diff --git a/uk/ac/sanger/artemis/components/DatabaseEntrySource.java b/uk/ac/sanger/artemis/components/DatabaseEntrySource.java
index f69cf39dae553d5d9fcccc82a89922884cc5c642..4b7bdedf44c5c47856608a21d1dca9aae9106901 100644
--- a/uk/ac/sanger/artemis/components/DatabaseEntrySource.java
+++ b/uk/ac/sanger/artemis/components/DatabaseEntrySource.java
@@ -28,10 +28,6 @@ import javax.swing.*;
import javax.swing.tree.DefaultMutableTreeNode;
import javax.swing.tree.TreeSelectionModel;
import javax.swing.tree.TreePath;
-import java.awt.event.MouseListener;
-import java.awt.event.MouseAdapter;
-import java.awt.event.MouseEvent;
-import java.awt.Cursor;
import java.awt.Container;
import java.awt.GridLayout;
import java.net.*;
@@ -189,7 +185,7 @@ public class DatabaseEntrySource implements EntrySource
DatabaseDocument doc = new DatabaseDocument(location);
entries = doc.getDatabaseEntries();
- Vector organism = doc.getOrganism();
+ Vector organism = doc.getOrganism();
DefaultMutableTreeNode top =
new DefaultMutableTreeNode("PSU Organism List");
@@ -206,12 +202,19 @@ public class DatabaseEntrySource implements EntrySource
* @return node that is currently selected
*
*/
- protected DefaultMutableTreeNode getSelectedNode(JTree tree)
+ protected String getSelectedNode(JTree tree)
{
TreePath path = tree.getLeadSelectionPath();
if(path == null)
return null;
- return (DefaultMutableTreeNode)path.getLastPathComponent();
+
+ DefaultMutableTreeNode seq_node = (DefaultMutableTreeNode)path.getLastPathComponent();
+ DefaultMutableTreeNode type_node = (DefaultMutableTreeNode)seq_node.getParent();
+ DefaultMutableTreeNode org_node = (DefaultMutableTreeNode)type_node.getParent();
+
+ return (String)org_node.getUserObject() + " - " +
+ (String)type_node.getUserObject() + " - " +
+ (String)seq_node.getUserObject();
}
/**
@@ -228,6 +231,7 @@ public class DatabaseEntrySource implements EntrySource
Enumeration enum_org = org.elements();
DefaultMutableTreeNode org_node;
DefaultMutableTreeNode seq_node;
+ DefaultMutableTreeNode typ_node;
while(enum_org.hasMoreElements())
{
@@ -235,14 +239,31 @@ public class DatabaseEntrySource implements EntrySource
org_node = new DefaultMutableTreeNode(name);
top.add(org_node);
+ Hashtable seq_type_node = new Hashtable();
+
Enumeration enum_seq = organism.keys();
while(enum_seq.hasMoreElements())
{
String seq_name = (String)enum_seq.nextElement();
if(seq_name.startsWith(name))
{
+ int ind1 = seq_name.indexOf( "- ");
+ int ind2 = seq_name.lastIndexOf("- ");
+
+ String type = seq_name.substring(ind1+2,ind2).trim();
+ seq_name = seq_name.substring(ind2+2).trim();
+
+ if(!seq_type_node.containsKey(type))
+ {
+ typ_node = new DefaultMutableTreeNode(type);
+ seq_type_node.put(type,typ_node);
+ org_node.add(typ_node);
+ }
+ else
+ typ_node= (DefaultMutableTreeNode)seq_type_node.get(type);
+
seq_node = new DefaultMutableTreeNode(seq_name);
- org_node.add(seq_node);
+ typ_node.add(seq_node);
}
}
}
diff --git a/uk/ac/sanger/artemis/components/DatabaseJFrame.java b/uk/ac/sanger/artemis/components/DatabaseJFrame.java
index 81d6236b9b39f89beedfe09f49def0d2e687fa44..0fb34b5f8c680fa814126a2fbb10b4b6b535127f 100644
--- a/uk/ac/sanger/artemis/components/DatabaseJFrame.java
+++ b/uk/ac/sanger/artemis/components/DatabaseJFrame.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/components/DatabaseJFrame.java,v 1.3 2005-06-01 15:07:31 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/DatabaseJFrame.java,v 1.4 2005-06-18 07:01:16 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
@@ -115,11 +115,8 @@ public class DatabaseJFrame extends JFrame
Cursor cbusy = new Cursor(Cursor.WAIT_CURSOR);
Cursor cdone = new Cursor(Cursor.DEFAULT_CURSOR);
- DefaultMutableTreeNode node = entry_source.getSelectedNode(tree);
- if(node == null || !node.isLeaf())
- return;
-
- String id = entry_source.getEntryID((String)node.getUserObject());
+ String node_name = entry_source.getSelectedNode(tree);
+ String id = entry_source.getEntryID(node_name);
if(id != null)
getEntryEditFromDatabase(id, entry_source, tree, art_main);
}
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index 7bd1affa4497180da556996f96487c3b9de4d7b0..bee313c20216f855f89418d59e78d74845fe70f2 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -189,6 +189,13 @@ public class DatabaseDocument extends Document
return null;
}
+
+ /**
+ *
+ * Given a parent (chromosome, contig, supercontig) retrieve the features
+ * in the form of a GFF stream.
+ *
+ */
private String getGFF(Connection conn, String parentFeatureID)
throws java.sql.SQLException
{
@@ -338,13 +345,7 @@ public class DatabaseDocument extends Document
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'";
-// ResultSet rs = st.executeQuery(sql);
-// rs.next();
-// String cvterm_id = rs.getString("cvterm_id");
-
- sql = new String("SELECT abbreviation, name, feature_id FROM organism, feature WHERE (");
+ sql = new String("SELECT abbreviation, name, feature_id, type_id FROM organism, feature WHERE (");
for(int i=0; i<cvterm_id.size(); i++)
{
@@ -356,16 +357,15 @@ public class DatabaseDocument extends Document
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);
while(rs.next())
{
- String org = rs.getString("abbreviation");
- db.put(org+" - "+rs.getString("name"), rs.getString("feature_id"));
+ String org = rs.getString("abbreviation");
+ String typeName = getCvtermName(conn,rs.getLong("type_id"));
+ db.put(org+" - "+typeName+" - "+rs.getString("name"),
+ rs.getString("feature_id"));
if(!organism.contains(org))
organism.add(org);
}