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tjc authored
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8846 ee4ac58c-ac51-4696-9907-e4b3aa274f04
tjc authoredgit-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8846 ee4ac58c-ac51-4696-9907-e4b3aa274f04
EntryFileDialog.java 18.20 KiB
/* EntryFileDialog.java
*
* created: Mon Dec 7 1998
*
* This file is part of Artemis
*
* Copyright(C) 1998-2003 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/EntryFileDialog.java,v 1.12 2008-09-16 08:19:20 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
import uk.ac.sanger.artemis.Options;
import uk.ac.sanger.artemis.util.*;
import uk.ac.sanger.artemis.io.DatabaseDocumentEntry;
import uk.ac.sanger.artemis.io.Entry;
import uk.ac.sanger.artemis.io.DocumentEntryFactory;
import uk.ac.sanger.artemis.io.ReadFormatException;
import uk.ac.sanger.artemis.io.EntryInformation;
import uk.ac.sanger.artemis.io.EntryInformationException;
import uk.ac.sanger.artemis.io.DocumentEntry;
import uk.ac.sanger.artemis.io.ReadAndWriteEntry;
import java.io.*;
import javax.swing.*;
/**
* This class is a JFileChooser that can read EMBL Entry objects.
*
* @author Kim Rutherford
* @version $Id: EntryFileDialog.java,v 1.12 2008-09-16 08:19:20 tjc Exp $
**/
public class EntryFileDialog extends StickyFileChooser
{
/** */
private static final long serialVersionUID = 1L;
/** JFrame reference that was passed to the constructor. */
private JFrame owner = null;
/**
* Create a new EntryFileDialog component.
* @param owner The component where this dialog was created.
* @param sequence_only If true default to showing only file that have
* suffixes that suggest that the files contain sequence(eg. .embl,
* .seq, .dna). Of false show all files that can be read.
**/
public EntryFileDialog(final JFrame owner,
final boolean show_sequence_only)
{
super();
this.owner = owner;
setFileSelectionMode(JFileChooser.FILES_ONLY); setMultiSelectionEnabled(false);
final StringVector sequence_suffixes =
Options.getOptions().getOptionValues("sequence_file_suffixes");
final StringVector feature_suffixes =
Options.getOptions().getOptionValues("feature_file_suffixes");
final javax.swing.filechooser.FileFilter artemis_filter =
new javax.swing.filechooser.FileFilter()
{
public boolean accept(final File file)
{
if(file.isDirectory())
return true;
for(int i = 0; i<sequence_suffixes.size(); ++i)
{
final String this_suffix = (String)sequence_suffixes.elementAt(i);
if(file.getName().endsWith("." + this_suffix) ||
file.getName().endsWith("." + this_suffix + ".gz"))
return true;
}
for(int i = 0; i<feature_suffixes.size(); ++i)
{
final String this_suffix = (String)feature_suffixes.elementAt(i);
if(file.getName().endsWith("." + this_suffix) ||
file.getName().endsWith("." + this_suffix + ".gz"))
return true;
}
return false;
}
public String getDescription()
{
return "Artemis files";
}
};
final javax.swing.filechooser.FileFilter feature_filter =
new javax.swing.filechooser.FileFilter()
{
public boolean accept(final File file)
{
if(file.isDirectory())
return true;
for(int i = 0 ; i < feature_suffixes.size() ; ++i)
{
final String this_suffix = (String)feature_suffixes.elementAt(i);
if(file.getName().endsWith("." + this_suffix) ||
file.getName().endsWith("." + this_suffix + ".gz"))
return true;
}
return false;
}
public String getDescription()
{
return "Feature files";
}
};
final javax.swing.filechooser.FileFilter sequence_filter =
new javax.swing.filechooser.FileFilter() {
public boolean accept(final File file)
{
if(file.isDirectory())
return true;
for(int i = 0 ; i<sequence_suffixes.size() ; ++i)
{
final String this_suffix = (String)sequence_suffixes.elementAt(i);
if(file.getName().endsWith("." + this_suffix) ||
file.getName().endsWith("." + this_suffix + ".gz"))
return true;
}
return false;
}
public String getDescription()
{
return "Sequence files";
}
};
addChoosableFileFilter(artemis_filter);
addChoosableFileFilter(feature_filter);
addChoosableFileFilter(sequence_filter);
if(show_sequence_only)
setFileFilter(sequence_filter);
else
setFileFilter(artemis_filter);
}
/**
* Return an uk.ac.sanger.artemis.io.Entry object representing the file
* the user has selected with the dialog or null if the read failed for any
* reason.
* @param entry_information The EntryInformation to use when reading. This
* supplies the list of valid keys and qualifiers. If a key or qualifier
* is read that is incompatible with this EntryInformation object the
* EntryInformation will be changed to cope.
* @param listener The object to which InputStreamProgressEvents will be
* send while reading.
* @exception EntryInformationException Thrown if an Entry using the given
* EntryInformation object cannot contain the Key, Qualifier or
* Key/Qualifier combination of one of the features in the Document.
* @param show_progress If true a InputStreamProgressDialog will be shown
* while loading.
**/
public Entry getEntry(final EntryInformation entry_information,
final InputStreamProgressListener listener,
final boolean show_progress)
{
setDialogTitle("Select a file ...");
setDialogType(JFileChooser.OPEN_DIALOG);
SecurityManager sm = System.getSecurityManager();
System.setSecurityManager(null);
final int status = showOpenDialog(owner);
System.setSecurityManager(sm);
if(status != JFileChooser.APPROVE_OPTION ||
getSelectedFile() == null)
return null;
final File file = new File(getCurrentDirectory(),
getSelectedFile().getName());
return getEntryFromFile(owner, new FileDocument(file),
entry_information, show_progress);
}
/**
* This exists only to get around a bug in the 1.1/1.2 code generator,
* which generates unverifiable code.
* @param frame Used when creating MessageDialog components.
* @param file_document The Document to read the Entry from(should be made
* from entry_file).
* @param entry_information The EntryInformation to use when reading. This
* supplies the list of valid keys and qualifiers. If a key or qualifier
* is read that is incompatible with this EntryInformation object the
* EntryInformation will be changed to cope.
**/
private static Entry getEntryFromFileHelper(final JFrame frame,
final Document file_document,
final EntryInformation entry_information)
throws ReadFormatException, IOException
{
final LogReadListener read_event_logger =
new LogReadListener(file_document.getName());
final Entry new_entry;
try
{
new_entry =
DocumentEntryFactory.makeDocumentEntry(entry_information,
file_document,read_event_logger);
}
catch(EntryInformationException e)
{
throw new Error("internal error - unexpected exception: " + e);
}
if(read_event_logger.seenMessage())
{
final YesNoDialog yes_no_dialog = new YesNoDialog(frame,
"there were warnings while reading - view now?");
if(yes_no_dialog.getResult())
Splash.showLog();
}
return new_entry;
}
/**
* Read and return an Entry from the given File.
* @param frame Used when creating MessageDialog components.
* @param entry_file The file to read the Entry from.
* @param entry_information The EntryInformation to use when reading. This
* supplies the list of valid keys and qualifiers. If a key or qualifier
* is read that is incompatible with this EntryInformation object the
* EntryInformation will be changed to cope.
* @param listener The object to which InputStreamProgressEvents will be
* send while reading.
* @param show_progress If true a InputStreamProgressDialog will be shown
* while loading.
**/
public static Entry getEntryFromFile(final JFrame frame,
final Document entry_document,
final EntryInformation entry_information,
final boolean show_progress)
{
InputStreamProgressDialog progress_dialog = null;
if(show_progress) {
// XXX FIXME
// This doesn't work because getEntryFromFile() is called from the Swing
// thread so the Dialog never gets updated
progress_dialog =
new InputStreamProgressDialog(frame, "Reading ...",
"Reading from " +
entry_document.getName(), false);
final InputStreamProgressListener listener =
progress_dialog.getInputStreamProgressListener();
entry_document.addInputStreamProgressListener(listener);
}
try
{
return getEntryFromFileHelper(frame, entry_document,
entry_information);
}
catch(ReadFormatException e)
{
final String message =
"failed to open " + entry_document.getName() + ": " +
e.getMessage() +(e.getLineNumber() > 1 ?
" at line: " + e.getLineNumber() :
"");
System.out.println(message);
new MessageDialog(frame, message);
}
catch(FileNotFoundException e)
{
final String message =
"failed to open " + entry_document.getName() + ": file not found";
new MessageDialog(frame, message);
}
catch(IOException e)
{
final String message =
"failed to open " + entry_document.getName() + ": " + e.getMessage();
new MessageDialog(frame, message);
}
finally
{
if(progress_dialog != null)
progress_dialog.dispose();
}
return null;
}
/**
* Save the given entry, prompting for a file name if necessary.
* @param include_diana_extensions If true then the any diana additions to
* the embl file format will be included in the output, otherwise they
* will be removed. Also possible problems that would cause an entry to
* bounce from the EMBL submission process will be flagged if this is
* true.
* @param ask_for_name If true then always prompt for a new filename,
* otherwise prompt only when the entry name is not set.
* @param keep_new_name If ask_for_name is true a file will be written with
* the new name the user selects - if keep_new_name is true as well, then
* the entry will have it's name set to the new name, otherwise it will
* be used for this save and then discarded.
* @param destination_type Should be one of EMBL_FORMAT, GENBANK_FORMAT or
* ANY_FORMAT. If ANY_FORMAT then the Entry will be saved in the
* same format it was created, otherwise it will be saved in the given
* format.
**/
void saveEntry(final uk.ac.sanger.artemis.Entry entry, final boolean include_diana_extensions,
final boolean ask_for_name,
final boolean keep_new_name,
final int destination_type)
{
JCheckBox remoteSave = new JCheckBox("Ssh/Remote Save",
true);
File file = null;
try
{
if(ask_for_name || entry.getName() == null)
{
Box yBox = Box.createVerticalBox();
boolean useAccessory = false;
JCheckBox emblHeader = new JCheckBox("Add EMBL Header",
false);
setDialogTitle("Save to ...");
setDialogType(JFileChooser.SAVE_DIALOG);
if( destination_type == DocumentEntryFactory.EMBL_FORMAT &&
(entry.getHeaderText() == null ||
!isHeaderEMBL(entry.getHeaderText())) )
{
yBox.add(emblHeader);
useAccessory = true;
}
JCheckBox flattenGeneModel = new JCheckBox("Flatten Gene Model",
true);
if(((DocumentEntry)entry.getEMBLEntry()).getDocument()
instanceof RemoteFileDocument)
{
yBox.add(remoteSave);
useAccessory = true;
}
else if(entry.getEMBLEntry() instanceof DatabaseDocumentEntry)
{
yBox.add(flattenGeneModel);
useAccessory = true;
}
if(useAccessory)
setAccessory(yBox);
int status = showSaveDialog(owner);
if(status != JFileChooser.APPROVE_OPTION ||
getSelectedFile() == null)
return;
if(emblHeader.isSelected())
{
Box bdown = Box.createVerticalBox();
JTextField idField = new JTextField("");
bdown.add(idField);
int n = JOptionPane.showConfirmDialog(null, bdown,
"Enter the entry ID",
JOptionPane.OK_CANCEL_OPTION,
JOptionPane.QUESTION_MESSAGE);
if(n != JOptionPane.CANCEL_OPTION &&
!idField.getText().trim().equals(""))
{
String header = "ID "+idField.getText().trim();
if(entry.getFeatureCount() > 0) header = header.concat("\nFH Key "+
"Location/Qualifiers\nFH\n");
entry.setHeaderText(header);
}
}
file = new File(getCurrentDirectory(),
getSelectedFile().getName());
if(file.exists())
{
final YesNoDialog yes_no_dialog = new YesNoDialog(owner,
"this file exists: " + file.getName() +
" overwrite it?");
if(!yes_no_dialog.getResult())
return;
}
final MessageDialog message = new MessageDialog(owner,
"saving to " + file.getName() + " ...",
false);
try
{
if(entry.getEMBLEntry() instanceof DatabaseDocumentEntry)
ReadAndWriteEntry.writeDatabaseEntryToFile(entry, file,
flattenGeneModel.isSelected(), false, destination_type, owner);
else if(include_diana_extensions)
entry.save(file, destination_type, false);
else
entry.saveStandardOnly(file, destination_type, true);
}
catch(EntryInformationException e)
{
final YesNoDialog yes_no_dialog = new YesNoDialog(owner,
"destination format can't handle all " +
"keys/qualifiers - continue?");
if(yes_no_dialog.getResult())
{
try
{
if(entry.getEMBLEntry() instanceof DatabaseDocumentEntry)
ReadAndWriteEntry.writeDatabaseEntryToFile(entry, file,
flattenGeneModel.isSelected(), true, destination_type, null);
else if(include_diana_extensions)
entry.save(file, destination_type, true);
else
entry.saveStandardOnly(file, destination_type, true);
}
catch(EntryInformationException e2)
{
throw new Error("internal error - unexpected exception: "+ e);
}
}
else
return;
}
finally
{
if(message != null)
message.dispose();
}
if(keep_new_name)
entry.setName(file.getName());
}
else
{
final MessageDialog message = new MessageDialog(owner, "saving to " + entry.getName() + " ...",
false);
try
{
if(include_diana_extensions)
entry.save(destination_type);
else
entry.saveStandardOnly(destination_type);
}
finally
{
message.dispose();
}
}
}
catch(ReadOnlyException e)
{
new MessageDialog(owner, "this entry is read only");
return;
}
catch(IOException e)
{
new MessageDialog(owner, "error while saving: " + e);
return;
}
catch(EntryInformationException e)
{
new MessageDialog(owner, "error while saving: " + e);
return;
}
// save it back to ssh server
if(((DocumentEntry)entry.getEMBLEntry()).getDocument()
instanceof RemoteFileDocument &&
remoteSave.isSelected())
{
RemoteFileDocument node =
(RemoteFileDocument)(((DocumentEntry)entry.getEMBLEntry()).getDocument());
if(file == null)
file = new File( ((DocumentEntry)entry.getEMBLEntry()).getDocument().getLocation().toString() );
node.saveEntry(file);
}
}
/**
*
* Test for that the header of an EMBL entry begins
* with an ID line.
* @param header embl header
*
*/
private boolean isHeaderEMBL(String header)
{
StringReader reader = new StringReader(header);
BufferedReader buff_reader = new BufferedReader(reader);
try
{
if(!buff_reader.readLine().startsWith("ID"))
return false;
}
catch(IOException ioe){}
return true;
}
}