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

@@ -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.

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)
       {

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();
 

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);
+      }  
     }
   }
 }