X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fseqfetcher%2FDbSourceProxy.java;h=9fa904a0b85e7284c2e00574b985a8df6da54cec;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=9c5356a50ac794618be1bef989b1dea6d1b19ea6;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/ws/seqfetcher/DbSourceProxy.java b/src/jalview/ws/seqfetcher/DbSourceProxy.java
index 9c5356a..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;
 
@@ -120,4 +124,14 @@ 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);
 }