X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2Fdas%2FDasSequenceSourceListener.java;h=13314bb7b800cabe7bf191b68e77aa95d72cbf44;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=fa961f03c8798ef66c374cfd18a4b72dfa54cd6f;hpb=54e003f9b2fff47dbfea6401c3944afdb7bd37b3;p=jalview.git

diff --git a/src/jalview/ws/dbsources/das/DasSequenceSourceListener.java b/src/jalview/ws/dbsources/das/DasSequenceSourceListener.java
index fa961f0..13314bb 100644
--- a/src/jalview/ws/dbsources/das/DasSequenceSourceListener.java
+++ b/src/jalview/ws/dbsources/das/DasSequenceSourceListener.java
@@ -1,3 +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/>.
+ */
 package jalview.ws.dbsources.das;
 
 import jalview.datamodel.AlignmentI;
@@ -11,25 +28,32 @@ import org.biojava.dasobert.eventmodel.SequenceEvent;
 import org.biojava.dasobert.eventmodel.SequenceListener;
 
 /**
- * Listen for sequence fetch events from a dasobert SequenceThread started with a 
- * query string and collect sequences returned from the DAS sequence source. 
+ * Listen for sequence fetch events from a dasobert SequenceThread started with
+ * a query string and collect sequences returned from the DAS sequence source.
+ * 
  * @author JimP
- *
+ * 
  */
 public class DasSequenceSourceListener implements SequenceListener
 {
-  
+
   String ourAccession = null;
-  DasSequenceSource oursource=null;
+
+  DasSequenceSource oursource = null;
+
   /**
    * 
-   * @param source the DAS Sequence DbProxy object containing database details for this source
-   * @param query the query string sent to the das source that we should be listening for.
+   * @param source
+   *          the DAS Sequence DbProxy object containing database details for
+   *          this source
+   * @param query
+   *          the query string sent to the das source that we should be
+   *          listening for.
    */
   public DasSequenceSourceListener(DasSequenceSource source, String query)
   {
-    oursource=source;
-    ourAccession=query;
+    oursource = source;
+    ourAccession = query;
   }
 
   public void clearSelection()
@@ -37,32 +61,38 @@ public class DasSequenceSourceListener implements SequenceListener
     // TODO Auto-generated method stub
 
   }
+
   java.util.Vector seqs = null;
+
   public void newSequence(SequenceEvent e)
   {
     if (!e.getAccessionCode().equals(ourAccession))
     {
-      System.err.println("Warning - received sequence event for strange accession code ("
-              +e.getAccessionCode()+") - we expected "+ourAccession);
-      
+      System.err
+              .println("Warning - received sequence event for strange accession code ("
+                      + e.getAccessionCode()
+                      + ") - we expected "
+                      + ourAccession);
+
       return;
     }
-    if (seqs==null)
+    if (seqs == null)
     {
-      if (e.getSequence().length()==0)
+      if (e.getSequence().length() == 0)
       {
         System.err.println("Empty sequence returned for accession code ("
-                +e.getAccessionCode()+") from "+oursource.getDbName());
-        called=true;
-        noSequences=true;
+                + e.getAccessionCode() + ") from " + oursource.getDbName());
+        called = true;
+        noSequences = true;
         return;
       }
       seqs = new java.util.Vector();
     }
     Sequence sq = new Sequence(e.getAccessionCode(), e.getSequence());
-    sq.addDBRef(new DBRefEntry(oursource.getDbSource(), oursource.getDbVersion()+":"+e.getVersion(), e.getAccessionCode()));
+    sq.addDBRef(new DBRefEntry(oursource.getDbSource(), oursource
+            .getDbVersion() + ":" + e.getVersion(), e.getAccessionCode()));
     seqs.addElement(sq);
-    called=true;
+    called = true;
   }
 
   public void selectedSeqPosition(int position)
@@ -88,19 +118,25 @@ public class DasSequenceSourceListener implements SequenceListener
     // TODO Auto-generated method stub
 
   }
-  boolean noSequences=false;
+
+  boolean noSequences = false;
+
   public void noObjectFound(String accessionCode)
   {
     if (accessionCode.equals(ourAccession))
     {
-      noSequences=true;
+      noSequences = true;
       called = true;
     }
   }
-  public boolean hasNoSequences() {
+
+  public boolean hasNoSequences()
+  {
     return noSequences;
   }
-  boolean called=false;
+
+  boolean called = false;
+
   public boolean isNotCalled()
   {
     return !called;
@@ -108,10 +144,10 @@ public class DasSequenceSourceListener implements SequenceListener
 
   public AlignmentI getSequences()
   {
-    if (noSequences || seqs!=null && seqs.size()==0)
+    if (noSequences || seqs != null && seqs.size() == 0)
       return null;
     SequenceI[] sqs = new SequenceI[seqs.size()];
-    for (int i=0,iSize=seqs.size(); i<iSize;i++)
+    for (int i = 0, iSize = seqs.size(); i < iSize; i++)
     {
       sqs[i] = (SequenceI) seqs.elementAt(i);
     }
@@ -120,11 +156,9 @@ public class DasSequenceSourceListener implements SequenceListener
     {
       java.util.Vector src = new java.util.Vector();
       src.addElement(oursource.getSource());
-      new jalview.ws.DasSequenceFeatureFetcher(sqs, 
-              null,
-              src, false, false);
+      new jalview.ws.DasSequenceFeatureFetcher(sqs, null, src, false, false);
     }
-    
+
     return al;
   }