change getOrganism() to get all features with residue independent of type

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@2865 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/util/DatabaseDocument.java

@@ -316,12 +316,13 @@ public class DatabaseDocument extends Document
 
       Statement st = conn.createStatement();
 
-      String sql = "select type_id from feature where residues notnull";
+      String sql = "SELECT DISTINCT type_id FROM feature WHERE residues notnull";
       appendToLogFile(sql,sqlLog);
 
+      Vector cvterm_id = new Vector();
       ResultSet rs = st.executeQuery(sql);
-      rs.next();
-      String cvterm_id = rs.getString("type_id");
+      while(rs.next())
+        cvterm_id.add(rs.getString("type_id"));
 
 //    String sql = "select cvterm.cvterm_id, cvterm.name FROM cvterm, cv "+
 //                 "WHERE cv.cv_id = cvterm.cv_id and cvterm.name = 'chromosome'";
@@ -329,9 +330,21 @@ public class DatabaseDocument extends Document
 //    rs.next();
 //    String cvterm_id = rs.getString("cvterm_id");
 
-      sql = new String("SELECT abbreviation, name, feature_id FROM organism, feature WHERE type_id = '"+
-                        cvterm_id+"' and organism.organism_id=feature.organism_id "+
-                        "ORDER BY abbreviation, name");
+      sql = new String("SELECT abbreviation, name, feature_id FROM organism, feature WHERE (");
+
+      for(int i=0; i<cvterm_id.size(); i++)
+      {
+        sql = sql + " type_id = "+ (String)cvterm_id.get(i);
+        if(i<cvterm_id.size()-1)
+          sql = sql + " OR ";
+      }
+
+      sql = sql + ") " + " and organism.organism_id=feature.organism_id "+
+            "ORDER BY abbreviation, name";
+
+//    sql = new String("SELECT abbreviation, name, feature_id FROM organism, feature WHERE type_id = '"+
+//                      cvterm_id+"' and organism.organism_id=feature.organism_id "+
+//                      "ORDER BY abbreviation, name");
       appendToLogFile(sql,sqlLog);
 
       rs = st.executeQuery(sql);