X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FDasSequenceSource.java;h=9283c66d18f2e4d2196b5c801639c654727ebe47;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=accb0b9bf17450c2ff50d79e7638acafa8676c5b;hpb=60f2d6c034560415fd0139c8bc7df0c19cae1186;p=jalview.git

diff --git a/src/jalview/ws/dbsources/DasSequenceSource.java b/src/jalview/ws/dbsources/DasSequenceSource.java
index accb0b9..9283c66 100644
--- a/src/jalview/ws/dbsources/DasSequenceSource.java
+++ b/src/jalview/ws/dbsources/DasSequenceSource.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
 package jalview.ws.dbsources;
 
 import java.util.Hashtable;
@@ -17,38 +35,52 @@ import jalview.ws.seqfetcher.*;
 import jalview.datamodel.AlignmentI;
 
 /**
- * an instance of this class is created for each unique DAS Sequence source (ie one capable of handling the 'sequence' for a particular MapMaster)
- *  
+ * an instance of this class is created for each unique DAS Sequence source (ie
+ * one capable of handling the 'sequence' for a particular MapMaster)
+ * 
  * @author JimP
- *
+ * 
  */
 public class DasSequenceSource extends DbSourceProxyImpl implements
         DbSourceProxy
 {
-  protected Das1Source source=null;
-  protected String dbname="DASCS";
-  protected String dbrefname="das:source";
+  protected Das1Source source = null;
+
+  protected String dbname = "DASCS";
+
+  protected String dbrefname = "das:source";
+
   protected DasCoordinateSystem coordsys = null;
+
   /**
    * create a new DbSource proxy for a DAS 1 source
-   * @param dbnbame Human Readable Name to use when fetching from this source
-   * @param dbrefname DbRefName for DbRefs attached to sequences retrieved from this source
-   * @param source Das1Source
-   * @param coordsys specific coordinate system to use for this source
-   * @throws Exception if source is not capable of the 'sequence' command
+   * 
+   * @param dbnbame
+   *                Human Readable Name to use when fetching from this source
+   * @param dbrefname
+   *                DbRefName for DbRefs attached to sequences retrieved from
+   *                this source
+   * @param source
+   *                Das1Source
+   * @param coordsys
+   *                specific coordinate system to use for this source
+   * @throws Exception
+   *                 if source is not capable of the 'sequence' command
    */
-  public DasSequenceSource(String dbname, String dbrefname, Das1Source source,
-            DasCoordinateSystem coordsys) throws Exception
+  public DasSequenceSource(String dbname, String dbrefname,
+          Das1Source source, DasCoordinateSystem coordsys) throws Exception
   {
     if (!source.hasCapability("sequence"))
     {
-      throw new Exception("Source "+source.getNickname()+" does not support the sequence command.");
+      throw new Exception("Source " + source.getNickname()
+              + " does not support the sequence command.");
     }
     this.source = source;
     this.dbname = dbname;
-    this.dbrefname=dbrefname;
+    this.dbrefname = dbrefname;
     this.coordsys = coordsys;
   }
+
   public String getAccessionSeparator()
   {
     // cope with single sequences only
@@ -57,14 +89,14 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
 
   public Regex getAccessionValidator()
   {
-    /** ? **/
+    /** ? * */
     return Regex.perlCode("\\S+");
   }
 
   public String getDbName()
   {
     // TODO: map to
-     return dbname+" (DAS)";
+    return dbname + " (DAS)";
   }
 
   public String getDbSource()
@@ -79,20 +111,37 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
 
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
-    SequenceThread seqfetcher = new org.biojava.dasobert.das.SequenceThread(queries, source);
-    DasSequenceSourceListener ourlistener = new DasSequenceSourceListener(this, queries);
+    SequenceThread seqfetcher = new org.biojava.dasobert.das.SequenceThread(
+            queries, source);
+    DasSequenceSourceListener ourlistener = new DasSequenceSourceListener(
+            this, queries);
     seqfetcher.addSequenceListener(ourlistener);
     seqfetcher.start();
-    try { Thread.sleep(5); } catch (Exception e) {};
+    try
+    {
+      Thread.sleep(5);
+    } catch (Exception e)
+    {
+    }
+    ;
     while (ourlistener.isNotCalled() && seqfetcher.isAlive())
     {
-      try { Thread.sleep(5); } catch (Exception e) { };
+      try
+      {
+        Thread.sleep(5);
+      } catch (Exception e)
+      {
+      }
+      ;
     }
     if (ourlistener.isNotCalled() || ourlistener.hasNoSequences())
     {
-      System.err.println("Sequence Query to "+source.getNickname()+" with '"+queries+"' returned no sequences.");
+      System.err.println("Sequence Query to " + source.getNickname()
+              + " with '" + queries + "' returned no sequences.");
       return null;
-    } else {
+    }
+    else
+    {
       return ourlistener.getSequences();
     }
   }
@@ -101,13 +150,15 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
   {
     return coordsys.getTestCode();
   }
+
   public boolean isValidReference(String accession)
   {
     // TODO try to validate an accession against source
     // We don't really know how to do this without querying source
-    
+
     return true;
   }
+
   /**
    * @return the source
    */
@@ -115,6 +166,7 @@ public class DasSequenceSource extends DbSourceProxyImpl implements
   {
     return source;
   }
+
   /**
    * @return the coordsys
    */