JTree implementation for database sequence selection

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@2726 ee4ac58c-ac51-4696-9907-e4b3aa274f04

uk/ac/sanger/artemis/components/ArtemisMain.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/ArtemisMain.java,v 1.12 2005-05-31 15:35:53 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/ArtemisMain.java,v 1.13 2005-06-01 11:06:43 tjc Exp $
  */
 
 package uk.ac.sanger.artemis.components;
@@ -38,20 +38,17 @@ import org.biojava.bio.seq.io.SequenceFormat;
 
 import java.awt.event.ActionListener;
 import java.awt.event.ActionEvent;
+import java.awt.Toolkit;
 import java.io.*;
-import java.util.Hashtable;
-import java.util.Enumeration;
 
+import javax.swing.tree.DefaultMutableTreeNode;
 import javax.swing.ListSelectionModel;
-import javax.swing.JList;
-import javax.swing.JOptionPane;
-import javax.swing.JScrollPane;
 
 /**
  *  The main window for the Artemis sequence editor.
  *
  *  @author Kim Rutherford <kmr@sanger.ac.uk>
- *  @version $Id: ArtemisMain.java,v 1.12 2005-05-31 15:35:53 tjc Exp $
+ *  @version $Id: ArtemisMain.java,v 1.13 2005-06-01 11:06:43 tjc Exp $
  **/
 
 public class ArtemisMain extends Splash 
@@ -117,10 +114,9 @@ public class ArtemisMain extends Splash
         if(!entry_source.setLocation())
           return;
 
-        String id = displayDatabases(entry_source);
-
-        if(id != null)
-          getEntryEditFromDatabase(id, entry_source);
+        final DatabaseJFrame frame = new DatabaseJFrame(entry_source,
+                                                   ArtemisMain.this);
+        frame.setVisible(true);
       }
     };
 
@@ -213,7 +209,6 @@ public class ArtemisMain extends Splash
         continue;
       }
 
-      
       if(new_entry_name.startsWith("+") && last_entry_edit != null ||
          seen_plus) 
       {
@@ -512,7 +507,7 @@ public class ArtemisMain extends Splash
   /**
    *  Make an EntryEdit component from the given Entry.
    **/
-  private EntryEdit makeEntryEdit(final Entry entry) 
+  protected EntryEdit makeEntryEdit(final Entry entry) 
   {
     final Bases bases = entry.getBases();
     final EntryGroup entry_group = new SimpleEntryGroup(bases);
@@ -551,91 +546,6 @@ public class ArtemisMain extends Splash
   }
 
 
-  /**
-  *
-  * Display a list of the available relational database entries.
-  *
-  */
-  private String displayDatabases(DatabaseEntrySource entry_source)
-  {
-    Hashtable db = entry_source.getDatabaseEntries();
-
-    String db_array[] = new String[db.size()];
-
-    Enumeration enum_db = db.keys();
-    for(int i=0; enum_db.hasMoreElements(); i++)
-      db_array[i] = (String)enum_db.nextElement();
-
-    java.util.Arrays.sort(db_array);
-    JList list_db = new JList(db_array);
-    list_db.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
-    JScrollPane scroll_list = new JScrollPane(list_db);
-
-    Object[] options = { "OPEN IN ARTEMIS >", "CANCEL"};
-    boolean selecting = true;
-
-    int select = JOptionPane.showOptionDialog(null, scroll_list,
-                                "Database Selection",
-                                 JOptionPane.YES_NO_CANCEL_OPTION,
-                                 JOptionPane.QUESTION_MESSAGE,
-                                 null,
-                                 options,
-                                 options[0]);
-    if(select == 1 || list_db.getSelectedValue() == null)
-      return null;
-
-    return (String)db.get((String)list_db.getSelectedValue());
-  }
-
-  /**
-  *
-  * Retrieve a database entry.
-  *
-  */
-  private void getEntryEditFromDatabase(final String id,
-                                        final DatabaseEntrySource entry_source)
-  {
-    SwingWorker entryWorker = new SwingWorker()
-    {
-      public Object construct()
-      {
-        try
-        {
-          final InputStreamProgressListener progress_listener =
-                                     getInputStreamProgressListener();
-
-//        DatabaseEntrySource entry_source = new DatabaseEntrySource();
-
-          final Entry entry = entry_source.getEntry(id, progress_listener);
-          if(entry == null)
-            return null;
-
-          final EntryEdit new_entry_edit = makeEntryEdit(entry);
-          new_entry_edit.setVisible(true);
-        }
-        catch(OutOfRangeException e)
-        {
-          new MessageDialog(ArtemisMain.this, "read failed: one of the features in " +
-                 " the entry has an out of range " +
-                 "location: " + e.getMessage());
-        }
-        catch(NoSequenceException e)
-        {
-          new MessageDialog(ArtemisMain.this, "read failed: entry contains no sequence");
-        }
-        catch(IOException e)
-        {
-          new MessageDialog(ArtemisMain.this, "read failed due to IO error: " + e);
-        }
-        return null;
-      }
-
-    };
-    entryWorker.start();
-
-  }
-
-
   /**
    *  Read an Entry from the given EntrySource and make a new EntryEdit
    *  component for the Entry.

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

@@ -24,11 +24,14 @@
 
 package uk.ac.sanger.artemis.components;
 
-import javax.swing.JOptionPane;
-import javax.swing.JLabel;
-import javax.swing.JTextField;
-import javax.swing.Box;
-
+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.net.*;
 import java.io.*;
 import java.util.*;
@@ -49,9 +52,10 @@ import uk.ac.sanger.artemis.io.EntryInformationException;
  *
  **/
 
-public class DatabaseEntrySource implements EntrySource 
+public class DatabaseEntrySource implements EntrySource
 {
   private String location;
+  private Hashtable entries;
 
   /**
    *  Create a new DatabaseEntrySource.
@@ -137,12 +141,83 @@ public class DatabaseEntrySource implements EntrySource
   }
 
 
-  protected Hashtable getDatabaseEntries()
+  /**
+  *
+  *  Given the entry name get the seq feature_id
+  *
+  */
+  protected String getEntryID(String name)
+  {
+    return (String)entries.get(name);
+  }
+
+  /**
+  *
+  * Create database organism JTree.
+  *
+  */
+  protected JTree getDatabaseTree()
   {
     DatabaseDocument doc = new DatabaseDocument(location);
-//  DatabaseDocument doc = new DatabaseDocument("jdbc:postgresql://localhost:13001/chadoCVS?user=es2");
-//  DatabaseDocument doc = new DatabaseDocument("jdbc:postgresql://tim1:2999/chadoCVS?user=tim");
-    return doc.getDatabaseEntries();
+
+    entries = doc.getDatabaseEntries();
+    Vector organism   = doc.getOrganism();
+
+    DefaultMutableTreeNode top =
+        new DefaultMutableTreeNode("PSU Organism List");
+    createNodes(top,organism,entries);
+    final JTree tree = new JTree(top);
+    tree.getSelectionModel().setSelectionMode(TreeSelectionModel.SINGLE_TREE_SELECTION);
+
+    return tree;
+  }
+
+  /**
+  *
+  * Get DefaultMutableTreeNode of selected node
+  * @return     node that is currently selected
+  *
+  */
+  protected DefaultMutableTreeNode getSelectedNode(JTree tree)
+  {
+    TreePath path = tree.getLeadSelectionPath();
+    if(path == null)
+      return null;
+    return (DefaultMutableTreeNode)path.getLastPathComponent();
+  }
+
+  /**
+  *
+  * Create the nodes of the organism JTree
+  * @param top		root node
+  * @param org  	organism collection
+  * @param organism 	sequences collection 
+  *
+  */
+  private void createNodes(DefaultMutableTreeNode top, Vector org,
+                           Hashtable organism)
+  {
+    Enumeration enum_org = org.elements();
+    DefaultMutableTreeNode org_node;
+    DefaultMutableTreeNode seq_node;
+
+    while(enum_org.hasMoreElements())
+    { 
+      String name = (String)enum_org.nextElement();
+      org_node = new DefaultMutableTreeNode(name);
+      top.add(org_node);
+
+      Enumeration enum_seq = organism.keys();
+      while(enum_seq.hasMoreElements())
+      {
+        String seq_name = (String)enum_seq.nextElement();
+        if(seq_name.startsWith(name))
+        {
+          seq_node = new DefaultMutableTreeNode(seq_name);
+          org_node.add(seq_node);
+        }
+      }
+    }
   }
 
 

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

+/* DatabaseJFrame.java
+ *
+ * created: June 2005
+ *
+ * This file is part of Artemis
+ *
+ * Copyright(C) 2000  Genome Research Limited
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or(at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * 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 1.1 2005-06-01 11:06:43 tjc Exp $
+ */
+
+package uk.ac.sanger.artemis.components;
+
+import uk.ac.sanger.artemis.Entry;
+import uk.ac.sanger.artemis.sequence.*;
+import uk.ac.sanger.artemis.util.InputStreamProgressListener;
+import uk.ac.sanger.artemis.util.OutOfRangeException;
+
+import javax.swing.JFrame;
+import javax.swing.JTree;
+import javax.swing.JScrollPane;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.awt.Dimension;
+import java.awt.Toolkit;
+import java.awt.Cursor;
+import java.io.*;
+import javax.swing.tree.DefaultMutableTreeNode;
+
+public class DatabaseJFrame extends JFrame
+{
+
+  public DatabaseJFrame(final DatabaseEntrySource entry_source,
+                        final ArtemisMain art_main)
+  {
+    super("PSU Organism");
+    final JTree tree = entry_source.getDatabaseTree();
+
+    //Listen for when the selection changes.
+    MouseListener mouseListener = new MouseAdapter()
+    {
+      private Cursor cbusy = new Cursor(Cursor.WAIT_CURSOR);
+      private Cursor cdone = new Cursor(Cursor.DEFAULT_CURSOR);
+
+      public void mouseClicked(MouseEvent e)
+      {
+        if(e.getClickCount() == 2 &&
+           !e.isPopupTrigger())
+        {
+          tree.setCursor(cbusy);
+          DefaultMutableTreeNode node = entry_source.getSelectedNode(tree);
+          if(!node.isLeaf())
+            return;
+          String id =  entry_source.getEntryID((String)node.getUserObject());
+          if(id != null)
+            getEntryEditFromDatabase(id, entry_source, art_main);
+
+          tree.setCursor(cdone);
+        }
+      }
+    };
+    tree.addMouseListener(mouseListener);
+
+    JScrollPane scroll = new JScrollPane(tree);
+
+    Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
+    Dimension dim_frame = new Dimension(screen.width*2 / 10, screen.height*6 / 10);
+    scroll.setPreferredSize(dim_frame);
+
+    getContentPane().add(scroll);
+    pack();
+    Utilities.rightJustifyFrame(this);
+  }
+
+  /**
+  *
+  * Retrieve a database entry.
+  *
+  */
+  private void getEntryEditFromDatabase(final String id,
+                                        final DatabaseEntrySource entry_source,
+                                        final ArtemisMain art_main)
+  {
+    SwingWorker entryWorker = new SwingWorker()
+    {
+      public Object construct()
+      {
+        try
+        {
+          final InputStreamProgressListener progress_listener =
+                                     art_main.getInputStreamProgressListener();
+
+          final Entry entry = entry_source.getEntry(id, progress_listener);
+          if(entry == null)
+            return null;
+
+          final EntryEdit new_entry_edit = art_main.makeEntryEdit(entry);
+          new_entry_edit.setVisible(true);
+        }
+        catch(OutOfRangeException e)
+        {
+          new MessageDialog(art_main, "read failed: one of the features in " +
+                 " the entry has an out of range " +
+                 "location: " + e.getMessage());
+        }
+        catch(NoSequenceException e)
+        {
+          new MessageDialog(art_main, "read failed: entry contains no sequence");
+        }
+        catch(IOException e)
+        {
+          new MessageDialog(art_main, "read failed due to IO error: " + e);
+        }
+        return null;
+      }
+
+    };
+    entryWorker.start();
+
+  }
+
+}

uk/ac/sanger/artemis/components/Utilities.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/Utilities.java,v 1.1 2004-06-09 09:47:57 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/Utilities.java,v 1.2 2005-06-01 11:06:43 tjc Exp $
  */
 
 package uk.ac.sanger.artemis.components;
@@ -37,7 +37,7 @@ import javax.swing.*;
  *  Utilities methods used by the uk.ac.sanger.artemis.components package.
  *
  *  @author Kim Rutherford <kmr@sanger.ac.uk>
- *  @version $Id: Utilities.java,v 1.1 2004-06-09 09:47:57 tjc Exp $
+ *  @version $Id: Utilities.java,v 1.2 2005-06-01 11:06:43 tjc Exp $
  **/
 
 public class Utilities 
@@ -69,6 +69,21 @@ public class Utilities
     frame.setLocation(new Point(x_position, y_position));
   }
 
+   /**
+   *  Move the given JFrame to the right of the screen.
+   **/
+  public static void rightJustifyFrame(final JFrame frame)
+  {
+    final Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
+    int y_position =(screen.height - frame.getSize().height) / 2;
+
+    if(y_position < 10)
+      y_position = 10;
+
+    frame.setLocation(new Point(0, y_position));
+  }
+
+
   /**
    *  Find the parent Frame of the given component and re-centre it on the
    *  screen.

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

@@ -27,6 +27,7 @@ package uk.ac.sanger.artemis.util;
 import java.sql.*;
 import java.io.*;
 import java.util.Hashtable;
+import java.util.Vector;
 import javax.swing.JOptionPane;
 
 /**
@@ -36,11 +37,12 @@ import javax.swing.JOptionPane;
 
 public class DatabaseDocument extends Document 
 {
-
   private String name = null;
   private String feature_id = "1";
   private Hashtable cvterm;
   private InputStreamProgressListener progress_listener;
+  private Hashtable db;
+  private Vector organism;
 
   /**
    *
@@ -278,7 +280,9 @@ public class DatabaseDocument extends Document
    **/
   public Hashtable getDatabaseEntries()
   {
-    Hashtable db = new Hashtable();
+    db = new Hashtable();
+    organism = new Vector();
+
     try
     {
       Connection conn = getConnection();
@@ -299,7 +303,12 @@ public class DatabaseDocument extends Document
 
       rs = st.executeQuery(sql);
       while(rs.next())
-        db.put(rs.getString("abbreviation")+" - "+rs.getString("name"), rs.getString("feature_id"));
+      {
+        String org = rs.getString("abbreviation");
+        db.put(org+" - "+rs.getString("name"), rs.getString("feature_id"));
+        if(!organism.contains(org))
+          organism.add(org);
+      }
     }
     catch(java.sql.SQLException sqlExp)
     {
@@ -319,6 +328,10 @@ public class DatabaseDocument extends Document
     return db;
   }
 
+  public Vector getOrganism()
+  {
+    return organism;
+  }
 
   public Connection getConnection() throws java.sql.SQLException,
                                            java.net.ConnectException