diff --git a/artemis_sqlmap/Feature.xml b/artemis_sqlmap/Feature.xml
index 97d468b53a93279549891eea4cac6f0cff5503c0..aef073ca6252daa25c5bd577657da64e7055392e 100644
--- a/artemis_sqlmap/Feature.xml
+++ b/artemis_sqlmap/Feature.xml
@@ -7,12 +7,12 @@
<sqlMap namespace="Feature">
- <parameterMap id="schema-cvlist" class="uk.ac.sanger.ibatis.SchemaCVList">
+ <parameterMap id="schema-cvlist" class="uk.ac.sanger.artemis.chado.SchemaCVList">
<parameter property="schema" javaType="java.lang.String"/>
<parameter property="cvlist" javaType="java.util.List"/>
</parameterMap>
- <resultMap id="select-feature-properties-result" class="uk.ac.sanger.ibatis.Feature">
+ <resultMap id="select-feature-properties-result" class="uk.ac.sanger.artemis.chado.ChadoFeature">
<result property="timelastmodified" column="timelastmodified"/>
<result property="id" column="id"/>
<result property="object_id" column="object_id"/>
@@ -26,7 +26,7 @@
<result property="phase" column="phase" nullValue="10"/>
</resultMap>
- <resultMap id="select-feature-result" class="uk.ac.sanger.ibatis.Feature">
+ <resultMap id="select-feature-result" class="uk.ac.sanger.artemis.chado.ChadoFeature">
<result property="id" column="id"/>
<result property="uniquename" column="uniquename"/>
<result property="name" column="name"/>
@@ -38,12 +38,12 @@
<result property="strand" column="strand" nullValue="0" />
</resultMap>
- <resultMap id="select-feature-sequence-result" class="uk.ac.sanger.ibatis.Feature">
+ <resultMap id="select-feature-sequence-result" class="uk.ac.sanger.artemis.chado.ChadoFeature">
<result property="name" column="name"/>
<result property="residues" column="residues"/>
</resultMap>
- <resultMap id="select-feature-with-residues-result" class="uk.ac.sanger.ibatis.Feature">
+ <resultMap id="select-feature-with-residues-result" class="uk.ac.sanger.artemis.chado.ChadoFeature">
<result property="abbreviation" column="abbreviation"/>
<result property="name" column="name"/>
<result property="id" column="feature_id"/>
@@ -52,7 +52,7 @@
<!-- get feature name -->
- <select id="getFeatureName" parameterClass="uk.ac.sanger.ibatis.Feature"
+ <select id="getFeatureName" parameterClass="uk.ac.sanger.artemis.chado.ChadoFeature"
resultClass="java.lang.String">
SELECT
name
@@ -68,7 +68,7 @@
</iterate>
</select>
- <select id="getGffLine" parameterClass="uk.ac.sanger.ibatis.Feature"
+ <select id="getGffLine" parameterClass="uk.ac.sanger.artemis.chado.ChadoFeature"
resultMap="select-feature-properties-result">
SELECT
timelastmodified,
@@ -99,7 +99,7 @@
ORDER BY f.type_id, uniquename
</select>
- <select id="getSequence" parameterClass="uk.ac.sanger.ibatis.Feature"
+ <select id="getSequence" parameterClass="uk.ac.sanger.artemis.chado.ChadoFeature"
resultMap="select-feature-sequence-result">
SELECT
name,
@@ -136,7 +136,7 @@
ORDER BY abbreviation
</select>
- <select id="getFeature" resultMap ="select-feature-result" parameterClass="uk.ac.sanger.ibatis.Feature">
+ <select id="getFeature" resultMap ="select-feature-result" parameterClass="uk.ac.sanger.artemis.chado.ChadoFeature">
SELECT
$schema$.feature.feature_id AS id,
uniquename,
diff --git a/uk/ac/sanger/artemis/chado/ChadoDAO.java b/uk/ac/sanger/artemis/chado/ChadoDAO.java
index 560840a542e7e73045f93e3deded2fba53d7973b..9d20a6ca42ecba82413aa5b440a1c336adb8d5c2 100644
--- a/uk/ac/sanger/artemis/chado/ChadoDAO.java
+++ b/uk/ac/sanger/artemis/chado/ChadoDAO.java
@@ -38,8 +38,8 @@ public interface ChadoDAO
* @param schema schema/organism name or null
*
*/
- public Feature getSequence(final int feature_id,
- final String schema)
+ public ChadoFeature getSequence(final int feature_id,
+ final String schema)
throws SQLException;
/**
@@ -91,7 +91,7 @@ public interface ChadoDAO
/**
*
- * Get available schemas (as a List of Feature objects).
+ * Get available schemas (as a List of ChadoFeature objects).
*
*/
public List getSchema()
diff --git a/uk/ac/sanger/artemis/chado/Feature.java b/uk/ac/sanger/artemis/chado/ChadoFeature.java
similarity index 99%
rename from uk/ac/sanger/artemis/chado/Feature.java
rename to uk/ac/sanger/artemis/chado/ChadoFeature.java
index 7127d5b8d2136da41caade1c9dd72226e475d55d..e4bbee52ed64ee72064aaa03ecfec7155a525634 100644
--- a/uk/ac/sanger/artemis/chado/Feature.java
+++ b/uk/ac/sanger/artemis/chado/ChadoFeature.java
@@ -1,4 +1,4 @@
-/* Feature.java
+/* ChadoFeature.java
*
* created: 2005
*
@@ -29,7 +29,7 @@ import java.util.Date;
import java.util.Hashtable;
import java.util.Vector;
-public class Feature
+public class ChadoFeature
{
/** schema */
diff --git a/uk/ac/sanger/artemis/chado/ChadoTransaction.java b/uk/ac/sanger/artemis/chado/ChadoTransaction.java
index fe8ba3f72d3ae6f3cd426f357df16f565c2fc33f..460e1ccd0d083feec01da1097d980531803225c7 100644
--- a/uk/ac/sanger/artemis/chado/ChadoTransaction.java
+++ b/uk/ac/sanger/artemis/chado/ChadoTransaction.java
@@ -35,12 +35,19 @@ import java.util.StringTokenizer;
**/
public class ChadoTransaction
{
+ //
+ // ATTRIBUTE TRANSACTIONS
/** update statement */
public static final int UPDATE = 1;
/** insert statement */
public static final int INSERT = 2;
/** delete statement */
public static final int DELETE = 3;
+
+ // FEATURE TRANSACTIONS
+ /** insert feature statement */
+ public static final int INSERT_FEATURE = 4;
+
/** properties store */
private List properties;
/** old properties store */
@@ -71,6 +78,17 @@ public class ChadoTransaction
this.chadoTable = chadoTable;
}
+ /**
+ *
+ * @param type transaction type
+ * @param uniquename uniquename of feature
+ *
+ */
+ public ChadoTransaction(int type, ChadoFeature new_feature)
+ {
+ this.type = type;
+ }
+
/**
*
*
@@ -144,7 +162,7 @@ public class ChadoTransaction
{
if(constraint == null)
constraint = new Vector();
- constraint.add(name+"="+"\'"+value+"\'");
+ constraint.add(name+"="+value);
}
@@ -183,7 +201,6 @@ public class ChadoTransaction
return propertiesName;
}
-
/**
*
* Get properties to this transaction that will be changed.
@@ -214,7 +231,6 @@ public class ChadoTransaction
return constraint;
}
-
/**
*
* Get uniquenames of features.
@@ -230,21 +246,26 @@ public class ChadoTransaction
}
return names;
-// String str_names[] = new String[names.size()];
-// for(int i=0; i<str_names.length; i++)
-// str_names[i] = (String)names.get(i);
-// return str_names;
}
+ /**
+ *
+ * Set the feature id
+ *
+ */
public void setFeature_id(final int feature_id)
{
this.feature_id = feature_id;
}
+ /**
+ *
+ * Get the feature id
+ *
+ */
public int getFeature_id()
{
return feature_id;
}
-
}
diff --git a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
index f8c6af39fb914557450dfe9dd3c7a52e82493747..a22fcf159a9a37eb2b82f1c7b78f5806dde27d98 100644
--- a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
+++ b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
@@ -146,7 +146,7 @@ public class ChadoTransactionManager
{
feature_uniquename = JOptionPane.showInputDialog(null,
"Provide a systematic_id : ",
- "systematic_id missing "+
+ "systematic_id missing in "+
feature.getIDString(),
JOptionPane.QUESTION_MESSAGE).trim();
}
@@ -161,7 +161,11 @@ public class ChadoTransactionManager
else
System.out.println("HERE feature_uniquename != null "+feature_uniquename);
-// ChadoTransaction tsn = new ChadoTransaction(ChadoTransaction.INSERT,
+/*
+
+ ChadoTransaction tsn = new ChadoTransaction(ChadoTransaction.INSERT_FEATURE,
+ feature);
+*/
}
diff --git a/uk/ac/sanger/artemis/chado/IBatisDAO.java b/uk/ac/sanger/artemis/chado/IBatisDAO.java
index 79497995ce7418587e755108a88762e9faa8556c..6374b8607adcb6325767ed7b97b03cc497d35272 100644
--- a/uk/ac/sanger/artemis/chado/IBatisDAO.java
+++ b/uk/ac/sanger/artemis/chado/IBatisDAO.java
@@ -42,7 +42,7 @@ public class IBatisDAO implements ChadoDAO
* Get feature name given the feature_id and schema
*
*/
- public String getFeatureName(final Feature feature)
+ public String getFeatureName(final ChadoFeature feature)
throws SQLException
{
SqlMapClient sqlMap = DbSqlConfig.getSqlMapInstance();
@@ -60,7 +60,7 @@ public class IBatisDAO implements ChadoDAO
final String schema)
throws SQLException
{
- Feature feature = new Feature();
+ ChadoFeature feature = new ChadoFeature();
feature.setId(feature_id);
if(schema != null)
feature.setSchema(schema);
@@ -81,7 +81,7 @@ public class IBatisDAO implements ChadoDAO
throws SQLException
{
SqlMapClient sqlMap = DbSqlConfig.getSqlMapInstance();
- Feature feature = new Feature();
+ ChadoFeature feature = new ChadoFeature();
feature.setId(feature_id);
if(schema != null)
feature.setSchema(schema);
@@ -99,16 +99,16 @@ public class IBatisDAO implements ChadoDAO
* @param schema schema/organism name or null
*
*/
- public Feature getSequence(final int feature_id,
+ public ChadoFeature getSequence(final int feature_id,
final String schema)
throws SQLException
{
SqlMapClient sqlMap = DbSqlConfig.getSqlMapInstance();
- Feature feature = new Feature();
+ ChadoFeature feature = new ChadoFeature();
feature.setId(feature_id);
if(schema != null)
feature.setSchema(schema);
- return (Feature)sqlMap.queryForObject("getSequence",
+ return (ChadoFeature)sqlMap.queryForObject("getSequence",
feature);
}
@@ -150,7 +150,7 @@ public class IBatisDAO implements ChadoDAO
/**
*
- * Get available schemas (as a List of Feature objects)
+ * Get available schemas (as a List of ChadoFeature objects)
*
*/
public List getSchema()
diff --git a/uk/ac/sanger/artemis/chado/JdbcDAO.java b/uk/ac/sanger/artemis/chado/JdbcDAO.java
index 32730b80d00e46490cd66e8a01553f50715fac87..8f9df8dadc62d758b2113017645d9441005402cc 100644
--- a/uk/ac/sanger/artemis/chado/JdbcDAO.java
+++ b/uk/ac/sanger/artemis/chado/JdbcDAO.java
@@ -58,7 +58,7 @@ public class JdbcDAO
return conn;
}
- public Feature getSequence(final int feature_id,
+ public ChadoFeature getSequence(final int feature_id,
final String schema)
throws SQLException
{
@@ -71,7 +71,7 @@ public class JdbcDAO
ResultSet rs = st.executeQuery(sql);
rs.next();
- Feature feature = new Feature();
+ ChadoFeature feature = new ChadoFeature();
feature.setName(rs.getString("name"));
feature.setResidues(rs.getBytes("residues"));
return feature;
@@ -135,7 +135,7 @@ public class JdbcDAO
List list = new Vector();
while(rs.next())
{
- Feature feature = new Feature();
+ ChadoFeature feature = new ChadoFeature();
feature.setFmin( rs.getInt("fmin") );
feature.setFmax( rs.getInt("fmax") );
feature.setType_id( rs.getLong("type_id") );
@@ -175,18 +175,18 @@ public class JdbcDAO
// merge same features in the list
int feature_size = list.size();
List flatten_list = new Vector();
- Feature featNext = null;
+ ChadoFeature featNext = null;
for(int i = 0; i < feature_size; i++)
{
- Feature feat = (Feature)list.get(i);
+ ChadoFeature feat = (ChadoFeature)list.get(i);
String name = feat.getUniquename();
feat.addQualifier(feat.getProp_type_id(),
feat.getValue());
if(i < feature_size - 1)
- featNext = (Feature)list.get(i + 1);
+ featNext = (ChadoFeature)list.get(i + 1);
// merge next line if part of the same feature
while(featNext != null && featNext.getUniquename().equals(name))
@@ -195,7 +195,7 @@ public class JdbcDAO
featNext.getValue());
i++;
if(i < feature_size - 1)
- featNext = (Feature)list.get(i + 1);
+ featNext = (ChadoFeature)list.get(i + 1);
else
break;
}
@@ -240,7 +240,7 @@ public class JdbcDAO
List list = new Vector();
while(rs.next())
{
- Feature feature = new Feature();
+ ChadoFeature feature = new ChadoFeature();
feature.setId( rs.getInt("feature_id") );
feature.setAbbreviation( rs.getString("abbreviation") );
feature.setName( rs.getString("name") );
@@ -279,7 +279,7 @@ public class JdbcDAO
/**
*
- * Get available schemas (as a List of Feature objects)
+ * Get available schemas (as a List of ChadoFeature objects)
*
*/
public List getSchema()
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index a922e773b6426d5258438f7a26e89d15c3642942..1d2bc059fabec3f9fac598648e81bb3b5eac3f50 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -370,7 +370,7 @@ public class DatabaseDocument extends Document
// build feature name store
for(int i = 0; i < feature_size; i++)
{
- Feature feat = (Feature)featList.get(i);
+ ChadoFeature feat = (ChadoFeature)featList.get(i);
String name = feat.getUniquename();
String feature_id = Integer.toString(feat.getId());
@@ -379,7 +379,7 @@ public class DatabaseDocument extends Document
for(int i = 0; i < feature_size; i++)
{
- Feature feat = (Feature)featList.get(i);
+ ChadoFeature feat = (ChadoFeature)featList.get(i);
int fmin = feat.getFmin() + 1;
int fmax = feat.getFmax();
long type_id = feat.getType_id();
@@ -536,7 +536,7 @@ public class DatabaseDocument extends Document
private ByteBuffer getSequence(ChadoDAO dao, ByteBuffer buff)
throws java.sql.SQLException
{
- Feature feature = dao.getSequence(Integer.parseInt(feature_id),
+ ChadoFeature feature = dao.getSequence(Integer.parseInt(feature_id),
schema);
buff.append("##FASTA\n>");
@@ -582,7 +582,7 @@ public class DatabaseDocument extends Document
Iterator it_residue_features = list_residue_features.iterator();
while(it_residue_features.hasNext())
{
- Feature feature = (Feature)it_residue_features.next();
+ ChadoFeature feature = (ChadoFeature)it_residue_features.next();
String org = feature.getAbbreviation();
String typeName = getCvtermName(feature.getType_id());
@@ -733,7 +733,7 @@ public class DatabaseDocument extends Document
DbSqlConfig.init(new JPasswordField());
SqlMapClient sqlMap = DbSqlConfig.getSqlMapInstance();
- Feature feature = new Feature();
+ ChadoFeature feature = new ChadoFeature();
feature.setId(Integer.parseInt(args[0]));
feature.setSchema(args[1]);
@@ -741,7 +741,7 @@ public class DatabaseDocument extends Document
for(int i = 0; i < featureList.size(); i++)
{
- feature = (Feature)featureList.get(i);
+ feature = (ChadoFeature)featureList.get(i);
int fmin = feature.getFmin() + 1;
int fmax = feature.getFmax();