X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fseqfetcher%2FDbSourceProxyImpl.java;h=6c612820839b26fb15bef44e93ee633812be05cf;hb=2763845dada91cdfe266200cf852146c70392ad7;hp=21272bebfad1cca641625286cbd7f2a1ecb7557a;hpb=6b406c397d41a0f2d84b75f13e7ab478932bf57d;p=jalview.git

diff --git a/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java b/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
index 21272be..6c61282 100644
--- a/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
+++ b/src/jalview/ws/seqfetcher/DbSourceProxyImpl.java
@@ -1,3 +1,21 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
+ * Copyright (C) 2009 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.seqfetcher;
 
 import jalview.datamodel.Alignment;
@@ -11,7 +29,7 @@ import java.util.Hashtable;
  * common methods for implementations of the DbSourceProxy interface.
  * 
  * @author JimP
- *
+ * 
  */
 public abstract class DbSourceProxyImpl implements DbSourceProxy
 {
@@ -19,14 +37,23 @@ public abstract class DbSourceProxyImpl implements DbSourceProxy
   {
     // default constructor - do nothing probably.
   }
-  private Hashtable props=null;
-  /* (non-Javadoc)
+
+  private Hashtable props = null;
+
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#getDbSourceProperties()
    */
   public Hashtable getDbSourceProperties()
   {
+    if (props==null)
+    {
+      props = new Hashtable();
+    }
     return props;
   }
+
   protected void addDbSourceProperty(Object propname)
   {
     addDbSourceProperty(propname, propname);
@@ -34,14 +61,17 @@ public abstract class DbSourceProxyImpl implements DbSourceProxy
 
   protected void addDbSourceProperty(Object propname, Object propvalue)
   {
-    if (props==null)
+    if (props == null)
     {
       props = new Hashtable();
     }
     props.put(propname, propvalue);
   }
-  boolean queryInProgress=false;
+
+  boolean queryInProgress = false;
+
   protected StringBuffer results = null;
+
   /*
    * (non-Javadoc)
    * 
@@ -52,45 +82,51 @@ public abstract class DbSourceProxyImpl implements DbSourceProxy
     return results;
   }
 
-  /* (non-Javadoc)
+  /*
+   * (non-Javadoc)
+   * 
    * @see jalview.ws.DbSourceProxy#queryInProgress()
    */
   public boolean queryInProgress()
   {
     return queryInProgress;
   }
+
   /**
    * call to set the queryInProgress flag
-   *
+   * 
    */
   protected void startQuery()
   {
-    queryInProgress=true;
+    queryInProgress = true;
   }
+
   /**
    * call to clear the queryInProgress flag
-   *
+   * 
    */
   protected void stopQuery()
   {
-    queryInProgress=false;
+    queryInProgress = false;
   }
 
   /**
    * create an alignment from raw text file...
+   * 
    * @param result
    * @return null or a valid alignment
    * @throws Exception
    */
-  protected Alignment parseResult(String result) throws Exception {
+  protected Alignment parseResult(String result) throws Exception
+  {
     Alignment sequences = null;
     String format = new IdentifyFile().Identify(result, "Paste");
     if (FormatAdapter.isValidFormat(format))
     {
       sequences = new FormatAdapter().readFile(result.toString(), "Paste",
-            format);
+              format);
     }
     return sequences;
   }
-  
+
 }