encode gff

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@3239 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/io/GFFStreamFeature.java

@@ -20,7 +20,7 @@
  * along with this program; if not, write to the Free Software
  * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
  *
- * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/GFFStreamFeature.java,v 1.16 2005-06-08 15:19:38 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/GFFStreamFeature.java,v 1.17 2005-07-20 13:28:24 tjc Exp $
  */
 
 package uk.ac.sanger.artemis.io;
@@ -35,7 +35,7 @@ import java.util.StringTokenizer;
  *  A StreamFeature that thinks it is a GFF feature.
  *
  *  @author Kim Rutherford
- *  @version $Id: GFFStreamFeature.java,v 1.16 2005-06-08 15:19:38 tjc Exp $
+ *  @version $Id: GFFStreamFeature.java,v 1.17 2005-07-20 13:28:24 tjc Exp $
  **/
 
 public class GFFStreamFeature extends SimpleDocumentFeature
@@ -295,7 +295,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
   * Add URL escaping rule (e.g. space="%20" or "+")
   *
   */
-  private String encode(String s)
+  public static String encode(String s)
   {
     final String map[][] = {
 //                           { " ",  "%20" },  // white space

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

@@ -24,6 +24,7 @@
 
 package uk.ac.sanger.artemis.util;
 
+import uk.ac.sanger.artemis.io.GFFStreamFeature;
 import java.sql.*;
 import java.io.*;
 import java.util.Hashtable;
@@ -264,14 +265,17 @@ public class DatabaseDocument extends Document
         cdsBuffer.append("Parent="+parent_id+";");
 
       cdsBuffer.append("timelastmodified="+timelastmodified+";");
-      cdsBuffer.append(propTypeName+"="+rs.getString("value")); // attributes
+   
+      String value = GFFStreamFeature.encode(rs.getString("value"));
+      cdsBuffer.append(propTypeName+"="+value); // attributes
 
       int rewind = 0;
       while(rs.next() && rs.getString("uniquename").equals(name))
       {
         prop_type_id = rs.getLong("prop_type_id");
         propTypeName = getCvtermName(conn,prop_type_id);
-        cdsBuffer.append(";"+propTypeName+"="+rs.getString("value"));
+        value = GFFStreamFeature.encode(rs.getString("value"));
+        cdsBuffer.append(";"+propTypeName+"="+value);
         rewind++;
       }