X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fseqfetcher%2FDbSourceProxy.java;h=9fa904a0b85e7284c2e00574b985a8df6da54cec;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=67097efe11ec68c0ba933ffd01629898cb42f988;hpb=56d8f0b05df600ea54388d58cf505d911beb630a;p=jalview.git

diff --git a/src/jalview/ws/seqfetcher/DbSourceProxy.java b/src/jalview/ws/seqfetcher/DbSourceProxy.java
index 67097ef..9fa904a 100644
--- a/src/jalview/ws/seqfetcher/DbSourceProxy.java
+++ b/src/jalview/ws/seqfetcher/DbSourceProxy.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview.
  * 
@@ -30,8 +30,7 @@ import com.stevesoft.pat.Regex;
  * add/define mechanism for retrieval of Trees and distance matrices from a
  * database (unify with io)
  * 
- * @author JimP
- * 
+ * @author JimP TODO: promote to API
  */
 public interface DbSourceProxy
 {
@@ -67,7 +66,9 @@ 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
    */
@@ -102,9 +103,12 @@ public interface DbSourceProxy
    * into an alignment
    * 
    * @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
+   *           - propagated from underlying transport to database (note -
+   *           exceptions are not raised if query not found in database)
+   * 
    */
   public AlignmentI getSequenceRecords(String queries) throws Exception;
 
@@ -121,10 +125,12 @@ public interface DbSourceProxy
    */
   public StringBuffer getRawRecords();
 
-  
   /**
    * Find out more info about the source.
-   * @param dbsourceproperty - one of the database reference source properties in jalview.datamodel.DBRefSource
+   * 
+   * @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);