X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fseqfetcher%2FDbSourceProxy.java;h=895c03e2df932dbf9f462f42f46f890d6aa80ae9;hb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;hp=5459ae9edea683788dc8d69062eda41fd89606b5;hpb=6b406c397d41a0f2d84b75f13e7ab478932bf57d;p=jalview.git

diff --git a/src/jalview/ws/seqfetcher/DbSourceProxy.java b/src/jalview/ws/seqfetcher/DbSourceProxy.java
index 5459ae9..895c03e 100644
--- a/src/jalview/ws/seqfetcher/DbSourceProxy.java
+++ b/src/jalview/ws/seqfetcher/DbSourceProxy.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.AlignmentI;
@@ -5,12 +23,16 @@ import jalview.datamodel.AlignmentI;
 import java.util.Hashtable;
 
 import com.stevesoft.pat.Regex;
+
 /**
- * generic Reference Retrieval interface for a particular database source/version as cited in DBRefEntry.
- * TODO: add/define property to describe max number of queries that this source can cope with at once.
- * TODO: add/define mechanism for retrieval of Trees and distance matrices from a database (unify with io)
+ * generic Reference Retrieval interface for a particular database
+ * source/version as cited in DBRefEntry. TODO: add/define property to describe
+ * max number of queries that this source can cope with at once. TODO:
+ * add/define mechanism for retrieval of Trees and distance matrices from a
+ * database (unify with io)
+ * 
  * @author JimP
- *
+ * 
  */
 public interface DbSourceProxy
 {
@@ -19,55 +41,83 @@ public interface DbSourceProxy
    * @return source string constant used for this DB source
    */
   public String getDbSource();
+
+  /**
+   * Short meaningful name for this data source for display in menus or
+   * selection boxes.
+   * 
+   * @return String
+   */
+  public String getDbName();
+
   /**
    * 
    * @return version string for this database.
    */
   public String getDbVersion();
+
   /**
-   * Separator between individual accession queries for a database that allows multiple IDs
-   * to be fetched in a single query. Null implies that only a single ID can be fetched at a time.
-   * @return string for separating concatenated queries (as individually validated by the accession validator)
+   * Separator between individual accession queries for a database that allows
+   * multiple IDs to be fetched in a single query. Null implies that only a
+   * single ID can be fetched at a time.
+   * 
+   * @return string for separating concatenated queries (as individually
+   *         validated by the accession validator)
    */
   public String getAccessionSeparator();
+
   /**
-   * Regular expression for checking form of query string understood by this source.
+   * Regular expression for checking form of query string understood by this
+   * source.
+   * 
    * @return null or a validation regex
    */
   public Regex getAccessionValidator();
+
   /**
-   * DbSource properties hash - define the capabilities of this source
-   * Property hash methods defined in DbSourceProxyImpl.
-   * See constants in jalview.datamodel.DBRefSource for definition of properties.
-   * @return 
+   * DbSource properties hash - define the capabilities of this source Property
+   * hash methods defined in DbSourceProxyImpl. See constants in
+   * jalview.datamodel.DBRefSource for definition of properties.
+   * 
+   * @return
    */
   public Hashtable getDbSourceProperties();
+
   /**
    * 
-   * @return a test/example query that can be used to validate retrieval and parsing mechanisms
+   * @return a test/example query that can be used to validate retrieval and
+   *         parsing mechanisms
    */
   public String getTestQuery();
+
   /**
    * optionally implemented
+   * 
    * @param accession
    * @return
    */
   public boolean isValidReference(String accession);
+
   /**
-   * make one or more queries to the database
-   * and attempt to parse the response into an alignment
+   * make one or more queries to the database and attempt to parse the response
+   * into an alignment
+   * 
    * @param queries
    * @return null if queries were successful but result was not parsable
-   * @throws Exception TODO
+   * @throws Exception
+   *                 TODO
    */
   public AlignmentI getSequenceRecords(String queries) throws Exception;
+
   /**
    * 
    * @return true if a query is currently being made
    */
   public boolean queryInProgress();
+
   /**
    * get the raw reponse from the last set of queries
+   * 
    * @return one or more string buffers for each individual query
    */
   public StringBuffer getRawRecords();