X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=14b69972a1276bd20bff2ac2425acb3c1103549f;hb=c330d4dad8fc78c8ec1d5c35e5fc137836c9776d;hp=b1d3f3c01d4b8793588efadda07a65cffa8f1bf3;hpb=92f7b5ee3bbdb5456d498f1c2780d90420491342;p=jalview.git

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index b1d3f3c..14b6997 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -1,20 +1,20 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- * 
- * This file is part of Jalview.
- * 
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
- * Jalview is distributed in the hope that it will be useful, but 
- * WITHOUT ANY WARRANTY; without even the implied warranty 
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
- * PURPOSE.  See the GNU General Public License for more details.
- * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
- */
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ */
 package jalview.ws;
 
 import jalview.datamodel.Alignment;
@@ -22,7 +22,6 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.SequenceI;
 import jalview.ws.dbsources.das.api.jalviewSourceI;
-import jalview.ws.dbsources.das.datamodel.DasSequenceSource;
 import jalview.ws.seqfetcher.ASequenceFetcher;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
@@ -48,6 +47,10 @@ 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 +63,9 @@ public class SequenceFetcher extends ASequenceFetcher
     // PFAM
     addDBRefSourceImpl(jalview.ws.dbsources.RfamFull.class);
     addDBRefSourceImpl(jalview.ws.dbsources.RfamSeed.class);
-    registerDasSequenceSources();
+    if (addDas) {
+      registerDasSequenceSources();
+    }
   }
 
   /**
@@ -73,15 +78,18 @@ public class SequenceFetcher extends ASequenceFetcher
     ArrayList<String> dassrc = new ArrayList<String>(), nondas = new ArrayList<String>();
     for (int i = 0; i < srcs.length; i++)
     {
-      boolean das = false,skip=false;
+      boolean das = false, skip = false;
       String nm;
       for (DbSourceProxy dbs : getSourceProxy(srcs[i]))
       {
-        // Skip the alignment databases for the moment - they're not useful for verifying a single sequence against its reference source
+        // Skip the alignment databases for the moment - they're not useful for
+        // verifying a single sequence against its reference source
         if (dbs.isA(DBRefSource.ALIGNMENTDB))
         {
-          skip=true;
-        } else {
+          skip = true;
+        }
+        else
+        {
           nm = dbs.getDbName();
           if (getSourceProxy(srcs[i]) instanceof jalview.ws.dbsources.das.datamodel.DasSequenceSource)
           {
@@ -208,12 +216,22 @@ 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 +241,11 @@ 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 +270,7 @@ 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++)
     {