X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fseqfetcher%2FDbSourceProxy.java;h=a02ffc9a01dc2837ea31846dac0fe39c1f60019e;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=1e62d1300c1395db84c0f273265296397649eb47;hpb=409fd993c6e32e999b24082aae107a043a590f8f;p=jalview.git

diff --git a/src/jalview/ws/seqfetcher/DbSourceProxy.java b/src/jalview/ws/seqfetcher/DbSourceProxy.java
index 1e62d13..a02ffc9 100644
--- a/src/jalview/ws/seqfetcher/DbSourceProxy.java
+++ b/src/jalview/ws/seqfetcher/DbSourceProxy.java
@@ -20,20 +20,19 @@
  */
 package jalview.ws.seqfetcher;
 
+import jalview.api.FeatureSettingsModelI;
 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)
+ * source/version as cited in DBRefEntry.
+ * 
+ * TODO: add/define mechanism for retrieval of Trees and distance matrices from
+ * a database (unify with io)
  * 
- * @author JimP TODO: promote to API
+ * @author JimP
  */
 public interface DbSourceProxy
 {
@@ -41,7 +40,7 @@ public interface DbSourceProxy
    * 
    * @return source string constant used for this DB source
    */
-  public String getDbSource();
+  String getDbSource();
 
   /**
    * Short meaningful name for this data source for display in menus or
@@ -49,13 +48,13 @@ public interface DbSourceProxy
    * 
    * @return String
    */
-  public String getDbName();
+  String getDbName();
 
   /**
    * 
    * @return version string for this database.
    */
-  public String getDbVersion();
+  String getDbVersion();
 
   /**
    * Separator between individual accession queries for a database that allows
@@ -65,7 +64,7 @@ public interface DbSourceProxy
    * @return string for separating concatenated queries (as individually
    *         validated by the accession validator)
    */
-  public String getAccessionSeparator();
+  String getAccessionSeparator();
 
   /**
    * Regular expression for checking form of query string understood by this
@@ -75,14 +74,14 @@ public interface DbSourceProxy
    * 
    * @return null or a validation regex
    */
-  public Regex getAccessionValidator();
+  Regex getAccessionValidator();
 
   /**
    * 
    * @return a test/example query that can be used to validate retrieval and
    *         parsing mechanisms
    */
-  public String getTestQuery();
+  String getTestQuery();
 
   /**
    * Required for sources supporting multiple query retrieval for use with the
@@ -92,7 +91,7 @@ public interface DbSourceProxy
    * @param accession
    * @return
    */
-  public boolean isValidReference(String accession);
+  boolean isValidReference(String accession);
 
   /**
    * make one or more queries to the database and attempt to parse the response
@@ -108,27 +107,27 @@ public interface DbSourceProxy
    *           exceptions are not raised if query not found in database)
    * 
    */
-  public AlignmentI getSequenceRecords(String queries) throws Exception;
+  AlignmentI getSequenceRecords(String queries) throws Exception;
 
   /**
    * 
    * @return true if a query is currently being made
    */
-  public boolean queryInProgress();
+  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();
+  StringBuffer getRawRecords();
 
   /**
    * Tier for this data source
    * 
    * @return 0 - primary datasource, 1 - das primary source, 2 - secondary
    */
-  public int getTier();
+  int getTier();
 
   /**
    * Extracts valid accession strings from a query string. If there is an
@@ -146,7 +145,7 @@ public interface DbSourceProxy
    * 
    * @return
    */
-  public int getMaximumQueryCount();
+  int getMaximumQueryCount();
 
   /**
    * Returns true if the source may provide coding DNA i.e. sequences with
@@ -154,7 +153,7 @@ public interface DbSourceProxy
    * 
    * @return
    */
-  public boolean isDnaCoding();
+  boolean isDnaCoding();
 
   /**
    * Answers true if the database is a source of alignments (for example, domain
@@ -162,5 +161,21 @@ public interface DbSourceProxy
    * 
    * @return
    */
-  public boolean isAlignmentSource();
+  boolean isAlignmentSource();
+
+  /**
+   * Returns an (optional) description of the source, suitable for display as a
+   * tooltip, or null
+   * 
+   * @return
+   */
+  String getDescription();
+
+  /**
+   * Returns the preferred feature colour configuration if there is one, else
+   * null
+   * 
+   * @return
+   */
+  FeatureSettingsModelI getFeatureColourScheme();
 }
\ No newline at end of file