diff --git a/uk/ac/sanger/artemis/components/EntryFileDialog.java b/uk/ac/sanger/artemis/components/EntryFileDialog.java
index d12145421298122c8c3af1aa9e6090faa6a94904..7da09025dad24b6e322260654d722a10846b776e 100644
--- a/uk/ac/sanger/artemis/components/EntryFileDialog.java
+++ b/uk/ac/sanger/artemis/components/EntryFileDialog.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/EntryFileDialog.java,v 1.9 2008-06-23 13:53:46 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/EntryFileDialog.java,v 1.10 2008-07-04 15:21:05 tjc Exp $
*/
package uk.ac.sanger.artemis.components;
@@ -34,6 +34,7 @@ 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.*;
@@ -42,7 +43,7 @@ import javax.swing.*;
* This class is a JFileChooser that can read EMBL Entry objects.
*
* @author Kim Rutherford
- * @version $Id: EntryFileDialog.java,v 1.9 2008-06-23 13:53:46 tjc Exp $
+ * @version $Id: EntryFileDialog.java,v 1.10 2008-07-04 15:21:05 tjc Exp $
**/
public class EntryFileDialog extends StickyFileChooser
diff --git a/uk/ac/sanger/artemis/components/ReadAndWriteEntry.java b/uk/ac/sanger/artemis/components/ReadAndWriteEntry.java
deleted file mode 100644
index 2a68f618ed71c7ce063ae6656d12d1644964d5a6..0000000000000000000000000000000000000000
--- a/uk/ac/sanger/artemis/components/ReadAndWriteEntry.java
+++ /dev/null
@@ -1,219 +0,0 @@
-/* ReadAndWriteEntry.java
-
- * This file is part of Artemis
- *
- * Copyright(C) 2008 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.
- *
- */
-
-package uk.ac.sanger.artemis.components;
-
-import java.io.File;
-import java.io.IOException;
-
-import uk.ac.sanger.artemis.components.database.DatabaseEntrySource;
-import uk.ac.sanger.artemis.components.genebuilder.GeneUtils;
-import uk.ac.sanger.artemis.io.DocumentEntryFactory;
-import uk.ac.sanger.artemis.io.EntryInformation;
-import uk.ac.sanger.artemis.io.EntryInformationException;
-import uk.ac.sanger.artemis.io.Feature;
-import uk.ac.sanger.artemis.io.Key;
-import uk.ac.sanger.artemis.io.KeyVector;
-import uk.ac.sanger.artemis.io.Qualifier;
-import uk.ac.sanger.artemis.io.QualifierInfo;
-import uk.ac.sanger.artemis.io.QualifierInfoException;
-import uk.ac.sanger.artemis.io.QualifierVector;
-import uk.ac.sanger.artemis.sequence.NoSequenceException;
-import uk.ac.sanger.artemis.util.DatabaseDocument;
-import uk.ac.sanger.artemis.util.InputStreamProgressEvent;
-import uk.ac.sanger.artemis.util.InputStreamProgressListener;
-import uk.ac.sanger.artemis.util.OutOfRangeException;
-import uk.ac.sanger.artemis.Entry;
-import uk.ac.sanger.artemis.FeatureVector;
-import uk.ac.sanger.artemis.Options;
-
-class ReadAndWriteEntry
-{
-
- private static org.apache.log4j.Logger logger4j =
- org.apache.log4j.Logger.getLogger(ReadAndWriteEntry.class);
-
- /**
- * Read from the database, given a srcFeature uniquename
- * @param uniqueName
- * @return
- * @throws OutOfRangeException
- * @throws NoSequenceException
- * @throws IOException
- */
- public static Entry readEntryFromDatabase(final String uniqueName)
- throws OutOfRangeException, NoSequenceException, IOException
- {
- final DatabaseEntrySource entry_source = new DatabaseEntrySource();
- boolean promptUser = true;
- if(System.getProperty("read_only") != null)
- promptUser = false;
-
- if(!entry_source.setLocation(promptUser))
- return null;
-
- String url = (String)entry_source.getLocation();
- int index = url.indexOf("?");
-
- String userName = url.substring(index+1).trim();
- if(userName.startsWith("user="))
- userName = userName.substring(5);
-
- final String srcFeatureId = getFeatureId(entry_source, uniqueName);
-
- final InputStreamProgressListener stream_progress_listener =
- new InputStreamProgressListener()
- {
- public void progressMade(final InputStreamProgressEvent event)
- {
- final int char_count = event.getCharCount();
- if(char_count != -1)
- logger4j.debug("chars read so far: " + char_count);
- }
- public void progressMade(String progress)
- {
- logger4j.debug(progress);
- }
- };
- return entry_source.getEntry(srcFeatureId, userName,
- stream_progress_listener);
- }
-
- /**
- * Write entry to a file
- * @param entry
- * @param file
- * @param flatten Flatten the gene model and combine the qualifiers if true.
- * If false it will write all features and qualifiers out.
- * @param force invalid qualifiers and any features with invalid keys will
- * be quietly thrown away when saving.
- * @param destination_type Should be one of EMBL_FORMAT, GENBANK_FORMAT,
- * GFF_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.
- * @throws IOException
- * @throws EntryInformationException
- */
- public static void writeDatabaseEntryToFile(final Entry entry, final File file,
- final boolean flatten,
- final boolean force,
- final int destination_type)
- throws IOException, EntryInformationException
- {
- GeneUtils.lazyLoadAll(entry, null);
-
- EntryInformation artemis_entry_information = Options.getArtemisEntryInformation();
- if(!flatten)
- {
- final FeatureVector features = entry.getAllFeatures();
- for(int i=0; i<features.size(); i++)
- addAllKeysQualifiers(artemis_entry_information, features.elementAt(i).getEmblFeature());
- }
- entry.save(file, destination_type, force, artemis_entry_information);
- }
-
- /**
- * Add all keys and qualifiers for a given feature to the EntryInformation
- * @param entry_information
- * @param feature
- */
- private static void addAllKeysQualifiers(final EntryInformation entry_information,
- final Feature feature)
- {
- final Key new_key = feature.getKey();
- boolean keyAdded = false;
- if(!entry_information.isValidKey(new_key))
- {
- entry_information.addKey(new_key);
- keyAdded = true;
- }
-
- final QualifierVector feature_qualifiers = feature.getQualifiers();
-
- // check the qualifiers
- for(int i = 0 ; i < feature_qualifiers.size() ; ++i)
- {
- final Qualifier this_qualifier = (Qualifier)feature_qualifiers.elementAt(i);
- final String this_qualifier_name = this_qualifier.getName();
-
- if(!entry_information.isValidQualifier(this_qualifier_name) ||
- !entry_information.isValidQualifier(new_key, this_qualifier_name) ||
- keyAdded)
- {
- QualifierInfo qualifierInfo = entry_information.getQualifierInfo(this_qualifier_name);
-
- if(qualifierInfo == null)
- {
- KeyVector keys = new KeyVector();
- qualifierInfo = new QualifierInfo(this_qualifier_name, QualifierInfo.QUOTED_TEXT,
- keys, null, false);
- try
- {
- entry_information.addQualifierInfo(qualifierInfo);
- }
- catch(QualifierInfoException e)
- {
- e.printStackTrace();
- }
- }
-
- if(qualifierInfo.getValidKeys() != null)
- qualifierInfo.getValidKeys().add(new_key);
- }
- }
-
- }
-
- /**
- * Get feature id
- * @param entry_source
- * @param srcUniqueName
- * @return
- */
- public static String getFeatureId(
- final DatabaseEntrySource entry_source, final String srcUniqueName)
- {
- final DatabaseDocument doc = entry_source.getDatabaseDocument();
- org.gmod.schema.sequence.Feature feature = doc.getFeatureByUniquename(srcUniqueName);
- return Integer.toString(feature.getFeatureId());
- }
-
- public static void main(final String args[])
- {
- try
- {
- Entry entry = ReadAndWriteEntry.readEntryFromDatabase("Pf3D7_03");
- ReadAndWriteEntry.writeDatabaseEntryToFile(
- entry, new File("Pf3D7_03.flatten"), true, false,
- DocumentEntryFactory.EMBL_FORMAT);
-
- ReadAndWriteEntry.writeDatabaseEntryToFile(
- entry, new File("Pf3D7_03.not-flatten"), false, false,
- DocumentEntryFactory.EMBL_FORMAT);
- }
- catch(Exception e)
- {
- e.printStackTrace();
- }
- }
-
-}
\ No newline at end of file