From cb1224a307ca2b1cb1cee44d01ada46ad1bb6d0a Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Fri, 10 Oct 2008 14:45:35 +0000
Subject: [PATCH] fix for creating nodes
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8981 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../components/database/DatabaseJPanel.java | 54 +++++++++----------
1 file changed, 27 insertions(+), 27 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/database/DatabaseJPanel.java b/uk/ac/sanger/artemis/components/database/DatabaseJPanel.java
index 4688f0807..58084694f 100644
--- a/uk/ac/sanger/artemis/components/database/DatabaseJPanel.java
+++ b/uk/ac/sanger/artemis/components/database/DatabaseJPanel.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/database/DatabaseJPanel.java,v 1.15 2008-09-15 10:49:56 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/database/DatabaseJPanel.java,v 1.16 2008-10-10 14:45:35 tjc Exp $
*/
package uk.ac.sanger.artemis.components.database;
@@ -50,7 +50,6 @@ import javax.swing.BorderFactory;
import javax.swing.border.Border;
import javax.swing.tree.TreePath;
-import org.gmod.schema.organism.Organism;
import org.gmod.schema.sequence.Feature;
import java.awt.BorderLayout;
@@ -70,6 +69,7 @@ import java.util.Arrays;
import java.util.Comparator;
import java.util.HashMap;
import java.util.List;
+import java.util.Vector;
public class DatabaseJPanel extends JPanel
{
@@ -432,7 +432,7 @@ public class DatabaseJPanel extends JPanel
entries = doc.getDatabaseEntries();
final DatabaseTreeNode top = new DatabaseTreeNode("");
- createNodes(top, doc.getSchema(), doc, entries);
+ createNodes(top, doc, entries);
return new DatabaseJTree(top);
}
catch(ConnectException e)
@@ -460,14 +460,10 @@ public class DatabaseJPanel extends JPanel
* @param doc DatabaseDocument
* @param organism sequences collection
*/
- private void createNodes(DatabaseTreeNode top, List schemas,
+ private void createNodes(DatabaseTreeNode top,
DatabaseDocument doc,
HashMap entries)
{
- DatabaseTreeNode schema_node;
- DatabaseTreeNode seq_node;
- DatabaseTreeNode typ_node;
-
final Object v_organism[] = entries.keySet().toArray();
final int v_organism_size = v_organism.length;
@@ -479,37 +475,42 @@ public class DatabaseJPanel extends JPanel
}
});
+ final List organisms = new Vector();
+ for(int i = 0; i < v_organism_size; i++)
+ {
+ String seqNames[] = ((String)v_organism[i]).split("-");
+ if(!organisms.contains(seqNames[0]))
+ organisms.add(seqNames[0]);
+ }
+
int start = 0;
boolean seen;
+ String seqFullName;
+ DatabaseTreeNode schema_node;
+ DatabaseTreeNode seq_node;
+ DatabaseTreeNode typ_node;
- for(int i=0; i<schemas.size(); i++)
+ for(int i=0; i<organisms.size(); i++)
{
int nchild = 0;
- String name;
+ String name = (String)organisms.get(i);
seen = false;
- if(schemas.get(i) instanceof String)
- name = (String)schemas.get(i);
- else
- name = ((Organism)schemas.get(i)).getCommonName();
-
schema_node = new DatabaseTreeNode(name);
final HashMap seq_type_node = new HashMap();
for(int j = start; j < v_organism_size; j++)
{
- String seq_name = (String)v_organism[j];
- int ind1 = seq_name.indexOf("- ");
-
- if(seq_name.substring(0, ind1).trim().toLowerCase().equals(name.toLowerCase()))
+ seqFullName = (String)v_organism[j];
+ String seqNames[] = seqFullName.split("-");
+
+ if(seqNames[0].trim().toLowerCase().equals(name.toLowerCase().trim()))
{
- final String featureId = (String)entries.get(seq_name);
+ final String featureId = (String)entries.get(seqFullName);
- int ind2 = seq_name.lastIndexOf("- ");
-
- final String schema = seq_name.substring(0, ind1).trim();
- String type = seq_name.substring(ind1 + 2, ind2 - 1);
- seq_name = seq_name.substring(ind2 + 2);
+ final String schema = seqNames[0].trim();
+ String type = seqNames[1].trim();
+ String thisSeqName = seqNames[2].trim();
if(!seq_type_node.containsKey(type))
{
@@ -520,11 +521,10 @@ public class DatabaseJPanel extends JPanel
else
typ_node = (DatabaseTreeNode) seq_type_node.get(type);
- seq_node = new DatabaseTreeNode(seq_name,
+ seq_node = new DatabaseTreeNode(thisSeqName,
featureId, schema,
doc.getUserName(),
doc.isSingleSchema());
-
typ_node.add(seq_node);
nchild++;
--
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