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/* FileDialogEntrySource.java
*
* created: Thu Jun 8 2000
*
* 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/FileDialogEntrySource.java,v 1.1 2004-06-09 09:46:49 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
import uk.ac.sanger.artemis.*;
import uk.ac.sanger.artemis.sequence.*;
import uk.ac.sanger.artemis.util.*;
import uk.ac.sanger.artemis.io.EntryInformation;
import uk.ac.sanger.artemis.io.SimpleEntryInformation;
import javax.swing.JFrame;
/**
* This is an EntrySource that reads Entry objects from the local filesystem.
*
* @author Kim Rutherford <kmr@sanger.ac.uk>
* @version $Id: FileDialogEntrySource.java,v 1.1 2004-06-09 09:46:49 tjc Exp $
**/
public class FileDialogEntrySource
implements EntrySource
{
/**
* The component that created this FileEntrySource. (Used for requesters.)
**/
final JFrame frame;
/** InputStreamProgressEvents are sent to this object. */
private final InputStreamProgressListener stream_progress_listener;
/**
* Create a new FileDialogEntrySource.
* @param frame The component that created this FileDialogEntrySource.
* (Used for requesters.)
* @param listener InputStreamProgressEvent objects will be sent to this
* listener as progress on reading is made.
**/
public FileDialogEntrySource (final JFrame frame,
final InputStreamProgressListener listener)
{
this.frame = frame;
this.stream_progress_listener = listener;
}
/**
* Get an Entry object from this source (by reading from a file).
* @param bases The Bases object to pass to the Entry constructor.
* @exception OutOfRangeException Thrown if one of the features in
* the Entry is out of range of the Bases object.
* @param show_progress If true a InputStreamProgressDialog will be shown
* while loading.
* @return null if and only if the user cancels the read.
**/
public Entry getEntry(final Bases bases,
final ProgressThread progress_thread,
final boolean show_progress)
throws OutOfRangeException
{
try
{
return getEntryInternal(bases, progress_thread, show_progress);
}
catch (NoSequenceException e)
{
throw new Error ("internal error - unexpected exception: " + e);
}
}
/**
* Get an Entry object from this source (by reading from a file).
* @param bases The Bases object to pass to the Entry constructor.
* @exception OutOfRangeException Thrown if one of the features in
* the Entry is out of range of the Bases object.
* @param show_progress If true a InputStreamProgressDialog will be shown
* while loading.
* @return null if and only if the user cancels the read.
**/
public Entry getEntry (final Bases bases,
final boolean show_progress)
throws OutOfRangeException
{
try
{
return getEntryInternal (bases, null, show_progress);
}
catch (NoSequenceException e)
{
throw new Error ("internal error - unexpected exception: " + e);
}
}
/**
* Get an Entry object from this source (by reading from a file).
* @exception OutOfRangeException Thrown if one of the features in
* the Entry is out of range of the Bases object.
* @exception NoSequenceException Thrown if the entry that we read has no
* sequence.
* @param show_progress If true a InputStreamProgressDialog will be shown
* while loading.
* @return null if and only if the user cancels the read.
**/
public Entry getEntry (final boolean show_progress)
throws OutOfRangeException, NoSequenceException
{
return getEntryInternal (null, null, show_progress);
}
/**
* Get an Entry object from this source (by reading from a file).
* @exception OutOfRangeException Thrown if one of the features in
* the Entry is out of range of the Bases object.
* @exception NoSequenceException Thrown if the entry that we read has no
* sequence.
* @param show_progress If true a InputStreamProgressDialog will be shown
* while loading.
* @return null if and only if the user cancels the read.
**/
public Entry getEntry (final boolean show_progress,
final ProgressThread progress_thread)
throws OutOfRangeException, NoSequenceException
{
return getEntryInternal (null, progress_thread, show_progress);
}
/**
* Returns true if and only if this EntrySource always returns "full"
* entries. ie. entries that contain features and sequence. Entries that
* are read from a file may contain just features so in this class this
* method returns false.
**/
public boolean isFullEntrySource ()
{
return false;
}
//// change ArtemisMain.readArgsAndOptions () to use this?:
// /**
// * Get an Entry object from this source by name (by reading from a file).
// * @exception OutOfRangeException Thrown if one of the features in
// * embl_entry is out of range of the Bases object.
// * @exception NoSequenceException Thrown if the entry that we read has no
// * sequence.
// * @return null if and only if there is no Entry with that name.
// **/
// public Entry getEntryByName (final String entry_file_name)
// throws OutOfRangeException, NoSequenceException, IOException {
// final Document new_document =
// new FileProgressDocument (new File (entry_file_name),
// getInputStreamProgressListener ());
// final EntryInformation new_entry_information =
// new SimpleEntryInformation (Options.getArtemisEntryInformation ());
// boolean seen_error = false;
// while (true) {
// try {
// final uk.ac.sanger.artemis.io.Entry new_entry =
// DocumentEntryFactory.makeDocumentEntry (new_entry_information,
// new_document);
// return new Entry (new_entry);
// } catch (EntryInformationException e) {
// if (!seen_error) {
// final String message =
// "warning while reading " + entry_file_name + " - " +
// e.getMessage ();
// System.err.println (message);
// new MessageDialog (frame, message);
// seen_error = true;
// }
// EntryFileDialog.handleOpenException (new_entry_information, e);
// // go around the loop again
// }
// }
// }
/**
* Make a new Entry.
* @param bases The Bases object to pass to the Entry constructor. If null
* a new Bases object will be created.
* @exception OutOfRangeException Thrown if one of the features in
* the Entry is out of range of the Bases object.
* @exception NoSequenceException Thrown if bases is null and the Entry that
* we read has no sequence.
**/
private Entry makeEntry (final Bases bases,
final uk.ac.sanger.artemis.io.Entry embl_entry)
throws OutOfRangeException, NoSequenceException
{
if (bases == null)
return new Entry (embl_entry);
else
return new Entry (bases, embl_entry);
}
/**
* Return the InputStreamProgressListener that was passed to the
* constructor.
**/
public InputStreamProgressListener getInputStreamProgressListener ()
{
return stream_progress_listener;
}
/**
* Return the name of this source (for display to the user in menus).
**/
public String getSourceName ()
{
return "Filesystem";
}
/**
* Implementation of getEntry ().
* @param bases The Bases object to pass to the Entry constructor.
* @exception OutOfRangeException Thrown if one of the features in
* Entry is out of range of the Bases object.
* @exception NoSequenceException Thrown if bases is null and the entry that
* we read has no sequence.
* @param show_progress If true a InputStreamProgressDialog will be shown
* while loading.
* @return null if and only if the user cancels the read.
**/
private Entry getEntryInternal(final Bases bases,
final ProgressThread progress_thread,
final boolean show_progress)
throws OutOfRangeException, NoSequenceException
{
final EntryInformation new_entry_information =
new SimpleEntryInformation(Options.getArtemisEntryInformation());
EntryFileDialog dialog;
if(bases == null)
dialog = new EntryFileDialog(frame, true);
else
dialog = new EntryFileDialog(frame, false);
uk.ac.sanger.artemis.io.Entry new_embl_entry =
dialog.getEntry(new_entry_information, stream_progress_listener,
progress_thread, show_progress);
if(new_embl_entry == null)
return null;
return makeEntry(bases, new_embl_entry);
}
}