X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FSequenceFetcher.java;h=6a612a0602665d356b50b18cf8c150dd2905bf4a;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=ce3e95214da0c9cdb4b7261605be02f2cd1edd43;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git

diff --git a/src/jalview/ws/SequenceFetcher.java b/src/jalview/ws/SequenceFetcher.java
index ce3e952..6a612a0 100644
--- a/src/jalview/ws/SequenceFetcher.java
+++ b/src/jalview/ws/SequenceFetcher.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * 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.
+ * 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ws;
@@ -50,6 +52,7 @@ public class SequenceFetcher extends ASequenceFetcher
   {
     this(true);
   }
+
   public SequenceFetcher(boolean addDas)
   {
     addDBRefSourceImpl(jalview.ws.dbsources.EmblSource.class);
@@ -58,13 +61,12 @@ public class SequenceFetcher extends ASequenceFetcher
     addDBRefSourceImpl(jalview.ws.dbsources.UnprotName.class);
     addDBRefSourceImpl(jalview.ws.dbsources.Pdb.class);
     addDBRefSourceImpl(jalview.ws.dbsources.PfamFull.class);
-    addDBRefSourceImpl(jalview.ws.dbsources.PfamSeed.class); // ensures Seed
-    // alignment is
-    // 'default' for
-    // PFAM
+    addDBRefSourceImpl(jalview.ws.dbsources.PfamSeed.class);
+    // ensures Seed alignment is 'default' for PFAM
     addDBRefSourceImpl(jalview.ws.dbsources.RfamFull.class);
     addDBRefSourceImpl(jalview.ws.dbsources.RfamSeed.class);
-    if (addDas) {
+    if (addDas)
+    {
       registerDasSequenceSources();
     }
   }
@@ -165,13 +167,11 @@ public class SequenceFetcher extends ASequenceFetcher
           {
             nm = nm.substring(4);
           }
-          dassrc.add(new String[]
-          { srcs[i], nm.toUpperCase() });
+          dassrc.add(new String[] { srcs[i], nm.toUpperCase() });
         }
         else
         {
-          nondas.add(new String[]
-          { srcs[i], nm.toUpperCase() });
+          nondas.add(new String[] { srcs[i], nm.toUpperCase() });
         }
       }
     }
@@ -222,13 +222,14 @@ public class SequenceFetcher extends ASequenceFetcher
             + "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"))
+    boolean withDas = true;
+    if (argv != null && argv.length > 0
+            && argv[0].toLowerCase().startsWith("-nodas"))
     {
-      withDas=false;
-      String targs[] = new String[argv.length-1];
+      withDas = false;
+      String targs[] = new String[argv.length - 1];
       System.arraycopy(argv, 1, targs, 0, targs.length);
-      argv=targs;
+      argv = targs;
     }
     if (argv != null && argv.length > 0)
     {
@@ -242,11 +243,13 @@ public class SequenceFetcher extends ASequenceFetcher
           AlignmentI al = null;
           try
           {
-            al = sp.getSequenceRecords(argv.length>1 ? argv[1] : sp.getTestQuery());
+            al = sp.getSequenceRecords(argv.length > 1 ? argv[1] : sp
+                    .getTestQuery());
           } catch (Exception e)
           {
             e.printStackTrace();
-            System.err.println("Error when retrieving " + (argv.length>1 ? argv[1] : sp.getTestQuery())
+            System.err.println("Error when retrieving "
+                    + (argv.length > 1 ? argv[1] : sp.getTestQuery())
                     + " from " + argv[0] + "\nUsage: " + usage);
           }
           SequenceI[] prod = al.getSequencesArray();
@@ -278,7 +281,9 @@ public class SequenceFetcher extends ASequenceFetcher
       String db = dbSources[dbsource];
       // skip me
       if (db.equals(DBRefSource.PDB))
+      {
         continue;
+      }
       for (DbSourceProxy sp : sfetcher.getSourceProxy(db))
       {
         System.out.println("Source: " + sp.getDbName() + " (" + db
@@ -324,9 +329,8 @@ public class SequenceFetcher extends ASequenceFetcher
             }
             else
             {
-              noProds.addElement((dna ? new Object[]
-              { al, al } : new Object[]
-              { al }));
+              noProds.addElement((dna ? new Object[] { al, al }
+                      : new Object[] { al }));
             }
 
           }
@@ -341,9 +345,13 @@ public class SequenceFetcher extends ASequenceFetcher
           System.out.println("ERROR:No alignment retrieved.");
           StringBuffer raw = sp.getRawRecords();
           if (raw != null)
+          {
             System.out.println(raw.toString());
+          }
           else
+          {
             System.out.println("ERROR:No Raw results.");
+          }
         }
         else
         {
@@ -358,8 +366,7 @@ public class SequenceFetcher extends ASequenceFetcher
             }
             if (ds == null)
             {
-              ds = new Alignment(new SequenceI[]
-              { sq });
+              ds = new Alignment(new SequenceI[] { sq });
 
             }
             else