sequence db fetcher and db reference validation/annotation transfer

[jalview.git] / src / jalview / ws / dbsources / GeneDbSource.java

diff --git a/src/jalview/ws/dbsources/GeneDbSource.java b/src/jalview/ws/dbsources/GeneDbSource.java
new file mode 100644 (file)
index 0000000..7cea532
--- /dev/null
+++ b/src/jalview/ws/dbsources/GeneDbSource.java
@@ -0,0 +1,98 @@
+/**\r
+ * \r
+ */\r
+package jalview.ws.dbsources;\r
+\r
+import java.io.File;\r
+import java.util.Hashtable;\r
+import java.util.Iterator;\r
+import java.util.StringTokenizer;\r
+\r
+import com.stevesoft.pat.Regex;\r
+\r
+import jalview.datamodel.Alignment;\r
+import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.DBRefSource;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.datamodel.xdb.embl.EmblEntry;\r
+import jalview.ws.ebi.EBIFetchClient;\r
+import jalview.ws.seqfetcher.DbSourceProxy;\r
+import jalview.ws.seqfetcher.DbSourceProxyImpl;\r
+\r
+/**\r
+ * @author JimP\r
+ *\r
+ */\r
+public class GeneDbSource extends EmblXmlSource implements DbSourceProxy\r
+{\r
+\r
+  public GeneDbSource() {\r
+    addDbSourceProperty(DBRefSource.DNASEQDB);\r
+    addDbSourceProperty(DBRefSource.CODINGSEQDB);\r
+  }\r
+  \r
+  /* (non-Javadoc)\r
+   * @see jalview.ws.DbSourceProxy#getAccessionSeparator()\r
+   */\r
+  public String getAccessionSeparator()\r
+  {\r
+    // TODO Auto-generated method stub\r
+    return null;\r
+  }\r
+\r
+  /* (non-Javadoc)\r
+   * @see jalview.ws.DbSourceProxy#getAccessionValidator()\r
+   */\r
+  public Regex getAccessionValidator()\r
+  {\r
+    // TODO Auto-generated method stub\r
+    return null;\r
+  }\r
+\r
+  /* (non-Javadoc)\r
+   * @see jalview.ws.DbSourceProxy#getDbSource()\r
+   */\r
+  public String getDbSource()\r
+  {\r
+    return DBRefSource.GENEDB;\r
+  }\r
+  /* (non-Javadoc)\r
+   * @see jalview.ws.DbSourceProxy#getDbVersion()\r
+   */\r
+  public String getDbVersion()\r
+  {\r
+    // TODO Auto-generated method stub\r
+    return "0";\r
+  }\r
+\r
+  /* (non-Javadoc)\r
+   * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])\r
+   */\r
+  public AlignmentI getSequenceRecords(String queries) throws Exception\r
+  {\r
+    // query of form http://www.genedb.org/genedb/ArtemisFormHandler?id=&dest=EMBL\r
+    // \r
+    return getEmblSequenceRecords(DBRefSource.GENEDB, queries);\r
+  }\r
+  /* (non-Javadoc)\r
+   * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)\r
+   */\r
+  public boolean isValidReference(String accession)\r
+  {\r
+    // TODO Auto-generated method stub\r
+    return false;\r
+  }\r
+\r
+  /**\r
+   * return T.Brucei Mannosyl-Transferase TbPIG-M \r
+   */\r
+  public String getTestQuery()\r
+  {\r
+    return "Tb927.6.3300";\r
+  }\r
+\r
+  public String getDbName()\r
+  {\r
+    return getDbSource();\r
+  }\r
+}\r