X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fseqfetcher%2FDbSourceProxy.java;h=3dacb1206abc26e93f758fdaecdd92e961d22f4e;hb=d904a499f1863e96cd699e0c5f7f0f81710e8ad9;hp=895c03e2df932dbf9f462f42f46f890d6aa80ae9;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/ws/seqfetcher/DbSourceProxy.java b/src/jalview/ws/seqfetcher/DbSourceProxy.java
index 895c03e..3dacb12 100644
--- a/src/jalview/ws/seqfetcher/DbSourceProxy.java
+++ b/src/jalview/ws/seqfetcher/DbSourceProxy.java
@@ -1,20 +1,19 @@
 /*
- * 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
+ * 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 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 file is part of Jalview.
  * 
- * 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.
+ * 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.
  * 
- * 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
+ * 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.seqfetcher;
 
@@ -32,7 +31,7 @@ import com.stevesoft.pat.Regex;
  * database (unify with io)
  * 
  * @author JimP
- * 
+ * TODO: promote to API
  */
 public interface DbSourceProxy
 {
@@ -68,7 +67,9 @@ public interface DbSourceProxy
 
   /**
    * Regular expression for checking form of query string understood by this
-   * source.
+   * source. If the Regex includes parenthesis, then the first parenthesis
+   * should yield the same accession string as the one used to annotate the
+   * sequence. This is used to match query strings to returned sequences.
    * 
    * @return null or a validation regex
    */
@@ -101,11 +102,10 @@ public interface DbSourceProxy
   /**
    * make one or more queries to the database and attempt to parse the response
    * into an alignment
-   * 
-   * @param queries
+   * @param queries - one or more queries for database in expected form
    * @return null if queries were successful but result was not parsable
-   * @throws Exception
-   *                 TODO
+   * @throws Exception - propagated from underlying transport to database (note - exceptions are not raised if query not found in database)
+   *           
    */
   public AlignmentI getSequenceRecords(String queries) throws Exception;
 
@@ -121,4 +121,12 @@ public interface DbSourceProxy
    * @return one or more string buffers for each individual query
    */
   public StringBuffer getRawRecords();
+
+  
+  /**
+   * Find out more info about the source.
+   * @param dbsourceproperty - one of the database reference source properties in jalview.datamodel.DBRefSource
+   * @return true if the source has this property
+   */
+  public boolean isA(Object dbsourceproperty);
 }