diff --git a/uk/ac/sanger/ibatis/Cvterm.java b/uk/ac/sanger/ibatis/Cvterm.java
new file mode 100644
index 0000000000000000000000000000000000000000..85492e0c4f6408d0b9b0f07a8b2fb2ec2b376552
--- /dev/null
+++ b/uk/ac/sanger/ibatis/Cvterm.java
@@ -0,0 +1,53 @@
+/* Cvterm.java
+ *
+ * created: 2005
+ *
+ * This file is part of Artemis
+ *
+ * Copyright (C) 2005 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.ibatis;
+
+
+public class Cvterm
+{
+
+ private long id;
+ private String name;
+
+ public long getId()
+ {
+ return id;
+ }
+
+ public void setId(long id)
+ {
+ this.id = id;
+ }
+
+ public String getName()
+ {
+ return name;
+ }
+
+ public void setName(String name)
+ {
+ this.name = name;
+ }
+}
diff --git a/uk/ac/sanger/ibatis/DbSqlConfig.java b/uk/ac/sanger/ibatis/DbSqlConfig.java
new file mode 100644
index 0000000000000000000000000000000000000000..6c6b08e2f0f3eaf26c24631e22d7742202197695
--- /dev/null
+++ b/uk/ac/sanger/ibatis/DbSqlConfig.java
@@ -0,0 +1,78 @@
+/* DbSqlConfig.java
+ *
+ * created: 2005
+ *
+ * This file is part of Artemis
+ *
+ * Copyright (C) 2005 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.ibatis;
+
+import com.ibatis.sqlmap.client.SqlMapClient;
+import com.ibatis.sqlmap.client.SqlMapClientBuilder;
+import com.ibatis.common.resources.Resources;
+
+import java.util.Properties;
+import java.io.Reader;
+
+public class DbSqlConfig
+{
+
+ private static final SqlMapClient sqlMap;
+
+ static
+ {
+ try
+ {
+ String resource = "artemis_sqlmap/chado_iBatis_config.xml";
+ Reader reader = Resources.getResourceAsReader(resource);
+
+ Properties properties = null;
+ if(System.getProperty("chado") != null)
+ {
+ String url = System.getProperty("chado");
+ int index = url.indexOf("?");
+ properties = new Properties();
+
+ properties.put("chado", url.substring(0,index));
+ properties.put("username", url.substring(index+1));
+ }
+
+ sqlMap = SqlMapClientBuilder.buildSqlMapClient(reader,
+ properties);
+ }
+ catch(Exception e)
+ {
+ // If you get an error at this point, it doesnt matter what it was. It is going to be
+ // unrecoverable and we will want the app to blow up hard so we are aware of the
+ // problem. You should always log such errors and re-throw them in such a way that
+ // you can be made immediately aware of the problem.
+ e.printStackTrace();
+ throw new RuntimeException("Error initializing DbSqlConfig class. Cause: " + e);
+ }
+ }
+
+ public static SqlMapClient getSqlMapInstance()
+ {
+ return sqlMap;
+ }
+
+}
+
diff --git a/uk/ac/sanger/ibatis/Feature.java b/uk/ac/sanger/ibatis/Feature.java
new file mode 100644
index 0000000000000000000000000000000000000000..1d3511fb59818dfaa3e917bfdaddb6618104a71a
--- /dev/null
+++ b/uk/ac/sanger/ibatis/Feature.java
@@ -0,0 +1,191 @@
+/* Feature.java
+ *
+ * created: 2005
+ *
+ * This file is part of Artemis
+ *
+ * Copyright (C) 2005 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.ibatis;
+
+import java.util.Date;
+
+public class Feature
+{
+
+ /** feature id */
+ private int id;
+ /** id of the parent feature */
+ private String object_id;
+ /** time last changed */
+ private Date timelastmodified;
+ /** +1 or -1 depending if on the forward or reverse */
+ private int strand;
+ /** start position */
+ private int fmin;
+ /** end position */
+ private int fmax;
+ /** features unique name */
+ private String uniquename;
+ /** features name */
+ private String name;
+ /** features residues */
+ private byte[] residues;
+ /** feature type id */
+ private long type_id;
+ /** feature property type id */
+ private long prop_type_id;
+ /** feature description value */
+ private String value;
+ /** feature organism abbreviation */
+ private String abbreviation;
+
+
+ public int getId()
+ {
+ return id;
+ }
+
+ public void setId(int id)
+ {
+ this.id = id;
+ }
+
+ public String getObject_id()
+ {
+ return object_id;
+ }
+
+ public void setObject_id(String object_id)
+ {
+ this.object_id = object_id;
+ }
+
+ public Date getTimelastmodified()
+ {
+ return timelastmodified;
+ }
+
+ public void setTimelastmodified(Date timelastmodified)
+ {
+ this.timelastmodified = timelastmodified;
+ }
+
+ public int getStrand()
+ {
+ return strand;
+ }
+
+ public void setStrand(int strand)
+ {
+ this.strand = strand;
+ }
+
+ public int getFmin()
+ {
+ return fmin;
+ }
+
+ public void setFmin(int fmin)
+ {
+ this.fmin = fmin;
+ }
+
+ public int getFmax()
+ {
+ return fmax;
+ }
+
+ public void setFmax(int fmax)
+ {
+ this.fmax = fmax;
+ }
+
+ public String getUniquename()
+ {
+ return uniquename;
+ }
+
+ public void setUniquename(String uniquename)
+ {
+ this.uniquename = uniquename;
+ }
+
+ public String getName()
+ {
+ return name;
+ }
+
+ public void setName(String name)
+ {
+ this.name = name;
+ }
+
+ public byte[] getResidues()
+ {
+ return residues;
+ }
+
+ public void setResidues(byte[] residues)
+ {
+ this.residues = residues;
+ }
+
+ public long getType_id()
+ {
+ return type_id;
+ }
+
+ public void setType_id(long type_id)
+ {
+ this.type_id = type_id;
+ }
+
+ public long getProp_type_id()
+ {
+ return prop_type_id;
+ }
+
+ public void setProp_type_id(long prop_type_id)
+ {
+ this.prop_type_id = prop_type_id;
+ }
+
+ public String getValue()
+ {
+ return value;
+ }
+
+ public void setValue(String value)
+ {
+ this.value = value;
+ }
+
+ public String getAbbreviation()
+ {
+ return abbreviation;
+ }
+
+ public void setAbbreviation(String abbreviation)
+ {
+ this.abbreviation = abbreviation;
+ }
+
+}
diff --git a/uk/ac/sanger/ibatis/Organism.java b/uk/ac/sanger/ibatis/Organism.java
new file mode 100644
index 0000000000000000000000000000000000000000..8d77b7a68735d1338663a6c577d26b318603ee67
--- /dev/null
+++ b/uk/ac/sanger/ibatis/Organism.java
@@ -0,0 +1,98 @@
+/* Organism.java
+ *
+ * created: 2005
+ *
+ * This file is part of Artemis
+ *
+ * Copyright (C) 2005 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.ibatis;
+
+
+public class Organism
+{
+
+ private int id;
+ private String abbreviation;
+ private String genus;
+ private String species;
+ private String common_name;
+ private String comment;
+
+ public int getId()
+ {
+ return id;
+ }
+
+ public void setId(int id)
+ {
+ this.id = id;
+ }
+
+ public String getAbbreviation()
+ {
+ return abbreviation;
+ }
+
+ public void setAbbreviation(String abbreviation)
+ {
+ this.abbreviation = abbreviation;
+ }
+
+ public String getGenus()
+ {
+ return genus;
+ }
+
+ public void setGenus(String genus)
+ {
+ this.genus = genus;
+ }
+
+ public String getSpecies()
+ {
+ return species;
+ }
+
+ public void setSpecies(String species)
+ {
+ this.species = species;
+ }
+
+ public String getCommon_name()
+ {
+ return common_name;
+ }
+
+ public void setCommon_name(String common_name)
+ {
+ this.common_name = common_name;
+ }
+
+ public String getComment()
+ {
+ return comment;
+ }
+
+ public void setComment()
+ {
+ this.comment = comment;
+ }
+
+}