected Hashtable<String, Map<String, DbSourceProxy>> FETCHABLEDBS;\r
 \r
   public ASequenceFetcher()\r
   {\r
@@ -259,7 +261,26 @@ public class ASequenceFetcher
    */\r
   public List<DbSourceProxy> getSourceProxy(String db)\r
   {\r
-    List<DbSourceProxy> dbs = FETCHABLEDBS.get(db);\r
+    List<DbSourceProxy> dbs;\r
+    Map<String,DbSourceProxy> dblist = FETCHABLEDBS.get(db);\r
+    if (dblist==null) {return new ArrayList<DbSourceProxy>();};\r
+    if (dblist.size()>1) {\r
+      DbSourceProxy[] l=dblist.values().toArray(new DbSourceProxy[0]);\r
+      int i=0;\r
+      String[] nm=new String[l.length];\r
+      for (DbSourceProxy s:l)\r
+      {\r
+        nm[i++]=s.getDbName().toLowerCase();\r
+      }\r
+      jalview.util.QuickSort.sort(nm,l);\r
+      dbs = new ArrayList<DbSourceProxy>();\r
+      for (i=l.length-1;i>=0; i--)\r
+      {\r
+        dbs.add(l[i]);\r
+      }\r
+    } else {\r
+      dbs = new ArrayList<DbSourceProxy>(dblist.values());\r
+    }\r
     return dbs;\r
   }\r
 \r
@@ -311,15 +332,15 @@ public class ASequenceFetcher
     {\r
       if (FETCHABLEDBS == null)\r
       {\r
-        FETCHABLEDBS = new Hashtable<String, List<DbSourceProxy>>();\r
+        FETCHABLEDBS = new Hashtable<String, Map<String,DbSourceProxy>>();\r
       }\r
-      List<DbSourceProxy> slist = FETCHABLEDBS.get(proxy.getDbSource());\r
+      Map<String,DbSourceProxy> slist = FETCHABLEDBS.get(proxy.getDbSource());\r
       if (slist == null)\r
       {\r
         FETCHABLEDBS.put(proxy.getDbSource(),\r
-                slist = new ArrayList<DbSourceProxy>());\r
+                slist = new Hashtable<String,DbSourceProxy>());\r
       }\r
-      slist.add(proxy);\r
+      slist.put(proxy.getDbName(),proxy);\r
     }\r
   }\r
 \r
@@ -373,7 +394,7 @@ public class ASequenceFetcher
     while (dbs.hasMoreElements())\r
     {\r
       String dbn = (String) dbs.nextElement();\r
-      for (DbSourceProxy dbp : FETCHABLEDBS.get(dbn))\r
+      for (DbSourceProxy dbp : FETCHABLEDBS.get(dbn).values())\r
       {\r
         if (class1.isAssignableFrom(dbp.getClass()))\r
         {\r
@@ -387,4 +408,20 @@ public class ASequenceFetcher
     }\r
     return sources;\r
   }\r
+  public DbSourceProxy[] getDbSourceProxyInstances(\r
+          Class class1)\r
+  {\r
+    ArrayList<DbSourceProxy> prlist=new ArrayList<DbSourceProxy>();\r
+    for (String fetchable:getSupportedDb())\r
+    for (DbSourceProxy pr:getSourceProxy(fetchable))\r
+    {\r
+      if (class1.isInstance(pr)) {prlist.add(pr);}\r
+    }\r
+    if (prlist.size()==0)\r
+    {\r
+      return null;\r
+    }\r
+    return prlist.toArray(new DbSourceProxy[0]);\r
+  }\r
+\r
 }\r