From fdaa085fd08221c3a5bc7b97c291ec9e29b3d861 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Fri, 4 Jul 2008 15:18:55 +0000
Subject: [PATCH] read and write db entry
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@8104 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
.../sanger/artemis/io/ReadAndWriteEntry.java | 213 ++++++++++++++++++
1 file changed, 213 insertions(+)
create mode 100644 uk/ac/sanger/artemis/io/ReadAndWriteEntry.java
diff --git a/uk/ac/sanger/artemis/io/ReadAndWriteEntry.java b/uk/ac/sanger/artemis/io/ReadAndWriteEntry.java
new file mode 100644
index 000000000..8b3f93e92
--- /dev/null
+++ b/uk/ac/sanger/artemis/io/ReadAndWriteEntry.java
@@ -0,0 +1,213 @@
+/* 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.io;
+
+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.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;
+
+public 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)
+ {
+ Key new_key = feature.getKey();
+
+ new_key = PublicDBDocumentEntry.mapKeys(new_key);
+
+ 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();
+ }
+ System.exit(0);
+ }
+
+}
\ No newline at end of file
--
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