From: jprocter <Jim Procter>
Date: Thu, 31 Jul 2008 10:09:55 +0000 (+0000)
Subject: added specific retrieval arguments to SequneceFetcher's main method.
X-Git-Tag: Release_2_4~77
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b7885c2f1d36f515354ede5793f5b3cddbc9db04;p=jalview.git

added specific retrieval arguments to SequneceFetcher's main method.
---

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index 208eb88..da2dab6 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -33,15 +33,46 @@ public class SequenceFetcher extends ASequenceFetcher
     addDBRefSourceImpl(jalview.ws.dbsources.Pdb.class);
     addDBRefSourceImpl(jalview.ws.dbsources.Pfam.class);
   };
-
+  /**
+   * simple run method to test dbsources.
+   * @param argv
+   */
   public static void main(String[] argv)
   {
     AlignmentI ds = null;
     Vector noProds = new Vector();
+    String usage = "SequenceFetcher.main [<DBNAME> <ACCNO>]\n"
+      +"With no arguments, all DbSources will be queried with their test Accession number.\n"
+      +"If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.";
     if (argv != null && argv.length > 0)
     {
+      DbSourceProxy sp = new SequenceFetcher().getSourceProxy(argv[0]);
+      if (sp!=null)
+      {
+        AlignmentI al = null;
+        try
+        {
+          al = sp.getSequenceRecords(argv[1]);
+        } catch (Exception e)
+        {
+          e.printStackTrace();
+          System.err.println("Error when retrieving "+argv[1]+" from "+argv[0]+"\nUsage: "+usage);
+        }
+        SequenceI[] prod = al.getSequencesArray();
+        if (al!=null)
+        {
+          for (int p = 0; p < prod.length; p++)
+          {
+            System.out.println("Prod " + p + ": "
+                    + prod[p].getDisplayId(true) + " : "+prod[p].getDescription());
+          }
+        }
+        return;
+      } else {
+        System.err.println("Can't resolve "+argv[0]+" as a database name. Allowed values are :\n"+new SequenceFetcher().getSupportedDb());
+      }
       System.out
-              .println("Ignoring arguments. Future Usage = dbname:query1;query2;...");
+              .println(usage);
     }
     ASequenceFetcher sfetcher = new SequenceFetcher();
     String[] dbSources = sfetcher.getSupportedDb();