From a049d57f4693f1b60ab02fdf2c9403a2e9c59444 Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Thu, 4 Oct 2012 16:12:25 +0100
Subject: [PATCH] JAL-636 tweak main() based test to allow DAS sources to be
 excluded from basic SequenceFetcher testing

---
 src/jalview/ws/SequenceFetcher.java |   30 +++++++++++++++++++++++-------
 1 file changed, 23 insertions(+), 7 deletions(-)

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index b1d3f3c..111c510 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -48,6 +48,10 @@ public class SequenceFetcher extends ASequenceFetcher
    */
   public SequenceFetcher()
   {
+    this(true);
+  }
+  public SequenceFetcher(boolean addDas)
+  {
     addDBRefSourceImpl(jalview.ws.dbsources.EmblSource.class);
     addDBRefSourceImpl(jalview.ws.dbsources.EmblCdsSouce.class);
     addDBRefSourceImpl(jalview.ws.dbsources.Uniprot.class);
@@ -60,7 +64,9 @@ public class SequenceFetcher extends ASequenceFetcher
     // PFAM
     addDBRefSourceImpl(jalview.ws.dbsources.RfamFull.class);
     addDBRefSourceImpl(jalview.ws.dbsources.RfamSeed.class);
-    registerDasSequenceSources();
+    if (addDas) {
+      registerDasSequenceSources();
+    }
   }
 
   /**
@@ -208,12 +214,22 @@ public class SequenceFetcher extends ASequenceFetcher
   {
     AlignmentI ds = null;
     Vector noProds = new Vector();
-    String usage = "SequenceFetcher.main [<DBNAME> <ACCNO>]\n"
+    String usage = "SequenceFetcher.main [-nodas] [<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.";
+            + "With one argument, the argument will be resolved to one or more db sources and each will be queried with their test accession only.\n"
+            + "If given two arguments, SequenceFetcher will try to find the DbFetcher corresponding to <DBNAME> and retrieve <ACCNO> from it.\n"
+            + "The -nodas option will exclude DAS sources from the database fetchers Jalview will try to use.";
+    boolean withDas=true;
+    if (argv!=null && argv.length>0 && argv[0].toLowerCase().startsWith("-nodas"))
+    {
+      withDas=false;
+      String targs[] = new String[argv.length-1];
+      System.arraycopy(argv, 1, targs, 0, targs.length);
+      argv=targs;
+    }
     if (argv != null && argv.length > 0)
     {
-      List<DbSourceProxy> sps = new SequenceFetcher()
+      List<DbSourceProxy> sps = new SequenceFetcher(withDas)
               .getSourceProxy(argv[0]);
 
       if (sps != null)
@@ -223,11 +239,11 @@ public class SequenceFetcher extends ASequenceFetcher
           AlignmentI al = null;
           try
           {
-            al = sp.getSequenceRecords(argv[1]);
+            al = sp.getSequenceRecords(argv.length>1 ? argv[1] : sp.getTestQuery());
           } catch (Exception e)
           {
             e.printStackTrace();
-            System.err.println("Error when retrieving " + argv[1]
+            System.err.println("Error when retrieving " + (argv.length>1 ? argv[1] : sp.getTestQuery())
                     + " from " + argv[0] + "\nUsage: " + usage);
           }
           SequenceI[] prod = al.getSequencesArray();
@@ -252,7 +268,7 @@ public class SequenceFetcher extends ASequenceFetcher
       System.out.println(usage);
       return;
     }
-    ASequenceFetcher sfetcher = new SequenceFetcher();
+    ASequenceFetcher sfetcher = new SequenceFetcher(withDas);
     String[] dbSources = sfetcher.getSupportedDb();
     for (int dbsource = 0; dbsource < dbSources.length; dbsource++)
     {
-- 
1.7.10.2