From 4cfcb454419bf016fc833f104a796c788f2f0c22 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Fri, 21 Apr 2006 09:26:22 +0000
Subject: [PATCH] synonym retrieval from chado
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@4286 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/chado/Alias.java | 78 +++++++++++++++++++
uk/ac/sanger/artemis/chado/ChadoDAO.java | 17 ++--
uk/ac/sanger/artemis/chado/Dbxref.java | 3 +-
uk/ac/sanger/artemis/chado/IBatisDAO.java | 36 +++++++++
uk/ac/sanger/artemis/chado/JdbcDAO.java | 40 ++++++++++
uk/ac/sanger/artemis/io/GFFStreamFeature.java | 6 +-
.../sanger/artemis/util/DatabaseDocument.java | 16 ++++
7 files changed, 186 insertions(+), 10 deletions(-)
create mode 100644 uk/ac/sanger/artemis/chado/Alias.java
diff --git a/uk/ac/sanger/artemis/chado/Alias.java b/uk/ac/sanger/artemis/chado/Alias.java
new file mode 100644
index 000000000..1058556d9
--- /dev/null
+++ b/uk/ac/sanger/artemis/chado/Alias.java
@@ -0,0 +1,78 @@
+/*
+ *
+ * created: 2006
+ *
+ * This file is part of Artemis
+ *
+ * Copyright (C) 2006 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.chado;
+
+/**
+ * Alias GFF tags - values are stored in the synonym table and
+ * linked to feature via feature_synonym table.
+ */
+public class Alias
+{
+ private Integer feature_id;
+ private String name;
+ private String schema;
+ private String uniquename;
+
+ public String getSchema()
+ {
+ return schema;
+ }
+
+ public void setSchema(String schema)
+ {
+ this.schema = schema;
+ }
+
+ public String getUniquename()
+ {
+ return uniquename;
+ }
+
+ public void setUniquename(String uniquename)
+ {
+ this.uniquename = uniquename;
+ }
+
+ public Integer getFeature_id()
+ {
+ return feature_id;
+ }
+
+ public void setFeature_id(Integer feature_id)
+ {
+ this.feature_id = feature_id;
+ }
+
+ public String getName()
+ {
+ return name;
+ }
+
+ public void setName(String name)
+ {
+ this.name = name;
+ }
+
+}
diff --git a/uk/ac/sanger/artemis/chado/ChadoDAO.java b/uk/ac/sanger/artemis/chado/ChadoDAO.java
index 90642635b..9fead21aa 100644
--- a/uk/ac/sanger/artemis/chado/ChadoDAO.java
+++ b/uk/ac/sanger/artemis/chado/ChadoDAO.java
@@ -145,7 +145,6 @@ public interface ChadoDAO
/**
- *
* Get dbxref for a feature.
* @param schema the postgres schema name
* @param uniquename the unique name for the feature. If set to NULL
@@ -156,11 +155,21 @@ public interface ChadoDAO
public Hashtable getDbxref(final String schema, final String uniquename)
throws SQLException;
+ /**
+ * Get dbxref for a feature.
+ * @param schema the postgres schema name
+ * @param uniquename the unique name for the feature. If set to NULL
+ * all <code>Dbxref</code> are returned.
+ * @return a <code>Hashtable</code> of dbxrefs.
+ * @throws SQLException
+ */
+ public Hashtable getAlias(final String schema, final String uniquename)
+ throws SQLException;
+
//
// WRITE BACK
//
/**
- *
* Update attributes defined by the <code>ChadoTransaction</code>.
* @param schema schema/organism name or null
* @param tsn the <code>ChadoTransaction</code>
@@ -172,7 +181,6 @@ public interface ChadoDAO
throws SQLException;
/**
- *
* Insert attributes defined by the <code>ChadoTransaction</code>.
* @param schema schema/organism name or null
* @param tsn the <code>ChadoTransaction</code>
@@ -183,7 +191,6 @@ public interface ChadoDAO
throws SQLException;
/**
- *
* Delete attributes defined by the <code>ChadoTransaction</code>.
* @param schema schema/organism name or null
* @param tsn the <code>ChadoTransaction</code>
@@ -194,7 +201,6 @@ public interface ChadoDAO
throws SQLException;
/**
- *
* Insert a feature into the database defined by the <code>ChadoTransaction</code>.
* @param schema schema/organism name or null
* @param tsn the <code>ChadoTransaction</code>
@@ -207,7 +213,6 @@ public interface ChadoDAO
throws SQLException;
/**
- *
* Delete a feature from the database defined by the <code>ChadoTransaction</code>.
* @param schema schema/organism name or null
* @param tsn the <code>ChadoTransaction</code>
diff --git a/uk/ac/sanger/artemis/chado/Dbxref.java b/uk/ac/sanger/artemis/chado/Dbxref.java
index 6924e9f90..60ac5c987 100644
--- a/uk/ac/sanger/artemis/chado/Dbxref.java
+++ b/uk/ac/sanger/artemis/chado/Dbxref.java
@@ -26,7 +26,8 @@ package uk.ac.sanger.artemis.chado;
/**
*
- * Java Object used by ORM to represent the chado feature_dbxref table.
+ * Java Object used by ORM to represent the chado feature_dbxref,
+ * dbxref and db tables.
*
*/
public class Dbxref
diff --git a/uk/ac/sanger/artemis/chado/IBatisDAO.java b/uk/ac/sanger/artemis/chado/IBatisDAO.java
index 8664cea1b..42eab274a 100644
--- a/uk/ac/sanger/artemis/chado/IBatisDAO.java
+++ b/uk/ac/sanger/artemis/chado/IBatisDAO.java
@@ -268,6 +268,42 @@ public class IBatisDAO implements ChadoDAO
return JdbcDAO.mergeDbxref(list);
}
+ /**
+ * Get dbxref for a feature.
+ * @param schema the postgres schema name
+ * @param uniquename the unique name for the feature. If set to NULL
+ * all <code>Dbxref</code> are returned.
+ * @return a <code>Hashtable</code> of dbxrefs.
+ * @throws SQLException
+ */
+ public Hashtable getAlias(final String schema, final String uniquename)
+ throws SQLException
+ {
+ Alias alias = new Alias();
+ alias.setSchema(schema);
+ alias.setUniquename(uniquename);
+ SqlMapClient sqlMap = DbSqlConfig.getSqlMapInstance();
+ List list = sqlMap.queryForList("getAlias", alias);
+
+ Hashtable synonym = new Hashtable();
+ Integer feature_id;
+ Vector value;
+ for(int i=0; i<list.size(); i++)
+ {
+ alias = (Alias)list.get(i);
+ feature_id = alias.getFeature_id();
+ if(synonym.containsKey(feature_id))
+ value = (Vector)synonym.get(feature_id);
+ else
+ value = new Vector();
+
+ value.add(alias.getName());
+ synonym.put(feature_id, value);
+ }
+
+ return synonym;
+ }
+
/**
*
* @param name cvterm name
diff --git a/uk/ac/sanger/artemis/chado/JdbcDAO.java b/uk/ac/sanger/artemis/chado/JdbcDAO.java
index f61a973b9..cbed0a166 100644
--- a/uk/ac/sanger/artemis/chado/JdbcDAO.java
+++ b/uk/ac/sanger/artemis/chado/JdbcDAO.java
@@ -457,6 +457,46 @@ public class JdbcDAO
return mergeDbxref(dbxrefs);
}
+ /**
+ * Get dbxref for a feature.
+ * @param schema the postgres schema name
+ * @param uniquename the unique name for the feature. If set to NULL
+ * all synonyms are returned.
+ * @return a <code>Hashtable</code> of synonym values with the
+ * feature_id as the key.
+ * @throws SQLException
+ */
+ public Hashtable getAlias(final String schema, final String uniquename)
+ throws SQLException
+ {
+ String sql = "SELECT s.name, f.feature_id FROM "+schema+".feature_synonym fs "+
+ "LEFT JOIN "+schema+".feature f ON f.feature_id=fs.feature_id "+
+ "LEFT JOIN "+schema+".synonym s ON fs.synonym_id=s.synonym_id ";
+
+ if(uniquename != null)
+ sql = sql + "WHERE uniquename='"+uniquename+"'";
+
+ appendToLogFile(sql, sqlLog);
+ Statement st = conn.createStatement();
+ ResultSet rs = st.executeQuery(sql);
+ Hashtable synonym = new Hashtable();
+ Integer feature_id;
+ Vector value;
+ while(rs.next())
+ {
+ feature_id = new Integer(rs.getInt("feature_id"));
+ if(synonym.containsKey(feature_id))
+ value = (Vector)synonym.get(feature_id);
+ else
+ value = new Vector();
+
+ value.add(rs.getString("name"));
+ synonym.put(feature_id, value);
+ }
+
+ return synonym;
+ }
+
/**
* Get the time a feature was last modified.
* @param schema schema/organism name or null
diff --git a/uk/ac/sanger/artemis/io/GFFStreamFeature.java b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
index 0049e7d4f..4f9de2ee8 100644
--- a/uk/ac/sanger/artemis/io/GFFStreamFeature.java
+++ b/uk/ac/sanger/artemis/io/GFFStreamFeature.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/GFFStreamFeature.java,v 1.32 2006-04-12 12:22:13 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/io/GFFStreamFeature.java,v 1.33 2006-04-21 09:26:22 tjc Exp $
*/
package uk.ac.sanger.artemis.io;
@@ -39,7 +39,7 @@ import java.text.SimpleDateFormat;
* A StreamFeature that thinks it is a GFF feature.
*
* @author Kim Rutherford
- * @version $Id: GFFStreamFeature.java,v 1.32 2006-04-12 12:22:13 tjc Exp $
+ * @version $Id: GFFStreamFeature.java,v 1.33 2006-04-21 09:26:22 tjc Exp $
**/
public class GFFStreamFeature extends SimpleDocumentFeature
@@ -760,7 +760,7 @@ public class GFFStreamFeature extends SimpleDocumentFeature
att_values.add(rest_of_token);
}
- if(att_name.equals("Dbxref")) // convert to multi-line
+ if(att_name.equals("Dbxref") || att_name.equals("Alias")) // convert to multi-line
{
StringTokenizer stok =
new StringTokenizer((String)att_values.get(0), ",");
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index 1e16a921d..5440b4087 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -371,6 +371,9 @@ public class DatabaseDocument extends Document
// get all dbrefs
Hashtable dbxrefs = dao.getDbxref(schema, null);
+
+ // get all synonyms
+ Hashtable synonym = dao.getAlias(schema, null);
for(int i = 0; i < feature_size; i++)
{
@@ -463,6 +466,19 @@ public class DatabaseDocument extends Document
}
}
+ if(synonym != null &&
+ synonym.containsKey(new Integer(feature_id)))
+ {
+ this_buff.append(";Alias=");
+ Vector v_synonyms = (Vector)synonym.get(new Integer(feature_id));
+ for(int j=0; j<v_synonyms.size(); j++)
+ {
+ this_buff.append((String)v_synonyms.get(j));
+ if(j<v_synonyms.size()-1)
+ this_buff.append(",");
+ }
+ }
+
this_buff.append("\n");
progress_listener.progressMade("Read from database: " + name);
--
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