JAL-1064 sequence database sources are stored and retrieved as lists associated with...

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index a919b9e..1886172 100644 (file)
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -31,8 +31,10 @@ import jalview.gui.Desktop;
 import jalview.gui.IProgressIndicator;\r
 import jalview.gui.OOMWarning;\r
 import jalview.ws.dbsources.das.api.jalviewSourceI;\r
+import jalview.ws.seqfetcher.DbSourceProxy;\r
 \r
 import java.lang.reflect.Array;\r
+import java.util.ArrayList;\r
 import java.util.Enumeration;\r
 import java.util.Hashtable;\r
 import java.util.List;\r
@@ -69,7 +71,7 @@ public class DBRefFetcher implements Runnable
   // The key will be the seq name or accession id of the seq\r
   Hashtable seqRefs;\r
 \r
-  String[] dbSources;\r
+  DbSourceProxy[] dbSources;\r
 \r
   SequenceFetcher sfetcher;\r
 \r
@@ -104,7 +106,7 @@ public class DBRefFetcher implements Runnable
    * @param sources\r
    *          array of database source strings to query references from\r
    */\r
-  public DBRefFetcher(SequenceI[] seqs, AlignFrame af, String[] sources)\r
+  public DBRefFetcher(SequenceI[] seqs, AlignFrame af, DbSourceProxy[] sources)\r
   {\r
     this.af = af;\r
     alseqs = new SequenceI[seqs.length];\r
@@ -125,25 +127,19 @@ public class DBRefFetcher implements Runnable
       // af.featureSettings_actionPerformed(null);\r
       String[] defdb = null, otherdb = sfetcher\r
               .getDbInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);\r
-      Vector selsources = new Vector(), dasselsrc = (af.featureSettings != null) ? af.featureSettings\r
+      List<DbSourceProxy> selsources = new ArrayList<DbSourceProxy>();\r
+      Vector dasselsrc = (af.featureSettings != null) ? af.featureSettings\r
               .getSelectedSources() : new jalview.gui.DasSourceBrowser()\r
               .getSelectedSources();\r
-      Enumeration en = dasselsrc.elements();\r
+      Enumeration<jalviewSourceI> en = dasselsrc.elements();\r
       while (en.hasMoreElements())\r
       {\r
-        jalviewSourceI src = (jalviewSourceI) en.nextElement();\r
-        selsources.addElement(src.getTitle());\r
-      }\r
-      int osel = 0;\r
-      for (int o = 0; otherdb != null && o < otherdb.length; o++)\r
-      {\r
-        if (!selsources.contains(otherdb[o]))\r
+        jalviewSourceI src = en.nextElement();\r
+        List<DbSourceProxy> sp=src.getSequenceSourceProxies();\r
+        selsources.addAll(sp);\r
+        if (sp.size()>1)\r
         {\r
-          otherdb[o] = null;\r
-        }\r
-        else\r
-        {\r
-          osel++;\r
+          Cache.log.debug("Added many Db Sources for :"+src.getTitle());\r
         }\r
       }\r
       // select appropriate databases based on alignFrame context.\r
@@ -155,17 +151,14 @@ public class DBRefFetcher implements Runnable
       {\r
         defdb = DBRefSource.PROTEINDBS;\r
       }\r
-      // append the selected sequence sources to the default dbs\r
-      dbSources = new String[defdb.length + osel];\r
-      System.arraycopy(defdb, 0, dbSources, 0, defdb.length);\r
-      for (int o = 0, op = defdb.length; otherdb != null\r
-              && o < otherdb.length; o++)\r
-      {\r
-        if (otherdb[o] != null)\r
-        {\r
-          dbSources[op++] = otherdb[o];\r
-        }\r
+      List<DbSourceProxy> srces=new ArrayList<DbSourceProxy>();\r
+      for (String ddb:defdb) {\r
+        srces.addAll(sfetcher.getSourceProxy(ddb));\r
       }\r
+      \r
+      // append the selected sequence sources to the default dbs\r
+      srces.addAll(selsources);\r
+      dbSources = srces.toArray(new DbSourceProxy[0]);\r
     }\r
     else\r
     {\r
@@ -183,15 +176,14 @@ public class DBRefFetcher implements Runnable
   {\r
     if (dbSources == null)\r
     {\r
-      dbSources = new String[]\r
-      {};\r
+      dbSources = new DbSourceProxy[0];\r
     }\r
     // append additional sources\r
-    String[] otherdb = sfetcher\r
-            .getDbInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);\r
+    DbSourceProxy[] otherdb=sfetcher\r
+            .getDbSourceProxyInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);\r
     if (otherdb != null && otherdb.length > 0)\r
     {\r
-      String[] newsrc = new String[dbSources.length + otherdb.length];\r
+      DbSourceProxy[] newsrc = new DbSourceProxy[dbSources.length + otherdb.length];\r
       System.arraycopy(dbSources, 0, newsrc, 0, dbSources.length);\r
       System.arraycopy(otherdb, 0, newsrc, dbSources.length, otherdb.length);\r
       dbSources = newsrc;\r
@@ -295,16 +287,8 @@ public class DBRefFetcher implements Runnable
     while (sdataset.size() > 0 && db < dbSources.length)\r
     {\r
       int maxqlen = 1; // default number of queries made to at one time\r
-      System.err.println("Verifying against " + dbSources[db]);\r
+      System.err.println("Verifying against " + dbSources[db].getDbName());\r
       boolean dn = false;\r
-      List<jalview.ws.seqfetcher.DbSourceProxy> srcs = sfetcher\r
-              .getSourceProxy(dbSources[db]);\r
-      if (srcs == null)\r
-      {\r
-        System.err.println("No proxy for " + dbSources[db]);\r
-        db++;\r
-        continue;\r
-      }\r
 \r
       // iterate through db for each remaining un-verified sequence\r
       SequenceI[] currSeqs = new SequenceI[sdataset.size()];\r
@@ -315,7 +299,7 @@ public class DBRefFetcher implements Runnable
 \r
       int seqIndex = 0;\r
 \r
-      for (jalview.ws.seqfetcher.DbSourceProxy dbsource : srcs)\r
+      jalview.ws.seqfetcher.DbSourceProxy dbsource = dbSources[db];\r
       {\r
         // for moment, we dumbly iterate over all retrieval sources for a particular database\r
         // TODO: introduce multithread multisource queries and logic to remove a query from other sources if any source for a database returns a record\r
@@ -373,7 +357,7 @@ public class DBRefFetcher implements Runnable
             }\r
             if (retrieved != null)\r
             {\r
-              transferReferences(sdataset, dbSources[db], retrieved);\r
+              transferReferences(sdataset, dbsource.getDbSource(), retrieved);\r
             }\r
           }\r
           else\r
@@ -384,7 +368,7 @@ public class DBRefFetcher implements Runnable
               SequenceI sequence = dataset[seqIndex];\r
               DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(\r
                       sequence.getDBRef(), new String[]\r
-                      { dbSources[db] }); // jalview.datamodel.DBRefSource.UNIPROT\r
+                      { dbsource.getDbSource() }); // jalview.datamodel.DBRefSource.UNIPROT\r
               // });\r
               // check for existing dbrefs to use\r
               if (uprefs != null && uprefs.length > 0)\r

diff --git a/src/jalview/ws/seqfetcher/ASequenceFetcher.java b/src/jalview/ws/seqfetcher/ASequenceFetcher.java
index c63e148..d4501d8 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
+    Collection<DbSourceProxy> dblist = FETCHABLEDBS.get(db).values();\r
+    if (dblist.size()>1)\r
+    {\r
+      DbSourceProxy[] l=dblist.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);\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