From f06e72c16c94b84230fd3e4cb18656f364a51ed6 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Wed, 26 Oct 2005 16:10:38 +0000
Subject: [PATCH] implement ssh file reading in act
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@3788 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/components/ActMain.java | 98 ++++++++++++-------
.../artemis/components/MultiComparator.java | 18 +++-
.../artemis/io/SimpleDocumentEntry.java | 15 ++-
.../sanger/artemis/util/DocumentFactory.java | 20 +++-
4 files changed, 108 insertions(+), 43 deletions(-)
diff --git a/uk/ac/sanger/artemis/components/ActMain.java b/uk/ac/sanger/artemis/components/ActMain.java
index dd1d8ced0..1fafc162d 100644
--- a/uk/ac/sanger/artemis/components/ActMain.java
+++ b/uk/ac/sanger/artemis/components/ActMain.java
@@ -20,11 +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/ActMain.java,v 1.7 2005-08-17 08:43:05 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/ActMain.java,v 1.8 2005-10-26 16:10:38 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
+import uk.ac.sanger.artemis.components.filetree.FileManager;
+import uk.ac.sanger.artemis.components.filetree.LocalAndRemoteFileManager;
import uk.ac.sanger.artemis.*;
import uk.ac.sanger.artemis.sequence.Bases;
import uk.ac.sanger.artemis.components.filetree.FileManager;
@@ -35,13 +37,14 @@ 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 1.7 2005-08-17 08:43:05 tjc Exp $
+ * @version $Id: ActMain.java,v 1.8 2005-10-26 16:10:38 tjc Exp $
**/
public class ActMain extends Splash
@@ -77,6 +80,20 @@ public class ActMain extends Splash
}
};
+ ActionListener menu_listener_ssh = new ActionListener()
+ {
+ private LocalAndRemoteFileManager fm;
+ public void actionPerformed(ActionEvent event)
+ {
+ if(fm == null)
+ fm = new LocalAndRemoteFileManager(ActMain.this);
+ else
+ fm.setVisible(true);
+ new ComparatorDialog(ActMain.this).setVisible(true);
+ }
+ };
+ makeMenuItem(file_menu, "Open SSH File Manager ...", menu_listener_ssh);
+
makeMenuItem(file_menu, "Quit", quit_listener);
}
@@ -116,40 +133,13 @@ public class ActMain extends Splash
new SimpleEntryInformation(Options.getArtemisEntryInformation());
final String this_file_name = file_names[i];
-
- final Document entry_document =
- DocumentFactory.makeDocument(this_file_name);
-
- if(progress_listener != null)
- entry_document.addInputStreamProgressListener(progress_listener);
-
- final uk.ac.sanger.artemis.io.Entry embl_entry =
- EntryFileDialog.getEntryFromFile(frame, entry_document,
- entry_information,
- false);
-
- // getEntryFromFile() has alerted the user so we just need to quit
- if(embl_entry == null)
- return null;
-
- final uk.ac.sanger.artemis.io.Sequence sequence =
- embl_entry.getSequence();
-
- if(sequence == null)
- {
- new MessageDialog(frame, "This file contains no sequence: " +
- this_file_name);
- return null;
- }
-
- final Bases embl_bases = new Bases(sequence);
- final EntryGroup entry_group = new SimpleEntryGroup(embl_bases);
-
+ File this_file = new File(this_file_name);
+
try
{
- final Entry entry = new Entry(entry_group.getBases(), embl_entry);
- entry_group.add(entry);
- entry_group_array[i / 2] = entry_group;
+ if(!openEntry(this_file_name, entry_group_array,
+ entry_information, i))
+ return null;
}
catch(OutOfRangeException e)
{
@@ -223,12 +213,52 @@ public class ActMain extends Splash
progress_thread.finished();
}
+ private boolean openEntry(String this_file_name, EntryGroup[] entry_group_array,
+ final EntryInformation entry_information, int i)
+ throws OutOfRangeException
+ {
+ final Document entry_document =
+ DocumentFactory.makeDocument(this_file_name);
+
+ if(progress_listener != null)
+ entry_document.addInputStreamProgressListener(progress_listener);
+
+ final uk.ac.sanger.artemis.io.Entry embl_entry =
+ EntryFileDialog.getEntryFromFile(frame, entry_document,
+ entry_information,
+ false);
+
+ // getEntryFromFile() has alerted the user so we just need to quit
+ if(embl_entry == null)
+ return false;
+
+ final uk.ac.sanger.artemis.io.Sequence sequence =
+ embl_entry.getSequence();
+
+ if(sequence == null)
+ {
+ new MessageDialog(frame, "This file contains no sequence: " +
+ this_file_name);
+ return false;
+ }
+
+ final Bases embl_bases = new Bases(sequence);
+ EntryGroup entry_group = new SimpleEntryGroup(embl_bases);
+ Entry entry = new Entry(entry_group.getBases(), embl_entry);
+
+ entry_group.add(entry);
+ entry_group_array[i / 2] = entry_group;
+ return true;
+ }
+
+
};
entryWorker.start();
return true;
}
+
/**
* Create a dialog that allow the user to the choose two files to compare
* and a file containing comparison data.
diff --git a/uk/ac/sanger/artemis/components/MultiComparator.java b/uk/ac/sanger/artemis/components/MultiComparator.java
index fc1ad94e3..2233b3a8a 100644
--- a/uk/ac/sanger/artemis/components/MultiComparator.java
+++ b/uk/ac/sanger/artemis/components/MultiComparator.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/MultiComparator.java,v 1.13 2005-08-17 08:43:05 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/MultiComparator.java,v 1.14 2005-10-26 16:10:38 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
@@ -28,6 +28,7 @@ package uk.ac.sanger.artemis.components;
import uk.ac.sanger.artemis.*;
import uk.ac.sanger.artemis.components.filetree.FileManager;
import uk.ac.sanger.artemis.components.filetree.FileNode;
+import uk.ac.sanger.artemis.util.RemoteFileDocument;
import uk.ac.sanger.artemis.util.FileDocument;
import uk.ac.sanger.artemis.util.OutOfRangeException;
import uk.ac.sanger.artemis.util.InputStreamProgressListener;
@@ -35,6 +36,7 @@ import uk.ac.sanger.artemis.io.EntryInformationException;
import uk.ac.sanger.artemis.io.DocumentEntryFactory;
import uk.ac.sanger.artemis.io.EntryInformation;
import uk.ac.sanger.artemis.io.SimpleEntryInformation;
+import uk.ac.sanger.artemis.io.DocumentEntry;
import java.awt.*;
import java.awt.event.*;
@@ -58,7 +60,7 @@ import javax.swing.border.BevelBorder;
* to keep them synchronized.
*
* @author Kim Rutherford <kmr@sanger.ac.uk>
- * @version $Id: MultiComparator.java,v 1.13 2005-08-17 08:43:05 tjc Exp $
+ * @version $Id: MultiComparator.java,v 1.14 2005-10-26 16:10:38 tjc Exp $
**/
public class MultiComparator extends JFrame
@@ -496,6 +498,18 @@ public class MultiComparator extends JFrame
try
{
entry.save(DocumentEntryFactory.ANY_FORMAT);
+
+ // save it back to ssh server
+ if(((DocumentEntry)entry.getEMBLEntry()).getDocument()
+ instanceof RemoteFileDocument)
+ {
+ RemoteFileDocument node =
+ (RemoteFileDocument)(((DocumentEntry)entry.getEMBLEntry()).getDocument());
+
+ File file = new File( ((DocumentEntry)entry.getEMBLEntry()).getDocument().toString() );
+ node.saveEntry(file);
+ }
+
}
catch(IOException e)
{
diff --git a/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java b/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java
index 44deb0848..be8a2474f 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 1.15 2005-10-11 14:20:31 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/SimpleDocumentEntry.java,v 1.16 2005-10-26 16:10:38 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 1.15 2005-10-11 14:20:31 tjc Exp $
+ * @version $Id: SimpleDocumentEntry.java,v 1.16 2005-10-26 16:10:38 tjc Exp $
**/
abstract public class SimpleDocumentEntry
@@ -1116,7 +1116,16 @@ abstract public class SimpleDocumentEntry
public void save(final Document document)
throws IOException
{
- final Writer out_file = document.getWriter();
+ final Writer out_file;
+ try
+ {
+ out_file = document.getWriter();
+ }
+ catch(NullPointerException npe)
+ {
+ return;
+ }
+
writeToStream(out_file);
out_file.close();
diff --git a/uk/ac/sanger/artemis/util/DocumentFactory.java b/uk/ac/sanger/artemis/util/DocumentFactory.java
index 35ca1fba1..1a48fff47 100644
--- a/uk/ac/sanger/artemis/util/DocumentFactory.java
+++ b/uk/ac/sanger/artemis/util/DocumentFactory.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/util/DocumentFactory.java,v 1.1 2004-06-09 09:52:58 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/util/DocumentFactory.java,v 1.2 2005-10-26 16:10:38 tjc Exp $
*/
package uk.ac.sanger.artemis.util;
@@ -28,11 +28,13 @@ package uk.ac.sanger.artemis.util;
import java.net.*;
import java.io.*;
+import uk.ac.sanger.artemis.components.filetree.RemoteFileNode;
+
/**
* A Factory for Document objects.
*
* @author Kim Rutherford <kmr@sanger.ac.uk>
- * @version $Id: DocumentFactory.java,v 1.1 2004-06-09 09:52:58 tjc Exp $
+ * @version $Id: DocumentFactory.java,v 1.2 2005-10-26 16:10:38 tjc Exp $
**/
public class DocumentFactory {
@@ -47,8 +49,18 @@ public class DocumentFactory {
} catch (MalformedURLException e) {
return new FileDocument (new File (source_string));
}
- } else {
- return new FileDocument (new File (source_string));
+ }
+ else
+ {
+ File file = new File (source_string);
+ if(file.exists()) // assume a local file
+ return new FileDocument(file);
+ else // assume a remote file
+ {
+ RemoteFileNode node = new RemoteFileNode("", file.getName(), null,
+ file.getParent(), false);
+ return new RemoteFileDocument(node);
+ }
}
}
}
--
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