From d52261d786e016d66515c001ef30f5728f05af54 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 20 Jul 2005 09:29:56 +0000
Subject: [PATCH] automatic hook-up to chado db with -Dchado option
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@3232 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../artemis/components/ArtemisMain.java | 44 ++++++++++++++-----
.../components/DatabaseEntrySource.java | 12 ++++-
.../artemis/io/SimpleDocumentEntry.java | 11 +----
3 files changed, 47 insertions(+), 20 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/ArtemisMain.java b/uk/ac/sanger/artemis/components/ArtemisMain.java
index 74a5564d2..95acf23b8 100644
--- a/uk/ac/sanger/artemis/components/ArtemisMain.java
+++ b/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 1.15 2005-06-22 19:39:41 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/ArtemisMain.java,v 1.16 2005-07-20 09:29:56 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
@@ -45,7 +45,7 @@ import java.io.*;
* The main window for the Artemis sequence editor.
*
* @author Kim Rutherford <kmr@sanger.ac.uk>
- * @version $Id: ArtemisMain.java,v 1.15 2005-06-22 19:39:41 tjc Exp $
+ * @version $Id: ArtemisMain.java,v 1.16 2005-07-20 09:29:56 tjc Exp $
**/
public class ArtemisMain extends Splash
@@ -107,13 +107,7 @@ public class ArtemisMain extends Splash
{
public void actionPerformed(ActionEvent event)
{
- DatabaseEntrySource entry_source = new DatabaseEntrySource();
- if(!entry_source.setLocation())
- return;
-
- final DatabaseJFrame frame = new DatabaseJFrame(entry_source,
- ArtemisMain.this);
- frame.setVisible(true);
+ launchDatabaseJFrame(true);
}
};
@@ -121,8 +115,12 @@ public class ArtemisMain extends Splash
Options.getOptions().getPropertyTruthValue("sanger_options");
if(sanger_options)
+ {
makeMenuItem(file_menu, "Database Entry ...", menu_listener);
-
+ if(System.getProperty("chado") != null)
+ launchDatabaseJFrame(false);
+ }
+
menu_listener = new ActionListener()
{
public void actionPerformed(ActionEvent event)
@@ -169,6 +167,32 @@ public class ArtemisMain extends Splash
// }
// }
+ /**
+ *
+ * Launch database manager window
+ *
+ */
+ private void launchDatabaseJFrame(final boolean prompt_user)
+ {
+ SwingWorker entryWorker = new SwingWorker()
+ {
+ public Object construct()
+ {
+ getStatusLabel().setText("Connecting ...");
+ DatabaseEntrySource entry_source = new DatabaseEntrySource();
+ if(!entry_source.setLocation(prompt_user))
+ return null;
+
+ final DatabaseJFrame frame = new DatabaseJFrame(entry_source,
+ ArtemisMain.this);
+ frame.setVisible(true);
+ getStatusLabel().setText("");
+ return null;
+ }
+ };
+ entryWorker.start();
+ }
+
/**
* Read the entries named in args and in the diana.ini file.
**/
diff --git a/uk/ac/sanger/artemis/components/DatabaseEntrySource.java b/uk/ac/sanger/artemis/components/DatabaseEntrySource.java
index 050c5f48b..03974a70a 100644
--- a/uk/ac/sanger/artemis/components/DatabaseEntrySource.java
+++ b/uk/ac/sanger/artemis/components/DatabaseEntrySource.java
@@ -123,7 +123,7 @@ public class DatabaseEntrySource implements EntrySource
* jdbc:postgresql://localhost:13001/chadoCVS?user=es2
*
*/
- protected boolean setLocation()
+ protected boolean setLocation(final boolean prompt_user)
{
Container bacross = new Container();
bacross.setLayout(new GridLayout(5,2,5,5));
@@ -165,6 +165,16 @@ public class DatabaseEntrySource implements EntrySource
{
inDB.setText(db_url.substring(index2+1,index3));
inUser.setText(db_url.substring(index3+1));
+
+ if(!prompt_user)
+ {
+ location = "jdbc:postgresql://"
+ +inServer.getText().trim()+ ":"
+ +inPort.getText().trim()+ "/"
+ +inDB.getText().trim()+ "?user="
+ +inUser.getText().trim();
+ return true;
+ }
}
}
}
diff --git a/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java b/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java
index 0eff47ed9..ec44d1455 100644
--- a/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java
+++ b/uk/ac/sanger/artemis/io/SimpleDocumentEntry.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/SimpleDocumentEntry.java,v 1.12 2005-06-03 16:04:18 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java,v 1.13 2005-07-20 09:29:56 tjc Exp $
*/
package uk.ac.sanger.artemis.io;
@@ -37,7 +37,7 @@ import java.util.Enumeration;
* This class contains the methods common to all DocumentEntry objects.
*
* @author Kim Rutherford <kmr@sanger.ac.uk>
- * @version $Id: SimpleDocumentEntry.java,v 1.12 2005-06-03 16:04:18 tjc Exp $
+ * @version $Id: SimpleDocumentEntry.java,v 1.13 2005-07-20 09:29:56 tjc Exp $
**/
abstract public class SimpleDocumentEntry
@@ -123,13 +123,6 @@ abstract public class SimpleDocumentEntry
while((new_line_group =
LineGroup.readNextLineGroup(pushback_reader)) != null)
{
-// if(document instanceof DatabaseDocument)
-// {
-// addLineGroup(new_line_group);
-// System.out.println("SimpleDocumentEntry DatabaseDocument ******************************");
-// if(new_line_group instanceof StreamSequence)
-// System.out.println("SimpleDocumentEntry StreamSequence ******************************");
-// }
if(new_line_group instanceof SimpleDocumentFeature)
{
final SimpleDocumentFeature new_feature =
--
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