diff --git a/uk/ac/sanger/artemis/components/ActMain.java b/uk/ac/sanger/artemis/components/ActMain.java
index 24cc2a37a382d726dccb75919f1f9fd1735e73e3..711a2068920ba82a177b67d6f76f0f8ac8721fed 100644
--- a/uk/ac/sanger/artemis/components/ActMain.java
+++ b/uk/ac/sanger/artemis/components/ActMain.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/ActMain.java,v 1.10 2006-10-18 14:25:23 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/ActMain.java,v 1.11 2006-10-23 13:34:12 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
@@ -31,7 +31,7 @@ import uk.ac.sanger.artemis.*;
import uk.ac.sanger.artemis.sequence.Bases;
import uk.ac.sanger.artemis.sequence.NoSequenceException;
import uk.ac.sanger.artemis.components.database.DatabaseEntrySource;
-import uk.ac.sanger.artemis.components.database.DatabaseJFrame;
+import uk.ac.sanger.artemis.components.database.DatabaseJPanel;
import uk.ac.sanger.artemis.components.database.DatabaseTreeNode;
import uk.ac.sanger.artemis.util.*;
@@ -41,14 +41,13 @@ import uk.ac.sanger.artemis.io.SimpleEntryInformation;
import java.awt.event.*;
import java.io.IOException;
-import java.io.File;
import javax.swing.JFrame;
/**
* The main window for the Artemis Comparison Tool.
*
* @author Kim Rutherford <kmr@sanger.ac.uk>
- * @version $Id: ActMain.java,v 1.10 2006-10-18 14:25:23 tjc Exp $
+ * @version $Id: ActMain.java,v 1.11 2006-10-23 13:34:12 tjc Exp $
**/
public class ActMain extends Splash
@@ -96,9 +95,13 @@ public class ActMain extends Splash
new ComparatorDialog(ActMain.this).setVisible(true);
}
};
- makeMenuItem(file_menu, "Open SSH File Manager ...", menu_listener_ssh);
+
+ if(System.getProperty("chado") != null)
+ makeMenuItem(file_menu, "Open Database and SSH File Manager ...", menu_listener_ssh);
+ else
+ makeMenuItem(file_menu, "Open SSH File Manager ...", menu_listener_ssh);
- final boolean sanger_options =
+/* final boolean sanger_options =
Options.getOptions().getPropertyTruthValue("sanger_options");
if(sanger_options)
@@ -114,7 +117,7 @@ public class ActMain extends Splash
makeMenuItem(file_menu, "Database Entry ...", menu_listener);
if(System.getProperty("chado") != null)
launchDatabaseJFrame(false);
- }
+ }*/
makeMenuItem(file_menu, "Quit", quit_listener);
}
@@ -340,9 +343,16 @@ public class ActMain extends Splash
DatabaseEntrySource entry_source = new DatabaseEntrySource();
if(!entry_source.setLocation(prompt_user))
return null;
-
- final DatabaseJFrame frame = new DatabaseJFrame(entry_source,
+
+ JFrame frame = new JFrame("Organism List");
+ final DatabaseJPanel pane = new DatabaseJPanel(entry_source,
ActMain.this);
+ frame.getContentPane().add(pane);
+ frame.pack();
+ Utilities.rightJustifyFrame(frame);
+ frame.setVisible(true);
+ frame.setJMenuBar(pane.makeMenuBar(entry_source, ActMain.this));
+
frame.setVisible(true);
getStatusLabel().setText("");
return null;
diff --git a/uk/ac/sanger/artemis/components/ArtemisMain.java b/uk/ac/sanger/artemis/components/ArtemisMain.java
index de4d9054851efaa66c3fe8bc5924f445bc6a549a..edbb2e7020d492d007f59df69f8e151e1005ba27 100644
--- a/uk/ac/sanger/artemis/components/ArtemisMain.java
+++ b/uk/ac/sanger/artemis/components/ArtemisMain.java
@@ -20,13 +20,13 @@
* 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 1.21 2006-10-18 14:25:23 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/ArtemisMain.java,v 1.22 2006-10-23 13:34:12 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
import uk.ac.sanger.artemis.components.database.DatabaseEntrySource;
-import uk.ac.sanger.artemis.components.database.DatabaseJFrame;
+import uk.ac.sanger.artemis.components.database.DatabaseJPanel;
import uk.ac.sanger.artemis.components.filetree.FileManager;
import uk.ac.sanger.artemis.components.filetree.LocalAndRemoteFileManager;
import uk.ac.sanger.artemis.*;
@@ -45,12 +45,13 @@ import java.awt.event.*;
import java.awt.Toolkit;
import java.io.*;
import java.awt.datatransfer.*;
+import javax.swing.JFrame;
/**
* The main window for the Artemis sequence editor.
*
* @author Kim Rutherford <kmr@sanger.ac.uk>
- * @version $Id: ArtemisMain.java,v 1.21 2006-10-18 14:25:23 tjc Exp $
+ * @version $Id: ArtemisMain.java,v 1.22 2006-10-23 13:34:12 tjc Exp $
**/
public class ArtemisMain extends Splash
@@ -62,6 +63,9 @@ public class ArtemisMain extends Splash
private EntryEditVector entry_edit_objects = new EntryEditVector();
protected static FileManager filemanager = null;
+
+ private LocalAndRemoteFileManager fm;
+
/**
* The constructor creates all the components for the main Artemis
* window and sets up all the menu callbacks.
@@ -82,10 +86,8 @@ public class ArtemisMain extends Splash
};
makeMenuItem(file_menu, "Open File Manager ...", menu_listener);
-
ActionListener menu_listener_ssh = new ActionListener()
{
- private LocalAndRemoteFileManager fm;
public void actionPerformed(ActionEvent event)
{
if(fm == null)
@@ -94,7 +96,11 @@ public class ArtemisMain extends Splash
fm.setVisible(true);
}
};
- makeMenuItem(file_menu, "Open SSH File Manager ...", menu_listener_ssh);
+
+ if(System.getProperty("chado") != null)
+ makeMenuItem(file_menu, "Open Database and SSH File Manager ...", menu_listener_ssh);
+ else
+ makeMenuItem(file_menu, "Open SSH File Manager ...", menu_listener_ssh);
final EntrySourceVector entry_sources = getEntrySources(this);
@@ -134,12 +140,12 @@ public class ArtemisMain extends Splash
final boolean sanger_options =
Options.getOptions().getPropertyTruthValue("sanger_options");
- if(sanger_options)
+/* if(sanger_options)
{
makeMenuItem(file_menu, "Database Entry ...", menu_listener);
if(System.getProperty("chado") != null)
- launchDatabaseJFrame(false);
- }
+ fm = new LocalAndRemoteFileManager(ArtemisMain.this);
+ }*/
menu_listener = new ActionListener()
{
@@ -259,9 +265,14 @@ public class ArtemisMain extends Splash
if(!entry_source.setLocation(prompt_user))
return null;
- final DatabaseJFrame frame = new DatabaseJFrame(entry_source,
+ JFrame frame = new JFrame("Organism List");
+ final DatabaseJPanel pane = new DatabaseJPanel(entry_source,
ArtemisMain.this);
+ frame.getContentPane().add(pane);
+ frame.pack();
+ Utilities.rightJustifyFrame(frame);
frame.setVisible(true);
+ frame.setJMenuBar(pane.makeMenuBar(entry_source, ArtemisMain.this));
getStatusLabel().setText("");
return null;
}
diff --git a/uk/ac/sanger/artemis/components/database/DatabaseJFrame.java b/uk/ac/sanger/artemis/components/database/DatabaseJPanel.java
similarity index 81%
rename from uk/ac/sanger/artemis/components/database/DatabaseJFrame.java
rename to uk/ac/sanger/artemis/components/database/DatabaseJPanel.java
index 52b50161cbb2d9644cb55f11bbb1c7b0224f5e01..b21599debb8eda334dc0b0d647350b7fa8f1c4de 100644
--- a/uk/ac/sanger/artemis/components/database/DatabaseJFrame.java
+++ b/uk/ac/sanger/artemis/components/database/DatabaseJPanel.java
@@ -1,4 +1,4 @@
-/* DatabaseJFrame.java
+/* DatabaseJPanel.java
*
* created: June 2005
*
@@ -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/DatabaseJFrame.java,v 1.1 2006-10-18 14:25:23 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/database/DatabaseJPanel.java,v 1.1 2006-10-23 13:34:12 tjc Exp $
*/
package uk.ac.sanger.artemis.components.database;
@@ -29,12 +29,12 @@ import uk.ac.sanger.artemis.components.*;
import uk.ac.sanger.artemis.Entry;
import uk.ac.sanger.artemis.sequence.*;
+import uk.ac.sanger.artemis.util.InputStreamProgressEvent;
import uk.ac.sanger.artemis.util.InputStreamProgressListener;
import uk.ac.sanger.artemis.util.OutOfRangeException;
import uk.ac.sanger.artemis.util.DatabaseDocument;
import uk.ac.sanger.artemis.io.DatabaseDocumentEntry;
-import javax.swing.JFrame;
import javax.swing.JTree;
import javax.swing.JScrollPane;
import javax.swing.JSeparator;
@@ -60,16 +60,17 @@ import java.awt.Cursor;
import java.awt.FontMetrics;
import java.io.*;
-public class DatabaseJFrame extends JFrame
+public class DatabaseJPanel extends JPanel
{
private JLabel status_line = new JLabel("");
private boolean splitGFFEntry = false;
-
- public DatabaseJFrame(final DatabaseEntrySource entry_source,
- final Splash splash_main)
+ private JTree tree;
+
+ public DatabaseJPanel(final DatabaseEntrySource entry_source,
+ final Splash splash_main)
{
- super("Organism List");
- final JTree tree = entry_source.getDatabaseTree();
+ setLayout(new BorderLayout());
+ tree = entry_source.getDatabaseTree();
// Listen for when the selection changes.
MouseListener mouseListener = new MouseAdapter()
@@ -89,10 +90,7 @@ public class DatabaseJFrame extends JFrame
screen.height * 6 / 10);
scroll.setPreferredSize(dim_frame);
- setJMenuBar(makeMenuBar(entry_source, tree, splash_main));
-
- JPanel pane = (JPanel)getContentPane();
- pane.add(scroll, BorderLayout.CENTER);
+ add(scroll, BorderLayout.CENTER);
final FontMetrics fm = this.getFontMetrics(status_line.getFont());
@@ -105,16 +103,20 @@ public class DatabaseJFrame extends JFrame
Border compound = BorderFactory.createCompoundBorder(raisedbevel,
loweredbevel);
status_line.setBorder(compound);
- pane.add(status_line, BorderLayout.SOUTH);
-
- pack();
- Utilities.rightJustifyFrame(this);
+ add(status_line, BorderLayout.SOUTH);
+
+ JLabel title_line = new JLabel("Database List");
+ title_line.setMinimumSize(new Dimension(100, font_height));
+ title_line.setPreferredSize(new Dimension(100, font_height));
+ title_line.setBorder(compound);
+ add(title_line, BorderLayout.NORTH);
}
/**
- *
* Show the selected sequence in the tree
- *
+ * @param entry_source
+ * @param tree
+ * @param splash_main
*/
private void showSelected(final DatabaseEntrySource entry_source,
final JTree tree, final Splash splash_main)
@@ -141,9 +143,13 @@ public class DatabaseJFrame extends JFrame
}
/**
- *
* Retrieve a database entry.
- *
+ * @param id
+ * @param entry_source
+ * @param tree
+ * @param splash_main
+ * @param node_name
+ * @param schema
*/
private void getEntryEditFromDatabase(final String id,
final DatabaseEntrySource entry_source, final JTree tree,
@@ -161,13 +167,10 @@ public class DatabaseJFrame extends JFrame
tree.setCursor(cbusy);
try
{
- final InputStreamProgressListener progress_listener =
- splash_main.getInputStreamProgressListener();
-
entry_source.setSplitGFF(splitGFFEntry);
final Entry entry = entry_source.getEntry(id, schema,
- progress_listener);
+ stream_progress_listener);
DatabaseDocumentEntry db_entry =
@@ -228,8 +231,14 @@ public class DatabaseJFrame extends JFrame
}
- private JMenuBar makeMenuBar(final DatabaseEntrySource entry_source,
- final JTree tree, final Splash splash_main)
+ /**
+ * Create a menu bar
+ * @param entry_source
+ * @param splash_main
+ * @return
+ */
+ public JMenuBar makeMenuBar(final DatabaseEntrySource entry_source,
+ final Splash splash_main)
{
JMenuBar mBar = new JMenuBar();
JMenu fileMenu = new JMenu("File");
@@ -275,4 +284,26 @@ public class DatabaseJFrame extends JFrame
return mBar;
}
+
+ /**
+ * An InputStreamProgressListener used to update the error label with the
+ * current number of chars read.
+ **/
+ private final InputStreamProgressListener stream_progress_listener =
+ new InputStreamProgressListener()
+ {
+ public void progressMade(final InputStreamProgressEvent event)
+ {
+ final int char_count = event.getCharCount();
+ if(char_count == -1)
+ status_line.setText("");
+ else
+ status_line.setText("chars read so far: " + char_count);
+ }
+
+ public void progressMade(String progress)
+ {
+ status_line.setText(progress);
+ }
+ };
}
diff --git a/uk/ac/sanger/artemis/components/filetree/LocalAndRemoteFileManager.java b/uk/ac/sanger/artemis/components/filetree/LocalAndRemoteFileManager.java
index 88309a378847b81099e740a652a059e8a93eb10e..731b8e41a35cfae1e7482d9768c59d0239e12260 100644
--- a/uk/ac/sanger/artemis/components/filetree/LocalAndRemoteFileManager.java
+++ b/uk/ac/sanger/artemis/components/filetree/LocalAndRemoteFileManager.java
@@ -21,6 +21,8 @@
package uk.ac.sanger.artemis.components.filetree;
+import uk.ac.sanger.artemis.components.database.DatabaseEntrySource;
+import uk.ac.sanger.artemis.components.database.DatabaseJPanel;
import uk.ac.sanger.artemis.j2ssh.SshLogin;
import uk.ac.sanger.artemis.j2ssh.SshFileManager;
import uk.ac.sanger.artemis.util.StringVector;
@@ -28,6 +30,7 @@ import uk.ac.sanger.artemis.Options;
import javax.swing.table.TableColumn;
import javax.swing.*;
+
import java.io.File;
import java.io.FileFilter;
import java.awt.event.*;
@@ -59,7 +62,7 @@ public class LocalAndRemoteFileManager extends JFrame
*/
public LocalAndRemoteFileManager(JFrame frame, FileFilter filter)
{
- super("File Manager");
+ super();
final JPanel localPanel = new JPanel(new BorderLayout());
@@ -78,7 +81,7 @@ public class LocalAndRemoteFileManager extends JFrame
//
final Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
final Dimension panelSize = new Dimension((int)(screen.getWidth()/3),
- (int)(screen.getHeight()/3));
+ (int)(screen.getHeight()/4));
String remote_name = "";
final JLabel remote_status_line = getStatusLabel("");
@@ -109,9 +112,11 @@ public class LocalAndRemoteFileManager extends JFrame
});
bdown.add(connect);
- int ypos = panelSize.height-connect.getPreferredSize().height;
+ /*int ypos = panelSize.height-connect.getPreferredSize().height;
if(ypos>0)
- bdown.add(Box.createVerticalStrut(ypos/2));
+ bdown.add(Box.createVerticalStrut(ypos/2));*/
+ bdown.add(Box.createVerticalGlue());
+
remotePanel.add(bdown, BorderLayout.SOUTH);
remotePanel.setPreferredSize(panelSize);
}
@@ -127,13 +132,41 @@ public class LocalAndRemoteFileManager extends JFrame
treePane = new JSplitPane(JSplitPane.VERTICAL_SPLIT,
localPanel,remotePanel);
-
+ treePane.setOneTouchExpandable(true);
+
JPanel pane = (JPanel)getContentPane();
pane.setLayout(new BorderLayout());
- pane.add(treePane, BorderLayout.CENTER);
-
- treePane.setDividerLocation((int)(screen.getHeight()/3));
- setJMenuBar(makeMenuBar(pane,ftree,sshtree,localPanel,remotePanel,treePane,panelSize));
+
+ if(System.getProperty("chado") != null)
+ {
+ setTitle("Database and File Manager");
+ DatabaseEntrySource entry_source = new DatabaseEntrySource();
+ if(!entry_source.setLocation(true))
+ return;
+
+ JLabel label = new JLabel(" Database Loading...");
+ JScrollPane dbScroll = new JScrollPane(label);
+
+ DbConnectionThread dbthread =
+ new DbConnectionThread(dbScroll, panelSize, entry_source);
+ dbthread.start();
+ dbScroll.setPreferredSize(panelSize);
+
+ JSplitPane mainSplit = new JSplitPane(JSplitPane.VERTICAL_SPLIT,
+ dbScroll, treePane);
+ treePane.setDividerLocation((int)(screen.getHeight()/4));
+ mainSplit.setOneTouchExpandable(true);
+ mainSplit.setDividerLocation((int)(screen.getHeight()/4));
+ pane.add(mainSplit, BorderLayout.CENTER);
+ }
+ else
+ {
+ setTitle("File Manager");
+ pane.add(treePane, BorderLayout.CENTER);
+ treePane.setDividerLocation((int)(screen.getHeight()/4));
+ }
+ setJMenuBar(makeMenuBar(pane,ftree,sshtree,localPanel,
+ remotePanel,treePane,panelSize));
localPanel.add(getFileFileterComboBox(ftree), BorderLayout.SOUTH);
localTree.setPreferredSize(panelSize);
@@ -534,61 +567,33 @@ public class LocalAndRemoteFileManager extends JFrame
return path;
}
-
- class UpButton extends JButton
+
+
+ public class DbConnectionThread extends Thread
{
- public void paintComponent(Graphics g)
+ private JScrollPane dbScroll;
+ private Dimension panelSize;
+ private DatabaseEntrySource entry_source;
+
+ public DbConnectionThread(final JScrollPane dbScroll,
+ final Dimension panelSize,
+ final DatabaseEntrySource entry_source)
{
- super.paintComponent(g);
- Graphics2D g2 = (Graphics2D)g;
-
- g2.setColor(new Color(0,128,0));
- float loc1[][] = { {11,18}, {7,18}, {7,14},
- {3,14}, {11,4} };
-
- g2.fill(makeShape(loc1));
- g2.setColor(Color.green);
-
- float loc2[][] = { {11,18}, {15,18}, {15,14},
- {19,14}, {11,4} };
- g2.fill(makeShape(loc2));
-
- setSize(22,24);
+ this.dbScroll = dbScroll;
+ this.panelSize = panelSize;
+ this.entry_source = entry_source;
}
- }
- class TextButton extends JButton
- {
- private String s1;
- private String s2;
- private Color c;
-
- public TextButton(String text)
+ public void run()
{
- this(text, Color.black);
+ final DatabaseJPanel dbPane = new DatabaseJPanel(entry_source,
+ null);
+ dbPane.setPreferredSize(panelSize);
+ dbScroll.setViewportView(dbPane);
}
+ }
- public TextButton(String text, Color c)
- {
- super();
- this.s1 = text.substring(0);
- this.s2 = text.substring(1);
- }
- public void paintComponent(Graphics g)
- {
- super.paintComponent(g);
- Graphics2D g2 = (Graphics2D)g;
- Font font = new Font("Monospaced", Font.BOLD, 14);
- g2.setFont(font);
-
- g2.setColor(c);
- g2.drawString(s1,4,18);
- g2.setColor(Color.red);
- g2.drawString(s2,10,15);
- setSize(22,24);
- }
- }
public static void main(String args[])
@@ -612,5 +617,6 @@ public class LocalAndRemoteFileManager extends JFrame
frame.pack();
frame.setVisible(true);
}
+
}