join exons and add parents to GFF generated from database

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@3201 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/components/DatabaseEntrySource.java

@@ -294,8 +294,8 @@ public class DatabaseEntrySource implements EntrySource
     {
       DatabaseDocumentEntry db_entry = null;
 
-      final EntryInformation entry_information =
-        new SimpleEntryInformation(Options.getArtemisEntryInformation());
+//    final EntryInformation entry_information =
+//      new SimpleEntryInformation(Options.getArtemisEntryInformation());
 
       if(read_only) 
       {
@@ -305,7 +305,7 @@ public class DatabaseEntrySource implements EntrySource
         DatabaseDocument doc = new DatabaseDocument(location, id, progress_listener);
 //      DatabaseDocument doc = new DatabaseDocument("jdbc:postgresql://localhost:13001/chadoCVS?user=es2",
 //                                                  id, progress_listener);
-        db_entry = new DatabaseDocumentEntry(entry_information, doc);
+        db_entry = new DatabaseDocumentEntry(doc);
       }
 
       final Bases real_bases;

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

@@ -34,15 +34,14 @@ import java.io.*;
  *  relational database entry
  **/
 
-public class DatabaseDocumentEntry extends SimpleDocumentEntry
+public class DatabaseDocumentEntry extends GFFDocumentEntry 
     implements DocumentEntry 
 {
 
-  public DatabaseDocumentEntry(final EntryInformation entry_information,
-                               final Document doc)
+  public DatabaseDocumentEntry(final Document doc)
          throws EntryInformationException, IOException
   {
-    super(entry_information, doc,  null);
+    super(doc,null);
   }
 
   /**

uk/ac/sanger/artemis/io/GFFDocumentEntry.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/GFFDocumentEntry.java,v 1.15 2005-07-15 10:33:56 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/GFFDocumentEntry.java,v 1.16 2005-07-18 19:20:25 tjc Exp $
  */
 
 package uk.ac.sanger.artemis.io;
@@ -36,7 +36,7 @@ import java.util.Vector;
  *  A DocumentEntry that can read an GFF entry from a Document.
  *
  *  @author Kim Rutherford
- *  @version $Id: GFFDocumentEntry.java,v 1.15 2005-07-15 10:33:56 tjc Exp $
+ *  @version $Id: GFFDocumentEntry.java,v 1.16 2005-07-18 19:20:25 tjc Exp $
  **/
 
 public class GFFDocumentEntry extends SimpleDocumentEntry
@@ -166,7 +166,8 @@ public class GFFDocumentEntry extends SimpleDocumentEntry
               this_feature.getQualifierByName("Parent").getValues();
             group_name = values.elementAt(0);
 
-            if(this_feature.getQualifierByName("ID") != null)
+            if(this_feature.getQualifierByName("ID") != null &&
+               !key.equals("exon"))
             {
               values =
                   this_feature.getQualifierByName("ID").getValues();

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

@@ -199,18 +199,24 @@ public class DatabaseDocument extends Document
   private String getGFF(Connection conn, String parentFeatureID) 
           throws java.sql.SQLException
   {
+
     Statement st = conn.createStatement(ResultSet.TYPE_SCROLL_INSENSITIVE, ResultSet.CONCUR_UPDATABLE);
-    String sql = "SELECT strand, fmin, fmax, uniquename, feature.type_id, featureprop.type_id AS prop_type_id, value"+
-                 " FROM feature, featureloc, featureprop WHERE srcfeature_id = "+parentFeatureID+
-                 " and featureloc.feature_id=featureprop.feature_id"+
-                 " and featureloc.feature_id=feature.feature_id ORDER BY uniquename";
+//  String sql = "SELECT feature_id, strand, fmin, fmax, uniquename, feature.type_id, featureprop.type_id AS prop_type_id, value"+
+//               " FROM feature, featureloc, featureprop WHERE srcfeature_id = "+parentFeatureID+
+//               " and featureloc.feature_id=featureprop.feature_id"+
+//               " and featureloc.feature_id=feature.feature_id";
+
+    String sql = "SELECT feature.feature_id, object_id, strand, fmin, fmax, uniquename, feature.type_id, "+
+                 " featureprop.type_id AS prop_type_id, featureprop.value FROM feature, featureloc, featureprop, feature_relationship "+
+                 " WHERE srcfeature_id = "+parentFeatureID+" and featureloc.feature_id=featureprop.feature_id and "+
+                 " featureloc.feature_id=feature.feature_id and feature_relationship.subject_id=feature.feature_id";
 
     appendToLogFile(sql,sqlLog);
     ResultSet rs = st.executeQuery(sql);
     StringBuffer cdsBuffer = new StringBuffer();
 
     String parentFeature = getFeatureName(parentFeatureID,conn);
-    int loop = 1;
+    Hashtable hstore = new Hashtable();
 
     while(rs.next())
     {
@@ -223,6 +229,13 @@ public class DatabaseDocument extends Document
       String typeName = getCvtermName(conn,type_id);
       String propTypeName = getCvtermName(conn,prop_type_id);
 
+      String feature_id = rs.getString("feature_id");
+      hstore.put(feature_id, name);
+
+      String parent_id  = rs.getString("object_id");
+      if(parent_id != null && hstore.containsKey(parent_id))
+        parent_id = (String)hstore.get(parent_id);
+      
 // make gff format
       cdsBuffer.append(parentFeature+"\t");    // seqid
       cdsBuffer.append("chado\t");             // source
@@ -237,6 +250,9 @@ public class DatabaseDocument extends Document
       cdsBuffer.append(".\t");                 // phase
       cdsBuffer.append("ID="+name+";"+propTypeName+"="+rs.getString("value")); // attributes
 
+      if(parent_id != null)
+        cdsBuffer.append(";Parent="+parent_id);
+
       int rewind = 0;
       while(rs.next() && rs.getString("uniquename").equals(name))
       {