diff --git a/artemis_sqlmap/Cvterm.xml b/artemis_sqlmap/Cvterm.xml
index 87c6694c5d0d6c9b76947e74e7a79b0be01f3cef..0fe20fb9b7338c9eac9650a0e20ca10687fc9ff7 100644
--- a/artemis_sqlmap/Cvterm.xml
+++ b/artemis_sqlmap/Cvterm.xml
@@ -7,13 +7,13 @@
<sqlMap namespace="Cvterm">
- <resultMap id="select-cvterm-names-result" class="uk.ac.sanger.artemis.chado.ChadoCvterm">
+ <resultMap id="select-cvterm-names-result" class="uk.ac.sanger.artemis.chado.Cvterm">
<result property="cvtermId" column="cvterm_id"/>
<result property="name" column="cvterm_name"/>
<result property="cv.name" column="cv_name"/>
</resultMap>
- <resultMap id="lazy-cvterm" class="uk.ac.sanger.artemis.chado.ChadoCvterm">
+ <resultMap id="lazy-cvterm" class="uk.ac.sanger.artemis.chado.Cvterm">
<result property="cvtermId" column="cvterm_id"/>
<result property="name" column="name"/>
<result property="definition" column="definition"/>
diff --git a/artemis_sqlmap/Dbxref.xml b/artemis_sqlmap/Dbxref.xml
index a9e4924bc3ff5c22c72cef03460b31c1a497cadc..b2da012b28745336f7f41c049a5619acc0f3a5a5 100644
--- a/artemis_sqlmap/Dbxref.xml
+++ b/artemis_sqlmap/Dbxref.xml
@@ -7,17 +7,17 @@
<sqlMap namespace="Dbxref">
- <typeAlias alias="ChadoFeatureDbxref"
- type="uk.ac.sanger.artemis.chado.ChadoFeatureDbxref"/>
+ <typeAlias alias="FeatureDbxref"
+ type="uk.ac.sanger.artemis.chado.FeatureDbxref"/>
- <typeAlias alias="ChadoDbxref"
- type="uk.ac.sanger.artemis.chado.ChadoDbxref"/>
+ <typeAlias alias="Dbxref"
+ type="uk.ac.sanger.artemis.chado.Dbxref"/>
- <typeAlias alias="ChadoDb"
- type="uk.ac.sanger.artemis.chado.ChadoDb"/>
+ <typeAlias alias="Db"
+ type="uk.ac.sanger.artemis.chado.Db"/>
<resultMap id="select-feature-dbxref"
- class="ChadoFeatureDbxref">
+ class="FeatureDbxref">
<result property="feature_id" column="feature_id"/>
<result property="dbxref.db.name" column="name"/>
<result property="dbxref.accession" column="accession"/>
@@ -25,7 +25,7 @@
</resultMap>
<select id="getFeatureDbxref"
- parameterClass="uk.ac.sanger.artemis.chado.ChadoFeature"
+ parameterClass="uk.ac.sanger.artemis.chado.Feature"
resultMap="select-feature-dbxref">
SELECT db.name, dbx.accession, dbx.version, dbx_f.feature_id
FROM feature_dbxref dbx_f
@@ -41,12 +41,12 @@
ORDER BY f.type_id, uniquename
</select>
- <select id="getDbId" parameterClass="ChadoDb"
+ <select id="getDbId" parameterClass="Db"
resultClass="java.lang.Integer">
SELECT db_id FROM db WHERE name=#name#
</select>
- <select id="getDbxrefId" parameterClass="ChadoDbxref"
+ <select id="getDbxrefId" parameterClass="Dbxref"
resultClass="java.lang.Integer">
SELECT dbxref_id FROM dbxref WHERE accession=#accession#
AND db_id=$db_id$;
@@ -54,14 +54,14 @@
- <select id="selectDbxref" resultClass="ChadoDbxref">
+ <select id="selectDbxref" resultClass="Dbxref">
SELECT * FROM dbxref WHERE dbxref_id=$dbxref_id$
</select>
<!-- WRITE BACK -->
- <delete id="deleteFeatureDbxref" parameterClass="ChadoFeatureDbxref">
+ <delete id="deleteFeatureDbxref" parameterClass="FeatureDbxref">
DELETE FROM feature_dbxref
WHERE dbxref_id=
(SELECT dbxref_id FROM dbxref WHERE accession=#dbxref.accession#
@@ -69,14 +69,14 @@
AND feature_id=$feature_id$
</delete>
- <insert id="insertFeatureDbxref" parameterClass="ChadoFeatureDbxref">
+ <insert id="insertFeatureDbxref" parameterClass="FeatureDbxref">
INSERT INTO feature_dbxref
(feature_id, dbxref_id, is_current)
VALUES
($feature_id$, $dbxref_id$, $current$)
</insert>
- <insert id="insertDbxref" parameterClass="ChadoDbxref">
+ <insert id="insertDbxref" parameterClass="Dbxref">
INSERT INTO dbxref ( db_id, accession )
VALUES ($db_id$, #accession#)
</insert>
diff --git a/artemis_sqlmap/Feature.xml b/artemis_sqlmap/Feature.xml
index 0ab5a1ccbfb5a281e06ded6bf49a56a3f9f25613..337577809e290d2955dd03231c94f6bc6c867bbe 100644
--- a/artemis_sqlmap/Feature.xml
+++ b/artemis_sqlmap/Feature.xml
@@ -7,20 +7,20 @@
<sqlMap namespace="Feature">
- <typeAlias alias="ChadoFeature"
- type="uk.ac.sanger.artemis.chado.ChadoFeature"/>
+ <typeAlias alias="Feature"
+ type="uk.ac.sanger.artemis.chado.Feature"/>
<typeAlias alias="ChadoTransaction"
type="uk.ac.sanger.artemis.chado.ChadoTransaction"/>
<parameterMap id="schema-cvlist"
- class="ChadoFeature">
+ class="Feature">
<parameter property="schema" javaType="java.lang.String"/>
<parameter property="featureCvterms" javaType="java.util.List"/>
</parameterMap>
<resultMap id="select-feature"
- class="ChadoFeature">
+ class="Feature">
<result property="timelastmodified" column="timelastmodified"/>
<result property="id" column="id"/>
<result property="feature_relationship.object_id" column="object_id"/>
@@ -40,7 +40,7 @@
<!-- mapping for feature table and lazy loading of feature_dbxref, feature_relationship,
featureprop, organism tables -->
<resultMap id="select-feature-lazy"
- class="ChadoFeature">
+ class="Feature">
<result property="timelastmodified" column="timelastmodified"/>
<result property="id" column="id"/>
<result property="uniquename" column="uniquename"/>
@@ -65,7 +65,7 @@
<resultMap id="select-feature-with-residues-result"
- class="ChadoFeature">
+ class="Feature">
<result property="organism.abbreviation" column="abbreviation"/>
<result property="name" column="name"/>
<result property="uniquename" column="uniquename"/>
@@ -74,14 +74,14 @@
</resultMap>
<resultMap id="select-featureprop"
- class="uk.ac.sanger.artemis.chado.ChadoFeatureProp">
+ class="uk.ac.sanger.artemis.chado.FeatureProp">
<result property="value" column="value" />
<result property="rank" column="rank" />
<result property="cvterm" column="type_id" select="selectCvterm" />
</resultMap>
<resultMap id="select-relationship"
- class="uk.ac.sanger.artemis.chado.ChadoFeatureRelationship">
+ class="uk.ac.sanger.artemis.chado.FeatureRelationship">
<result property="subject_id" column="subject_id" />
<result property="object_id" column="object_id" />
<result property="value" column="value" />
@@ -90,7 +90,7 @@
</resultMap>
<resultMap id="select-location"
- class="uk.ac.sanger.artemis.chado.ChadoFeatureLoc">
+ class="uk.ac.sanger.artemis.chado.FeatureLoc">
<result property="srcfeature_id" column="srcfeature_id" nullValue="-999" />
<result property="fmin" column="fmin" nullValue="-999" />
<result property="fmax" column="fmax" nullValue="-999" />
@@ -136,7 +136,7 @@
<!-- get feature id -->
<select id="getFeatureID" parameterClass="ChadoTransaction"
- resultClass="ChadoFeature">
+ resultClass="Feature">
SELECT feature_id AS id, uniquename FROM feature WHERE
<dynamic>
<isNotNull property="uniquename">
@@ -159,7 +159,7 @@
</dynamic>
</select>
- <select id="getFeature" parameterClass="ChadoFeature"
+ <select id="getFeature" parameterClass="Feature"
resultMap="select-feature">
SELECT
timelastmodified,
@@ -193,7 +193,7 @@
</select>
<select id="getLazyFeature" resultMap ="select-feature-lazy"
- parameterClass="ChadoFeature">
+ parameterClass="Feature">
SELECT
timelastmodified,
f.feature_id AS id,
@@ -258,7 +258,7 @@
<select id="getOrganismID" resultClass="java.lang.Integer"
- parameterClass="ChadoFeature">
+ parameterClass="Feature">
SELECT organism_id FROM feature f WHERE
f.feature_id=$featureloc.srcfeature_id$
</select>
@@ -327,7 +327,7 @@
</delete>
<insert id="insertFeature"
- parameterClass="ChadoFeature">
+ parameterClass="Feature">
INSERT INTO feature
( feature_id, organism_id, name, uniquename, type_id )
VALUES
@@ -339,7 +339,7 @@
</insert>
<insert id="insertFeatureLoc"
- parameterClass="ChadoFeature">
+ parameterClass="Feature">
INSERT INTO featureloc
( featureloc_id, feature_id, srcfeature_id, fmin, fmax, strand, phase )
VALUES
@@ -353,13 +353,13 @@
</insert>
<delete id="deleteFeature"
- parameterClass="ChadoFeature">
+ parameterClass="Feature">
DELETE FROM feature
WHERE uniquename=#uniquename#
</delete>
<insert id="insertFeatureRelationship"
- parameterClass="ChadoFeature">
+ parameterClass="Feature">
INSERT INTO feature_relationship
( subject_id, object_id, type_id )
VALUES
diff --git a/artemis_sqlmap/Organism.xml b/artemis_sqlmap/Organism.xml
index 898724b4f7d92015206ac8380977772beca243fa..1f8cd895db66a6e498492d7a4dbe53054f4af005 100644
--- a/artemis_sqlmap/Organism.xml
+++ b/artemis_sqlmap/Organism.xml
@@ -6,7 +6,7 @@
<sqlMap namespace="Organism">
- <select id="getOrganism" resultClass="uk.ac.sanger.artemis.chado.ChadoOrganism">
+ <select id="getOrganism" resultClass="uk.ac.sanger.artemis.chado.Organism">
SELECT organism_id AS id, abbreviation, genus, species, common_name, comment
FROM organism
WHERE organism_id=#value#
diff --git a/artemis_sqlmap/Synonym.xml b/artemis_sqlmap/Synonym.xml
index 1838f7d25a12c1b169ea04e160d60f9c4dcc8d68..d993e7eca38cd87c6b97db7e43ecbb28cd5efd50 100644
--- a/artemis_sqlmap/Synonym.xml
+++ b/artemis_sqlmap/Synonym.xml
@@ -7,14 +7,14 @@
<sqlMap namespace="Synonym">
- <typeAlias alias="ChadoFeatureSynonym"
- type="uk.ac.sanger.artemis.chado.ChadoFeatureSynonym"/>
+ <typeAlias alias="FeatureSynonym"
+ type="uk.ac.sanger.artemis.chado.FeatureSynonym"/>
- <typeAlias alias="ChadoSynonym"
- type="uk.ac.sanger.artemis.chado.ChadoSynonym"/>
+ <typeAlias alias="Synonym"
+ type="uk.ac.sanger.artemis.chado.Synonym"/>
<resultMap id="select-alias"
- class="ChadoFeatureSynonym">
+ class="FeatureSynonym">
<result property="feature_id" column="feature_id"/>
<result property="synonym_id" column="synonym_id"/>
<result property="pub_id" column="pub_id"/>
@@ -27,7 +27,7 @@
</resultMap>
<resultMap id="select-alias-part-lazy"
- class="ChadoFeatureSynonym">
+ class="FeatureSynonym">
<result property="feature_id" column="feature_id"/>
<result property="synonym_id" column="synonym_id"/>
<result property="pub_id" column="pub_id"/>
@@ -37,7 +37,7 @@
</resultMap>
<resultMap id="select-alias-lazy"
- class="ChadoFeatureSynonym">
+ class="FeatureSynonym">
<result property="feature_id" column="feature_id"/>
<result property="pub_id" column="pub_id"/>
<result property="current" column="is_current"/>
@@ -46,7 +46,7 @@
</resultMap>
<resultMap id="select-synonym-lazy"
- class="ChadoSynonym">
+ class="Synonym">
<result property="synonym_id" column="synonym_id"/>
<result property="name" column="name"/>
<result property="synonym_sgml" column="synonym_sgml"/>
@@ -57,7 +57,7 @@
<!-- SQL -->
<select id="getFeatureSynonymsByUniquename" resultMap="select-alias"
- parameterClass="ChadoFeature">
+ parameterClass="Feature">
SELECT fs.*, s.name, s.synonym_sgml, s.type_id
FROM feature_synonym fs
LEFT JOIN feature f ON f.feature_id=fs.feature_id
@@ -68,7 +68,7 @@
</select>
<select id="getLazyFeatureSynonymsByUniquename" resultMap="select-alias-part-lazy"
- parameterClass="ChadoFeatureSynonym">
+ parameterClass="FeatureSynonym">
SELECT fs.*
FROM feature_synonym fs
LEFT JOIN feature f ON f.feature_id=fs.feature_id
@@ -78,15 +78,15 @@
</select>
<select id="getFeatureSynonymsByName" resultMap="select-alias-lazy"
- parameterClass="ChadoSynonym">
+ parameterClass="Synonym">
SELECT * FROM feature_synonym
WHERE
synonym_id=(SELECT synonym_id FROM synonym WHERE
name=#name#) AND is_current
</select>
- <select id="getSynonymByNameAndType" resultClass="ChadoSynonym"
- parameterClass="ChadoSynonym">
+ <select id="getSynonymByNameAndType" resultClass="Synonym"
+ parameterClass="Synonym">
SELECT * FROM synonym WHERE
<isNotNull property="name">
name=#name# AND
@@ -104,25 +104,25 @@
<!-- WRITE BACK -->
- <delete id="deleteFeatureAlias" parameterClass="ChadoFeatureSynonym">
+ <delete id="deleteFeatureAlias" parameterClass="FeatureSynonym">
DELETE FROM feature_synonym WHERE
synonym_id=$synonym_id$ AND
feature_id=(SELECT feature_id FROM feature WHERE
uniquename=#uniquename#)
</delete>
- <insert id="insertFeatureAlias" parameterClass="ChadoFeatureSynonym">
+ <insert id="insertFeatureAlias" parameterClass="FeatureSynonym">
INSERT INTO feature_synonym ( synonym_id, feature_id, pub_id )
VALUES ( $synonym_id$ ,
(SELECT feature_id FROM feature WHERE uniquename=#uniquename#),
1)
</insert>
- <delete id="deleteAlias" parameterClass="ChadoFeatureSynonym">
+ <delete id="deleteAlias" parameterClass="FeatureSynonym">
DELETE FROM synonym WHERE synonym_id=$synonym_id$
</delete>
- <insert id="insertAlias" parameterClass="ChadoFeatureSynonym">
+ <insert id="insertAlias" parameterClass="FeatureSynonym">
INSERT INTO synonym ( name, type_id, synonym_sgml )
VALUES ( #synonym.name#, $synonym.cvterm.cvtermId$, #synonym.name# )
</insert>
diff --git a/uk/ac/sanger/artemis/chado/ChadoDAO.java b/uk/ac/sanger/artemis/chado/ChadoDAO.java
index 33a6eaf96de49315736cb8edc5af6f38eb60790b..baa3fbf797ce78a578515d8b68c69a7b86777dbf 100644
--- a/uk/ac/sanger/artemis/chado/ChadoDAO.java
+++ b/uk/ac/sanger/artemis/chado/ChadoDAO.java
@@ -26,7 +26,6 @@ package uk.ac.sanger.artemis.chado;
import java.sql.*;
import java.util.List;
-import java.util.Hashtable;
/**
*
@@ -44,7 +43,7 @@ public interface ChadoDAO
* @param id the systematic id
* @return the Feature, or null
*/
- public ChadoFeature getFeatureById(int id)
+ public Feature getFeatureById(int id)
throws SQLException;
/**
@@ -53,18 +52,18 @@ public interface ChadoDAO
* @param name the systematic id
* @return the Feature, or null
*/
- public ChadoFeature getFeatureByUniqueName(String name)
+ public Feature getFeatureByUniqueName(String name)
throws SQLException;
/**
* This can be used to get individual features or children.
- * If ChadoFeature.featureloc.srcfeature_id is set this is used
+ * If Feature.featureloc.srcfeature_id is set this is used
* to return the children of that srcfeature_id.
* @param feature the feature used to query
- * @return the <code>List</code> of child <code>ChadoFeature</code> objects
+ * @return the <code>List</code> of child <code>Feature</code> objects
* @throws SQLException
*/
- public List getFeaturesByLocatedOnFeature(ChadoFeature parent)
+ public List getFeaturesByLocatedOnFeature(Feature parent)
throws SQLException;
/**
@@ -91,7 +90,7 @@ public interface ChadoDAO
* with residues.
* @param cvterm_ids list of cvterm_id/type_id's
* @param schema schema/organism name or null
- * @return the <code>List</code> of <code>ChadoFeature</code> objects
+ * @return the <code>List</code> of <code>Feature</code> objects
* @throws SQLException
*/
public List getResidueFeatures(List cvterm_ids,
@@ -130,7 +129,7 @@ public interface ChadoDAO
/**
* Get dbxref for a feature.
* @param uniquename the unique name for the feature. If set to NULL
- * all <code>ChadoFeatureDbxref</code> are returned.
+ * all <code>FeatureDbxref</code> are returned.
* @return a <code>List</code> of feature_dbxrefs.
* @throws SQLException
*/
@@ -138,9 +137,9 @@ public interface ChadoDAO
throws SQLException;
/**
- * Return a list of ChadoFeatureSynonyms for a uniquename
+ * Return a list of FeatureSynonyms for a uniquename
* @param uniquename the unique name for the feature. If set to NULL
- * all <code>ChadoFeatureSynonym</code> are returned.
+ * all <code>FeatureSynonym</code> are returned.
* @return
* @throws SQLException
*/
@@ -154,19 +153,19 @@ public interface ChadoDAO
* @param type the type of the Synonym
* @return a Synonym, or null
*/
- public ChadoSynonym getSynonymByNameAndCvTerm(String name, ChadoCvterm type)
+ public Synonym getSynonymByNameAndCvTerm(String name, Cvterm type)
throws SQLException;
/**
- * Return a list of ChadoFeatureSynonyms which link a given Feature and Synonym
+ * Return a list of FeatureSynonyms which link a given Feature and Synonym
*
* @param feature the test Feature
* @param synonym the test Synonym
* @return a (possibly empty) List<FeatureSynonym>
*/
public List getFeatureSynonymsByFeatureAndSynonym(
- ChadoFeature feature, ChadoSynonym synonym)
+ Feature feature, Synonym synonym)
throws SQLException;
diff --git a/uk/ac/sanger/artemis/chado/ChadoDemo.java b/uk/ac/sanger/artemis/chado/ChadoDemo.java
index 12f65dd9de91421d45fb1b5d03d057952b428bdd..f2ff149894cf447aa9b101f92e46c7a160c5156d 100644
--- a/uk/ac/sanger/artemis/chado/ChadoDemo.java
+++ b/uk/ac/sanger/artemis/chado/ChadoDemo.java
@@ -88,7 +88,7 @@ public class ChadoDemo
/** feature attributes */
private JTextArea attr_text;
- /** <code>List</code> of <code>ChadoFeature</code> objects */
+ /** <code>List</code> of <code>Feature</code> objects */
private List featureList;
/**
@@ -254,7 +254,7 @@ public class ChadoDemo
{
int row = result_table.getSelectedRow();
StringBuffer attr_buff = new StringBuffer();
- ChadoFeature chado_feature = (ChadoFeature)featureList.get(row);
+ Feature chado_feature = (Feature)featureList.get(row);
List attributes = chado_feature.getFeaturepropList();
List dbxrefs = chado_feature.getFeatureDbxrefs();
@@ -263,7 +263,7 @@ public class ChadoDemo
attr_buff.append("/Dbxref=");
for(int i = 0; i < dbxrefs.size(); i++)
{
- ChadoFeatureDbxref dbxref = (ChadoFeatureDbxref) dbxrefs.get(i);
+ FeatureDbxref dbxref = (FeatureDbxref) dbxrefs.get(i);
attr_buff.append(dbxref.getDbxref().getDb().getName() + ":"
+ dbxref.getDbxref().getAccession() + "; ");
}
@@ -275,11 +275,11 @@ public class ChadoDemo
// append synonyms
if(synonyms.size() > 0)
{
- ChadoFeatureSynonym alias;
+ FeatureSynonym alias;
for(int i = 0; i < synonyms.size(); i++)
{
- alias = (ChadoFeatureSynonym) synonyms.get(i);
+ alias = (FeatureSynonym) synonyms.get(i);
attr_buff.append("/");
attr_buff.append(alias.getSynonym().getCvterm().getName() + "=");
attr_buff.append(alias.getSynonym().getName());
@@ -292,7 +292,7 @@ public class ChadoDemo
if(attributes != null)
for(int i = 0; i < attributes.size(); i++)
{
- ChadoFeatureProp featprop = (ChadoFeatureProp) attributes.get(i);
+ FeatureProp featprop = (FeatureProp) attributes.get(i);
attr_buff.append("/" + featprop.getCvterm().getName() + "="
+ GFFStreamFeature.decode(featprop.getValue()) + "\n");
@@ -318,7 +318,7 @@ public class ChadoDemo
ChadoDAO dao) throws SQLException, ConnectException
{
final String search_name = search_gene.replaceAll("[*]","%");
- ChadoFeature feature = new ChadoFeature();
+ Feature feature = new Feature();
//feature.setUniquename(search_gene.replaceAll("[*]","%"));
featureList = new Vector();
@@ -333,14 +333,14 @@ public class ChadoDemo
for(int i = 0; i < featureList.size(); i++)
{
- feature = (ChadoFeature) featureList.get(i);
+ feature = (Feature) featureList.get(i);
// assume only one featureloc
List locs = feature.getFeaturelocsForFeatureId();
if(locs.size() > 0)
{
- ChadoFeatureLoc loc = (ChadoFeatureLoc)locs.get(0);
+ FeatureLoc loc = (FeatureLoc)locs.get(0);
int fmin = loc.getFmin() + 1;
int fmax = loc.getFmax();
rowData[i][4] = fmin + "..." + fmax;
diff --git a/uk/ac/sanger/artemis/chado/ChadoTransaction.java b/uk/ac/sanger/artemis/chado/ChadoTransaction.java
index a90d40a45cc21f5102dd1ab93566fa6283c9874e..ec4e78fcc038bd3661e5efa548bd2f96bf4b619b 100644
--- a/uk/ac/sanger/artemis/chado/ChadoTransaction.java
+++ b/uk/ac/sanger/artemis/chado/ChadoTransaction.java
@@ -79,11 +79,11 @@ public class ChadoTransaction
/** feature id */
private int feature_id;
/** chado feature */
- private ChadoFeature chadoFeature;
+ private Feature chadoFeature;
/** feature dbxref */
- private ChadoFeatureDbxref dbxref;
+ private FeatureDbxref dbxref;
/** feature synonym */
- private ChadoFeatureSynonym alias;
+ private FeatureSynonym alias;
/** last time feature was modified */
private Timestamp lastmodified;
/** the feature object */
@@ -136,19 +136,19 @@ public class ChadoTransaction
* be used to describe a SQL transaction.
*
* <i>e.g.</i> to INSERT a feature and where chado_feature is a
- * <code>ChadoFeature</code>:
+ * <code>Feature</code>:
* <blockquote><pre>
* ChadoTransaction tsn = new ChadoTransaction(ChadoTransaction.INSERT_FEATURE,
* chado_feature);
* </pre></blockquote>
*
* @param type the transaction type
- * @param chado_feature the <code>ChadoFeature</code> to be inserted
+ * @param chado_feature the <code>Feature</code> to be inserted
* @param parents <code>Vector</code> of parent uniquenames
* @param derives_from <code>Vector</code> of derives_from names
*/
public ChadoTransaction(final int type,
- final ChadoFeature chadoFeature,
+ final Feature chadoFeature,
final Vector parents,
final Vector derives_from)
{
@@ -166,7 +166,7 @@ public class ChadoTransaction
*/
public ChadoTransaction(final int type,
final String uniquename,
- final ChadoFeatureDbxref dbxref,
+ final FeatureDbxref dbxref,
final Timestamp lastmodified,
final Object feature_obj)
{
@@ -178,7 +178,7 @@ public class ChadoTransaction
}
public ChadoTransaction(final int type,
- final ChadoFeatureSynonym alias,
+ final FeatureSynonym alias,
final Object feature_obj)
{
this.type = type;
@@ -187,7 +187,7 @@ public class ChadoTransaction
}
public ChadoTransaction(final int type,
- final ChadoFeature chadoFeature,
+ final Feature chadoFeature,
final String parent_uniquename)
{
this.type = type;
@@ -199,16 +199,16 @@ public class ChadoTransaction
* The <code>Dbxref</code> used in a transaction.
* @return the feature dbxref
*/
- public ChadoFeatureDbxref getFeatureDbxref()
+ public FeatureDbxref getFeatureDbxref()
{
return dbxref;
}
/**
- * The <code>ChadoFeature</code> feature used in a transaction.
- * @return chado_feature the <code>ChadoFeature</code>
+ * The <code>Feature</code> feature used in a transaction.
+ * @return chado_feature the <code>Feature</code>
*/
- public ChadoFeature getChadoFeature()
+ public Feature getChadoFeature()
{
return chadoFeature;
}
@@ -406,12 +406,12 @@ public class ChadoTransaction
return feature_obj;
}
- public ChadoFeatureSynonym getAlias()
+ public FeatureSynonym getAlias()
{
return alias;
}
- public void setAlias(ChadoFeatureSynonym alias)
+ public void setAlias(FeatureSynonym alias)
{
this.alias = alias;
}
diff --git a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
index 208511d8fc7974e37dc9a88f6bb2dbcfe462a6ec..c834a9b0554d15245036a4116f60232798b459c7 100644
--- a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
+++ b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
@@ -392,7 +392,8 @@ public class ChadoTransactionManager
Range range = (Range)rv_new.elementAt(i);
String seq_id = feature.getSegmentID(range);
- ChadoFeature chado_feature = new ChadoFeature();
+ uk.ac.sanger.artemis.chado.Feature chado_feature =
+ new uk.ac.sanger.artemis.chado.Feature();
chado_feature.setUniquename(seq_id);
tsn = new ChadoTransaction(
@@ -444,8 +445,9 @@ public class ChadoTransactionManager
roe.printStackTrace();
}
- ChadoFeature chado_feature = new ChadoFeature();
- ChadoFeatureLoc featureloc = new ChadoFeatureLoc();
+ uk.ac.sanger.artemis.chado.Feature chado_feature =
+ new uk.ac.sanger.artemis.chado.Feature();
+ FeatureLoc featureloc = new FeatureLoc();
chado_feature.setFeatureloc(featureloc);
if(feature.isForwardFeature())
@@ -509,7 +511,7 @@ public class ChadoTransactionManager
String key = feature.getKey().toString();
- ChadoCvterm cvterm = new ChadoCvterm();
+ Cvterm cvterm = new Cvterm();
cvterm.setCvtermId(DatabaseDocument.getCvtermID(key).longValue());
chado_feature.setCvterm(cvterm);
@@ -529,8 +531,9 @@ public class ChadoTransactionManager
private void insertFeatureSegment(final FeatureSegment segment,
final String segment_uniquename)
{
- ChadoFeature chado_feature = new ChadoFeature();
- ChadoFeatureLoc featureloc = new ChadoFeatureLoc();
+ uk.ac.sanger.artemis.chado.Feature chado_feature =
+ new uk.ac.sanger.artemis.chado.Feature();
+ FeatureLoc featureloc = new FeatureLoc();
chado_feature.setFeatureloc(featureloc);
if(segment.isForwardSegment())
@@ -590,7 +593,7 @@ public class ChadoTransactionManager
String key = feature.getKey().toString();
- ChadoCvterm cvterm = new ChadoCvterm();
+ Cvterm cvterm = new Cvterm();
cvterm.setCvtermId(DatabaseDocument.getCvtermID(key).longValue());
chado_feature.setCvterm(cvterm);
@@ -622,7 +625,7 @@ public class ChadoTransactionManager
* @param chado_feature the <code>ChadoFeature</code>
*/
private void addQualifiers(final QualifierVector qualifiers,
- final ChadoFeature chado_feature)
+ final uk.ac.sanger.artemis.chado.Feature chado_feature)
{
// add qualifiers/attributes
for(int qualifier_index = 0; qualifier_index < qualifiers.size();
@@ -652,7 +655,7 @@ public class ChadoTransactionManager
// else
// {
// happens when duplicating features
- ChadoFeatureProp featureprop = new ChadoFeatureProp();
+ FeatureProp featureprop = new FeatureProp();
featureprop.setValue((String)qualifier_values.elementAt(value_index));
chado_feature.addQualifier(type_id, featureprop);
// }
@@ -972,9 +975,9 @@ public class ChadoTransactionManager
System.out.println(uniquename+" in handleReservedTags() DELETE db="+
qualifier_string.substring(0,index)+" acc="+qualifier_string.substring(index+1));
- ChadoFeatureDbxref old_dbxref = new ChadoFeatureDbxref();
- ChadoDbxref dbxref = new ChadoDbxref();
- ChadoDb db = new ChadoDb();
+ FeatureDbxref old_dbxref = new FeatureDbxref();
+ Dbxref dbxref = new Dbxref();
+ Db db = new Db();
db.setName(qualifier_string.substring(0,index));
dbxref.setAccession(qualifier_string.substring(index+1));
dbxref.setDb(db);
@@ -990,8 +993,8 @@ public class ChadoTransactionManager
System.out.println(uniquename+" in handleReservedTags() DELETE "+qualifier_name+" "+
qualifier_string);
- ChadoFeatureSynonym alias = new ChadoFeatureSynonym();
- ChadoSynonym synonym = new ChadoSynonym();
+ FeatureSynonym alias = new FeatureSynonym();
+ Synonym synonym = new Synonym();
synonym.setName(qualifier_string);
alias.setSynonym(synonym);
alias.setUniquename(uniquename);
@@ -1023,9 +1026,9 @@ public class ChadoTransactionManager
System.out.println(uniquename+" in handleReservedTags() INSERT db="+
qualifier_string.substring(0,index)+" acc="+qualifier_string.substring(index+1));
- ChadoFeatureDbxref new_dbxref = new ChadoFeatureDbxref();
- ChadoDbxref dbxref = new ChadoDbxref();
- ChadoDb db = new ChadoDb();
+ FeatureDbxref new_dbxref = new FeatureDbxref();
+ Dbxref dbxref = new Dbxref();
+ Db db = new Db();
db.setName(qualifier_string.substring(0,index));
dbxref.setDb(db);
dbxref.setAccession(qualifier_string.substring(index+1));
@@ -1041,9 +1044,9 @@ public class ChadoTransactionManager
System.out.println(uniquename+" in handleReservedTags() INSERT "+qualifier_name+" "+
qualifier_string);
Long lcvterm_id = DatabaseDocument.getCvtermID(qualifier_name);
- ChadoFeatureSynonym alias = new ChadoFeatureSynonym();
- ChadoSynonym synonym = new ChadoSynonym();
- ChadoCvterm cvterm = new ChadoCvterm();
+ FeatureSynonym alias = new FeatureSynonym();
+ Synonym synonym = new Synonym();
+ Cvterm cvterm = new Cvterm();
cvterm.setCvtermId(lcvterm_id.longValue());
synonym.setName(qualifier_string);
synonym.setCvterm(cvterm);
diff --git a/uk/ac/sanger/artemis/chado/ChadoCv.java b/uk/ac/sanger/artemis/chado/Cv.java
similarity index 98%
rename from uk/ac/sanger/artemis/chado/ChadoCv.java
rename to uk/ac/sanger/artemis/chado/Cv.java
index 3e3cf1591ccfe48452b5dae255ddaee6ca3186a1..389aff65afddcdd5fda9f76a891dc6c14a795d3c 100644
--- a/uk/ac/sanger/artemis/chado/ChadoCv.java
+++ b/uk/ac/sanger/artemis/chado/Cv.java
@@ -27,7 +27,7 @@ package uk.ac.sanger.artemis.chado;
/**
* Representation of cv table.
*/
-public class ChadoCv
+public class Cv
{
private int cvId;
private String name;
diff --git a/uk/ac/sanger/artemis/chado/ChadoCvterm.java b/uk/ac/sanger/artemis/chado/Cvterm.java
similarity index 93%
rename from uk/ac/sanger/artemis/chado/ChadoCvterm.java
rename to uk/ac/sanger/artemis/chado/Cvterm.java
index 09125dfeaa216a4546808da02de832e801c23af0..f3a53247fff9cad4f41a0e2583abc475ae7e19e2 100644
--- a/uk/ac/sanger/artemis/chado/ChadoCvterm.java
+++ b/uk/ac/sanger/artemis/chado/Cvterm.java
@@ -28,12 +28,12 @@ package uk.ac.sanger.artemis.chado;
/**
* Representation of cvterm table.
*/
-public class ChadoCvterm
+public class Cvterm
{
private long cvtermId;
private String name;
- private ChadoCv cv;
- private ChadoDbxref dbxref;
+ private Cv cv;
+ private Dbxref dbxref;
private String definition;
private int isObsolete;
private int isRelationshiptype;
@@ -53,7 +53,7 @@ public class ChadoCvterm
* Note that a cvterm may have multiple secondary dbxrefs.
* @return
*/
- public ChadoDbxref getDbxref()
+ public Dbxref getDbxref()
{
return dbxref;
}
@@ -63,17 +63,17 @@ public class ChadoCvterm
* Note that a cvterm may have multiple secondary dbxrefs.
* @param dbxref
*/
- public void setDbxref(ChadoDbxref dbxref)
+ public void setDbxref(Dbxref dbxref)
{
this.dbxref = dbxref;
}
- public ChadoCv getCv()
+ public Cv getCv()
{
return cv;
}
- public void setCv(ChadoCv cv)
+ public void setCv(Cv cv)
{
this.cv = cv;
}
diff --git a/uk/ac/sanger/artemis/chado/ChadoDb.java b/uk/ac/sanger/artemis/chado/Db.java
similarity index 98%
rename from uk/ac/sanger/artemis/chado/ChadoDb.java
rename to uk/ac/sanger/artemis/chado/Db.java
index 742431e5c236615612349eabae156dd69108a791..c5d71229ddfa008169b4bb084c125eb03dd62c19 100644
--- a/uk/ac/sanger/artemis/chado/ChadoDb.java
+++ b/uk/ac/sanger/artemis/chado/Db.java
@@ -27,7 +27,7 @@ package uk.ac.sanger.artemis.chado;
/**
* Representation of the chado db table.
*/
-public class ChadoDb
+public class Db
{
private int db_id;
private String name;
diff --git a/uk/ac/sanger/artemis/chado/ChadoDbxref.java b/uk/ac/sanger/artemis/chado/Dbxref.java
similarity index 94%
rename from uk/ac/sanger/artemis/chado/ChadoDbxref.java
rename to uk/ac/sanger/artemis/chado/Dbxref.java
index 31b2c4423ea3b5342907419e35ab41fc6d37e6f9..29970726719f8b01ad4e994cf1f8db94bf2373b8 100644
--- a/uk/ac/sanger/artemis/chado/ChadoDbxref.java
+++ b/uk/ac/sanger/artemis/chado/Dbxref.java
@@ -27,13 +27,13 @@ package uk.ac.sanger.artemis.chado;
/**
* Representation of the chado dbxref table.
*/
-public class ChadoDbxref
+public class Dbxref
{
private int db_id;
private String accession;
private String version;
private String description;
- private ChadoDb db;
+ private Db db;
public String getAccession()
{
@@ -45,12 +45,12 @@ public class ChadoDbxref
this.accession = accession;
}
- public ChadoDb getDb()
+ public Db getDb()
{
return db;
}
- public void setDb(ChadoDb db)
+ public void setDb(Db db)
{
this.db = db;
}
diff --git a/uk/ac/sanger/artemis/chado/ChadoFeature.java b/uk/ac/sanger/artemis/chado/Feature.java
similarity index 83%
rename from uk/ac/sanger/artemis/chado/ChadoFeature.java
rename to uk/ac/sanger/artemis/chado/Feature.java
index 36a6f6dba4f8f4242c3c98306e2cda6e85931da1..165dbbb45498eb5f6c62c79e292f54dcb50ec053 100644
--- a/uk/ac/sanger/artemis/chado/ChadoFeature.java
+++ b/uk/ac/sanger/artemis/chado/Feature.java
@@ -1,4 +1,4 @@
-/* ChadoFeature.java
+/* Feature.java
*
* created: 2006
*
@@ -35,7 +35,7 @@ import java.util.List;
* Chado feature representation of the feature table and with references
* to the featureloc, featureprop, feature_relationship tables.
*/
-public class ChadoFeature
+public class Feature
{
/** schema */
@@ -57,26 +57,26 @@ public class ChadoFeature
/** whether this feature has been obsoleted */
private boolean obsolete;
/** feature cvterm */
- private ChadoCvterm cvterm;
+ private Cvterm cvterm;
/** feature property */
- private ChadoFeatureProp featureprop;
+ private FeatureProp featureprop;
/** feature location (for a given srcfeature) */
- private ChadoFeatureLoc featureloc;
+ private FeatureLoc featureloc;
/** feature relationship */
- private ChadoFeatureRelationship feature_relationship;
+ private FeatureRelationship feature_relationship;
/** feature organism */
- private ChadoOrganism organism;
+ private Organism organism;
/** optional primary public stable identifier */
- private ChadoFeatureDbxref feature_dbxref;
+ private FeatureDbxref feature_dbxref;
/** merged featureprops */
private Hashtable qualifiers;
- /** list of ChadoFeatureProp */
+ /** list of FeatureProp */
private List featurepropList;
- /** list of ChadoFeatureRelationship children */
+ /** list of FeatureRelationship children */
private List featureRelationshipsForObjectId;
- /** list of ChadoFeatureRelationship parent */
+ /** list of FeatureRelationship parent */
private List featureRelationshipsForSubjectId;
- /** list of feature dbxrefs (ChadoFeatureDbxref) */
+ /** list of feature dbxrefs (FeatureDbxref) */
private List featureDbxrefs;
/** list of feature locations for a feature_id */
private List featurelocsForFeatureId;
@@ -262,7 +262,7 @@ public class ChadoFeature
* This will typically be a Sequence Ontology identifier.
* @return the feature SO cvterm
*/
- public ChadoCvterm getCvterm()
+ public Cvterm getCvterm()
{
return cvterm;
}
@@ -272,16 +272,16 @@ public class ChadoFeature
* This will typically be a Sequence Ontology identifier.
* @param cvterm the feature SO cvterm
*/
- public void setCvterm(ChadoCvterm cvterm)
+ public void setCvterm(Cvterm cvterm)
{
this.cvterm = cvterm;
}
/**
* Get the the feature property.
- * @return the <code>ChadoFeatureProp</code>
+ * @return the <code>FeatureProp</code>
*/
- public ChadoFeatureProp getFeatureprop()
+ public FeatureProp getFeatureprop()
{
return featureprop;
}
@@ -290,16 +290,16 @@ public class ChadoFeature
* Set the feature property.
* @param featureprop the feature property
*/
- public void setFeatureprop(ChadoFeatureProp featureprop)
+ public void setFeatureprop(FeatureProp featureprop)
{
this.featureprop = featureprop;
}
/**
* Reference to the featureloc table.
- * @return featureloc the <code>ChadoFeatureLoc</code> object.
+ * @return featureloc the <code>FeatureLoc</code> object.
*/
- public ChadoFeatureLoc getFeatureloc()
+ public FeatureLoc getFeatureloc()
{
return featureloc;
}
@@ -308,46 +308,46 @@ public class ChadoFeature
* Reference to the featureloc table.
* @param featureloc the feature location
*/
- public void setFeatureloc(ChadoFeatureLoc featureloc)
+ public void setFeatureloc(FeatureLoc featureloc)
{
this.featureloc = featureloc;
}
/**
* Reference to the feature_relationship table.
- * @return feature_relationship the <code>ChadoFeatureRelationship</code>
+ * @return feature_relationship the <code>FeatureRelationship</code>
* object.
*/
- public ChadoFeatureRelationship getFeature_relationship()
+ public FeatureRelationship getFeature_relationship()
{
return feature_relationship;
}
/**
* Reference to the feature_relationship table.
- * @param feature_relationship the <code>ChadoFeatureRelationship</code>
+ * @param feature_relationship the <code>FeatureRelationship</code>
* object.
*/
public void setFeature_relationship(
- ChadoFeatureRelationship feature_relationship)
+ FeatureRelationship feature_relationship)
{
this.feature_relationship = feature_relationship;
}
/**
* Reference to the organism table for this feature.
- * @return the <code>ChadoOrganism</code> object
+ * @return the <code>Organism</code> object
*/
- public ChadoOrganism getOrganism()
+ public Organism getOrganism()
{
return organism;
}
/**
* Reference to the organism table for this feature.
- * @param organism the <code>ChadoOrganism</code> object
+ * @param organism the <code>Organism</code> object
*/
- public void setOrganism(ChadoOrganism organism)
+ public void setOrganism(Organism organism)
{
this.organism = organism;
}
@@ -358,7 +358,7 @@ public class ChadoFeature
* Secondary identifiers and external dbxrefs go in table:feature_dbxref
* @return
*/
- public ChadoFeatureDbxref getFeature_dbxref()
+ public FeatureDbxref getFeature_dbxref()
{
return feature_dbxref;
}
@@ -368,7 +368,7 @@ public class ChadoFeature
* Secondary identifiers and external dbxrefs go in table:feature_dbxref
* @param dbxref
*/
- public void setFeature_dbxref(ChadoFeatureDbxref feature_dbxref)
+ public void setFeature_dbxref(FeatureDbxref feature_dbxref)
{
this.feature_dbxref = feature_dbxref;
}
@@ -404,13 +404,13 @@ public class ChadoFeature
for(int i=0; i<featurepropList.size(); i++)
{
- ChadoFeatureProp featureprop = (ChadoFeatureProp)featurepropList.get(i);
+ FeatureProp featureprop = (FeatureProp)featurepropList.get(i);
addQualifier(featureprop.getCvterm().getCvtermId(), featureprop);
}
}
/**
- * Get a list of <code>ChadoFeatureRelationship</code> children
+ * Get a list of <code>FeatureRelationship</code> children
* @return
*/
public List getFeatureRelationshipsForObjectId()
@@ -419,7 +419,7 @@ public class ChadoFeature
}
/**
- * Set a list of <code>ChadoFeatureRelationship</code> children
+ * Set a list of <code>FeatureRelationship</code> children
* @param featureRelationshipsForObjectId
*/
public void setFeatureRelationshipsForObjectId(
@@ -429,7 +429,7 @@ public class ChadoFeature
}
/**
- * Get a list of <code>ChadoFeatureRelationship</code> parent
+ * Get a list of <code>FeatureRelationship</code> parent
* @return
*/
public List getFeatureRelationshipsForSubjectId()
@@ -438,7 +438,7 @@ public class ChadoFeature
}
/**
- * Set a list of <code>ChadoFeatureRelationship</code> parent
+ * Set a list of <code>FeatureRelationship</code> parent
* @param featureRelationshipsForSubjectId
*/
public void setFeatureRelationshipsForSubjectId(
@@ -448,7 +448,7 @@ public class ChadoFeature
}
/**
- * Get a list of feature dbxrefs (<code>ChadoFeatureDbxref</code>)
+ * Get a list of feature dbxrefs (<code>FeatureDbxref</code>)
* @return
*/
public List getFeatureDbxrefs()
@@ -457,7 +457,7 @@ public class ChadoFeature
}
/**
- * Set a list of feature dbxrefs (<code>ChadoFeatureDbxref</code>)
+ * Set a list of feature dbxrefs (<code>FeatureDbxref</code>)
* @param featureDbxrefs
*/
public void setFeatureDbxrefs(List featureDbxrefs)
@@ -502,7 +502,7 @@ public class ChadoFeature
* @param the cvterm type_id of the property name
* @param the property value
*/
- public void addQualifier(long prop_type_id, ChadoFeatureProp featprop)
+ public void addQualifier(long prop_type_id, FeatureProp featprop)
{
if(qualifiers == null)
qualifiers = new Hashtable();
@@ -535,15 +535,15 @@ public class ChadoFeature
/**
* Utility for finding a feature location from a List that corresponds
* to a particular srcfeature.
- * @param locs List of ChadoFeatureLoc
+ * @param locs List of FeatureLoc
* @param srcfeature_id srcfeature id
* @return
*/
- public static ChadoFeatureLoc getFeatureLoc(List locs, int srcfeature_id)
+ public static FeatureLoc getFeatureLoc(List locs, int srcfeature_id)
{
for(int i=0; i<locs.size(); i++)
{
- ChadoFeatureLoc loc = (ChadoFeatureLoc)locs.get(i);
+ FeatureLoc loc = (FeatureLoc)locs.get(i);
if(loc.getSrcfeature_id() == srcfeature_id)
return loc;
}
diff --git a/uk/ac/sanger/artemis/chado/ChadoFeatureDbxref.java b/uk/ac/sanger/artemis/chado/FeatureDbxref.java
similarity index 90%
rename from uk/ac/sanger/artemis/chado/ChadoFeatureDbxref.java
rename to uk/ac/sanger/artemis/chado/FeatureDbxref.java
index 9ce00ee894bca83b6bda6ae6cf4700e423ccf1a4..bc4ecd83f8f4fc6c65a128aa07d6bb18eae4843a 100644
--- a/uk/ac/sanger/artemis/chado/ChadoFeatureDbxref.java
+++ b/uk/ac/sanger/artemis/chado/FeatureDbxref.java
@@ -27,7 +27,7 @@ package uk.ac.sanger.artemis.chado;
/**
* Representation of the chado feature_dbxref.
*/
-public class ChadoFeatureDbxref
+public class FeatureDbxref
{
private String schema;
@@ -35,11 +35,7 @@ public class ChadoFeatureDbxref
private int feature_id;
private int dbxref_id;
private boolean current = true;
- private ChadoDbxref dbxref;
-
- public ChadoFeatureDbxref()
- {
- }
+ private Dbxref dbxref;
public int getFeature_id()
{
@@ -81,12 +77,12 @@ public class ChadoFeatureDbxref
this.dbxref_id = dbxref_id;
}
- public ChadoDbxref getDbxref()
+ public Dbxref getDbxref()
{
return dbxref;
}
- public void setDbxref(ChadoDbxref dbxref)
+ public void setDbxref(Dbxref dbxref)
{
this.dbxref = dbxref;
}
diff --git a/uk/ac/sanger/artemis/chado/ChadoFeatureLoc.java b/uk/ac/sanger/artemis/chado/FeatureLoc.java
similarity index 99%
rename from uk/ac/sanger/artemis/chado/ChadoFeatureLoc.java
rename to uk/ac/sanger/artemis/chado/FeatureLoc.java
index e0e69f6a6d560639c67b5d8250da86ae7500445e..c329b5b3ca475e7f1f37c3cf90e12add922d5223 100644
--- a/uk/ac/sanger/artemis/chado/ChadoFeatureLoc.java
+++ b/uk/ac/sanger/artemis/chado/FeatureLoc.java
@@ -27,7 +27,7 @@ package uk.ac.sanger.artemis.chado;
/**
* Representation of featureloc table.
*/
-public class ChadoFeatureLoc
+public class FeatureLoc
{
/** id of the parent feature */
private int srcfeature_id = 0;
diff --git a/uk/ac/sanger/artemis/chado/ChadoFeatureProp.java b/uk/ac/sanger/artemis/chado/FeatureProp.java
similarity index 94%
rename from uk/ac/sanger/artemis/chado/ChadoFeatureProp.java
rename to uk/ac/sanger/artemis/chado/FeatureProp.java
index c4ff2caabce0ea66173538891a62f8575467d1c1..857aea56743be57a54a2c5539c7794c4be71cc60 100644
--- a/uk/ac/sanger/artemis/chado/ChadoFeatureProp.java
+++ b/uk/ac/sanger/artemis/chado/FeatureProp.java
@@ -27,10 +27,10 @@ package uk.ac.sanger.artemis.chado;
/**
* Representation of featureprop table.
*/
-public class ChadoFeatureProp
+public class FeatureProp
{
- public ChadoCvterm cvterm;
+ public Cvterm cvterm;
public String value;
public int rank;
@@ -38,7 +38,7 @@ public class ChadoFeatureProp
* Get the cv term
* @return cvterm
*/
- public ChadoCvterm getCvterm()
+ public Cvterm getCvterm()
{
return cvterm;
}
@@ -47,7 +47,7 @@ public class ChadoFeatureProp
* Set the cv term
* @param cvterm
*/
- public void setCvterm(ChadoCvterm cvterm)
+ public void setCvterm(Cvterm cvterm)
{
this.cvterm = cvterm;
}
diff --git a/uk/ac/sanger/artemis/chado/ChadoFeatureRelationship.java b/uk/ac/sanger/artemis/chado/FeatureRelationship.java
similarity index 95%
rename from uk/ac/sanger/artemis/chado/ChadoFeatureRelationship.java
rename to uk/ac/sanger/artemis/chado/FeatureRelationship.java
index 848fc968b7e01a6338afb5580a9fd9a672fcf7eb..73952055ca7faa1d8a5be293129cfea3715a4b84 100644
--- a/uk/ac/sanger/artemis/chado/ChadoFeatureRelationship.java
+++ b/uk/ac/sanger/artemis/chado/FeatureRelationship.java
@@ -27,14 +27,14 @@ package uk.ac.sanger.artemis.chado;
/**
* Representation of feature_relationship table.
*/
-public class ChadoFeatureRelationship
+public class FeatureRelationship
{
public int subject_id;
/** id of the parent feature */
public int object_id;
/** cv term of feature relationship (e.g. part_of) */
- public ChadoCvterm cvterm;
+ public Cvterm cvterm;
/** Additional notes/comments */
public String value;
/** ordering of subject features */
@@ -45,7 +45,7 @@ public class ChadoFeatureRelationship
* subject and object (e.g. part_of).
* @return cvterm
*/
- public ChadoCvterm getCvterm()
+ public Cvterm getCvterm()
{
return cvterm;
}
@@ -55,7 +55,7 @@ public class ChadoFeatureRelationship
* subject and object (e.g. part_of).
* @param cvterm
*/
- public void setCvterm(ChadoCvterm cvterm)
+ public void setCvterm(Cvterm cvterm)
{
this.cvterm = cvterm;
}
diff --git a/uk/ac/sanger/artemis/chado/ChadoFeatureSynonym.java b/uk/ac/sanger/artemis/chado/FeatureSynonym.java
similarity index 93%
rename from uk/ac/sanger/artemis/chado/ChadoFeatureSynonym.java
rename to uk/ac/sanger/artemis/chado/FeatureSynonym.java
index 06ed53e7ebb731c2f2adb7aae451ae0d6ab7b176..4020a3dd8bd57a50092feb8341e4eee0db1f5405 100644
--- a/uk/ac/sanger/artemis/chado/ChadoFeatureSynonym.java
+++ b/uk/ac/sanger/artemis/chado/FeatureSynonym.java
@@ -28,7 +28,7 @@ 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 ChadoFeatureSynonym
+public class FeatureSynonym
{
private String schema;
private String uniquename;
@@ -40,7 +40,7 @@ public class ChadoFeatureSynonym
private boolean current;
private boolean internal;
- private ChadoSynonym synonym;
+ private Synonym synonym;
public String getSchema()
{
@@ -112,12 +112,12 @@ public class ChadoFeatureSynonym
this.internal = internal;
}
- public ChadoSynonym getSynonym()
+ public Synonym getSynonym()
{
return synonym;
}
- public void setSynonym(ChadoSynonym synonym)
+ public void setSynonym(Synonym synonym)
{
this.synonym = synonym;
}
diff --git a/uk/ac/sanger/artemis/chado/IBatisDAO.java b/uk/ac/sanger/artemis/chado/IBatisDAO.java
index ea7271854d65709cf18810582219a9332caec49e..166f39908b47e53781322604afffd39c52ead7ac 100644
--- a/uk/ac/sanger/artemis/chado/IBatisDAO.java
+++ b/uk/ac/sanger/artemis/chado/IBatisDAO.java
@@ -35,7 +35,7 @@ import javax.swing.JPasswordField;
/**
*
- * iBATIS implemetation of the <code>ChadoDAO</code> data
+ * iBATIS implemetation of the <code>DAO</code> data
* access interface.
*
*/
@@ -64,18 +64,18 @@ public class IBatisDAO implements ChadoDAO
* @return the Feature, or null
* @throws SQLException
*/
- public ChadoFeature getFeatureById(int id)
+ public Feature getFeatureById(int id)
throws SQLException
{
- ChadoFeature feature = new ChadoFeature();
+ Feature feature = new Feature();
feature.setId(id);
return getLazyFeature(feature);
}
- public ChadoFeature getFeatureByUniqueName(String uniquename)
+ public Feature getFeatureByUniqueName(String uniquename)
throws SQLException
{
- ChadoFeature feature = new ChadoFeature();
+ Feature feature = new Feature();
feature.setUniquename(uniquename);
return getLazyFeature(feature);
}
@@ -83,13 +83,13 @@ public class IBatisDAO implements ChadoDAO
/**
* This can be used to get individual features or children.
- * If ChadoFeature.featureloc.srcfeature_id is set this is used
+ * If Feature.featureloc.srcfeature_id is set this is used
* to return the children of that srcfeature_id.
* @param feature the feature to query
- * @return the <code>List</code> of child <code>ChadoFeature</code> objects
+ * @return the <code>List</code> of child <code>Feature</code> objects
* @throws SQLException
*/
- public List getFeaturesByLocatedOnFeature(final ChadoFeature feature)
+ public List getFeaturesByLocatedOnFeature(final Feature feature)
throws SQLException
{
List feature_list = sqlMap.queryForList("getFeature", feature);
@@ -107,13 +107,13 @@ public class IBatisDAO implements ChadoDAO
public List getFeaturesByAnyCurrentName(String name)
throws SQLException
{
- final ChadoSynonym alias = new ChadoSynonym();
+ final Synonym alias = new Synonym();
alias.setName(name);
List feature_synonym_list =
sqlMap.queryForList("getFeatureSynonymsByName", alias);
- ChadoFeature feature = new ChadoFeature();
+ Feature feature = new Feature();
feature.setUniquename(name);
feature.setFeatureSynonymsForFeatureId(feature_synonym_list);
@@ -137,13 +137,13 @@ public class IBatisDAO implements ChadoDAO
/**
* Get the properties of a feature.
* @param uniquename the unique name of the feature
- * @return the <code>List</code> of <code>ChadoFeature</code>
+ * @return the <code>List</code> of <code>Feature</code>
* @throws SQLException
*/
- private ChadoFeature getLazyFeature(final ChadoFeature feature)
+ private Feature getLazyFeature(final Feature feature)
throws SQLException
{
- return (ChadoFeature)sqlMap.queryForObject("getLazyFeature", feature);
+ return (Feature)sqlMap.queryForObject("getLazyFeature", feature);
}
/**
@@ -153,14 +153,14 @@ public class IBatisDAO implements ChadoDAO
* with residues.
* @param cvterm_ids list of cvterm_id/type_id's
* @param schema schema/organism name or null
- * @return the <code>List</code> of <code>ChadoFeature</code> objects
+ * @return the <code>List</code> of <code>Feature</code> objects
* @throws SQLException
*/
public List getResidueFeatures(List cvterm_ids,
final String schema)
throws SQLException
{
- ChadoFeature feature = new ChadoFeature();
+ Feature feature = new Feature();
feature.setSchema(schema);
feature.setFeatureCvterms(cvterm_ids);
@@ -211,30 +211,30 @@ public class IBatisDAO implements ChadoDAO
/**
* Get dbxref for a feature.
* @param uniquename the unique name for the feature. If set to NULL
- * all <code>ChadoFeatureDbxref</code> are returned.
+ * all <code>FeatureDbxref</code> are returned.
* @return a <code>List</code> of feature_dbxrefs.
* @throws SQLException
*/
public List getFeatureDbxrefByUniquename(final String uniquename)
throws SQLException
{
- ChadoFeature feature = new ChadoFeature();
+ Feature feature = new Feature();
feature.setUniquename(uniquename);
return sqlMap.queryForList("getFeatureDbxref", feature);
}
/**
- * Return a list of ChadoFeatureSynonyms for a uniquename
+ * Return a list of FeatureSynonyms for a uniquename
* @param uniquename the unique name for the feature. If set to NULL
- * all <code>ChadoFeatureSynonym</code> are returned.
+ * all <code>FeatureSynonym</code> are returned.
* @return
* @throws SQLException
*/
public List getFeatureSynonymsByUniquename(final String uniquename)
throws SQLException
{
- ChadoFeature feature = new ChadoFeature();
+ Feature feature = new Feature();
feature.setUniquename(uniquename);
return sqlMap.queryForList("getFeatureSynonymsByUniquename", feature);
@@ -246,27 +246,27 @@ public class IBatisDAO implements ChadoDAO
* @param type the type of the Synonym
* @return a Synonym, or null
*/
- public ChadoSynonym getSynonymByNameAndCvTerm(
- String name, ChadoCvterm type)
+ public Synonym getSynonymByNameAndCvTerm(
+ String name, Cvterm type)
throws SQLException
{
- ChadoSynonym synonym = new ChadoSynonym();
+ Synonym synonym = new Synonym();
synonym.setName(name);
synonym.setCvterm(type);
- return (ChadoSynonym)sqlMap.queryForObject("getSynonymByNameAndType",
+ return (Synonym)sqlMap.queryForObject("getSynonymByNameAndType",
synonym);
}
/**
- * Return a list of ChadoFeatureSynonyms which link a given Feature
+ * Return a list of FeatureSynonyms which link a given Feature
* and Synonym
* @param feature the test Feature
* @param synonym the test Synonym
* @return a (possibly empty) List<FeatureSynonym>
*/
public List getFeatureSynonymsByFeatureAndSynonym(
- ChadoFeature feature, ChadoSynonym synonym)
+ Feature feature, Synonym synonym)
throws SQLException
{
return
@@ -281,16 +281,16 @@ public class IBatisDAO implements ChadoDAO
* @param cv_name ontology name (e.g. gene, sequence)
* @throws SQLException
*/
- public ChadoCvterm getCvtermID(String name, String cv_name)
+ public Cvterm getCvtermID(String name, String cv_name)
throws SQLException
{
- ChadoCvterm cvterm = new ChadoCvterm();
- ChadoCv cv = new ChadoCv();
+ Cvterm cvterm = new Cvterm();
+ Cv cv = new Cv();
cv.setName(cv_name);
cvterm.setCv(cv);
cvterm.setName(name);
- return (ChadoCvterm)sqlMap.queryForObject("getCvterm", cvterm);
+ return (Cvterm)sqlMap.queryForObject("getCvterm", cvterm);
}
//
@@ -298,8 +298,8 @@ public class IBatisDAO implements ChadoDAO
//
/**
*
- * Update attributes defined by the <code>ChadoTransaction</code>.
- * @param tsn the <code>ChadoTransaction</code>
+ * Update attributes defined by the <code>Transaction</code>.
+ * @param tsn the <code>Transaction</code>
* @return number of rows changed
* @throws SQLException
*/
@@ -311,8 +311,8 @@ public class IBatisDAO implements ChadoDAO
}
/**
- * Insert attributes defined by the <code>ChadoTransaction</code>.
- * @param tsn the <code>ChadoTransaction</code>
+ * Insert attributes defined by the <code>Transaction</code>.
+ * @param tsn the <code>Transaction</code>
* @throws SQLException
*/
public void insertAttributes
@@ -324,14 +324,14 @@ public class IBatisDAO implements ChadoDAO
for(int i=0; i<feature_ids.size(); i++)
{
- tsn.setFeature_id( ((ChadoFeature)feature_ids.get(i)).getId() );
+ tsn.setFeature_id( ((Feature)feature_ids.get(i)).getId() );
sqlMap.insert("insertAttributes", tsn);
}
}
/**
- * Delete attributes defined by the <code>ChadoTransaction</code>.
- * @param tsn the <code>ChadoTransaction</code>
+ * Delete attributes defined by the <code>Transaction</code>.
+ * @param tsn the <code>Transaction</code>
* @throws SQLException
*/
public void deleteAttributes
@@ -343,14 +343,14 @@ public class IBatisDAO implements ChadoDAO
for(int i=0; i<feature_ids.size(); i++)
{
- tsn.setFeature_id( ((ChadoFeature)feature_ids.get(i)).getId() );
+ tsn.setFeature_id( ((Feature)feature_ids.get(i)).getId() );
sqlMap.delete("deleteAttributes", tsn);
}
}
/**
- * Insert a feature into the database defined by the <code>ChadoTransaction</code>.
- * @param tsn the <code>ChadoTransaction</code>
+ * Insert a feature into the database defined by the <code>Transaction</code>.
+ * @param tsn the <code>Transaction</code>
* @parma srcfeature_id the parent feature identifier
* @throws SQLException
*/
@@ -360,8 +360,8 @@ public class IBatisDAO implements ChadoDAO
throws SQLException
{
// get the organism id from the srcfeature_id
- ChadoFeature feature = new ChadoFeature();
- ChadoFeatureLoc featureloc = new ChadoFeatureLoc();
+ Feature feature = new Feature();
+ FeatureLoc featureloc = new FeatureLoc();
feature.setFeatureloc(featureloc);
featureloc.setSrcfeature_id(Integer.parseInt(srcfeature_id));
@@ -370,8 +370,8 @@ public class IBatisDAO implements ChadoDAO
//
// insert feature into feature table
- ChadoFeature chadoFeature = tsn.getChadoFeature();
- ChadoOrganism organism = new ChadoOrganism();
+ Feature chadoFeature = tsn.getChadoFeature();
+ Organism organism = new Organism();
organism.setId(organism_id.intValue());
chadoFeature.setOrganism(organism);
sqlMap.insert("insertFeature", chadoFeature);
@@ -395,14 +395,14 @@ public class IBatisDAO implements ChadoDAO
for(int i=0; i<feature_ids.size(); i++)
{
- ChadoFeatureRelationship feature_relationship =
- new ChadoFeatureRelationship();
- feature_relationship.setObject_id( ((ChadoFeature)feature_ids.get(i)).getId() );
+ FeatureRelationship feature_relationship =
+ new FeatureRelationship();
+ feature_relationship.setObject_id( ((Feature)feature_ids.get(i)).getId() );
feature_relationship.setSubject_id(feature_id);
- ChadoCvterm cvterm = new ChadoCvterm();
+ Cvterm cvterm = new Cvterm();
if(tsn.getParents().contains(
- ((ChadoFeature)feature_ids.get(i)).getUniquename() ))
+ ((Feature)feature_ids.get(i)).getUniquename() ))
cvterm.setName("part_of");
else
cvterm.setName("derives_from");
@@ -417,8 +417,8 @@ public class IBatisDAO implements ChadoDAO
/**
- * Delete a feature from the database defined by the <code>ChadoTransaction</code>.
- * @param tsn the <code>ChadoTransaction</code>
+ * Delete a feature from the database defined by the <code>Transaction</code>.
+ * @param tsn the <code>Transaction</code>
* @return number of rows deleted
* @throws SQLException
*/
@@ -426,7 +426,7 @@ public class IBatisDAO implements ChadoDAO
(final ChadoTransaction tsn)
throws SQLException
{
- ChadoFeature chadoFeature = new ChadoFeature();
+ Feature chadoFeature = new Feature();
chadoFeature.setUniquename(tsn.getUniqueName());
return sqlMap.delete("deleteFeature", chadoFeature);
@@ -434,14 +434,14 @@ public class IBatisDAO implements ChadoDAO
/**
* Insert a dbxref for a feature.
- * @param tsn the <code>ChadoTransaction</code>
+ * @param tsn the <code>Transaction</code>
* @return number of rows changed
* @throws SQLException
*/
public int insertFeatureDbxref(final ChadoTransaction tsn)
throws SQLException
{
- ChadoFeatureDbxref dbxref = tsn.getFeatureDbxref();
+ FeatureDbxref dbxref = tsn.getFeatureDbxref();
Integer db_id = (Integer)sqlMap.queryForObject("getDbId",
dbxref.getDbxref().getDb());
@@ -466,7 +466,7 @@ public class IBatisDAO implements ChadoDAO
// get the feature id's
List feature_ids = sqlMap.queryForList("getFeatureID", tsn);
- dbxref.setFeature_id( ((ChadoFeature)feature_ids.get(0)).getId() );
+ dbxref.setFeature_id( ((Feature)feature_ids.get(0)).getId() );
sqlMap.insert("insertFeatureDbxref", dbxref);
@@ -475,35 +475,35 @@ public class IBatisDAO implements ChadoDAO
/**
* Delete a dbxref for a feature.
- * @param tsn the <code>ChadoTransaction</code>
+ * @param tsn the <code>Transaction</code>
* @return number of rows changed
* @throws SQLException
*/
public int deleteFeatureDbxref(final ChadoTransaction tsn)
throws SQLException
{
- ChadoFeatureDbxref dbxref = tsn.getFeatureDbxref();
+ FeatureDbxref dbxref = tsn.getFeatureDbxref();
// get the feature id's
List feature_ids = sqlMap.queryForList("getFeatureID", tsn);
- dbxref.setFeature_id( ((ChadoFeature)feature_ids.get(0)).getId() );
+ dbxref.setFeature_id( ((Feature)feature_ids.get(0)).getId() );
return sqlMap.delete("deleteFeatureDbxref", dbxref);
}
/**
* Insert a synonym for a feature.
- * @param tsn the <code>ChadoTransaction</code>
+ * @param tsn the <code>Transaction</code>
* @return number of rows changed
* @throws SQLException
*/
public int insertFeatureAlias(final ChadoTransaction tsn)
throws SQLException
{
- final ChadoFeatureSynonym alias = tsn.getAlias();
+ final FeatureSynonym alias = tsn.getAlias();
- ChadoSynonym synonym =
- (ChadoSynonym)sqlMap.queryForObject("getSynonymByNameAndType",
+ Synonym synonym =
+ (Synonym)sqlMap.queryForObject("getSynonymByNameAndType",
alias.getSynonym());
if(synonym == null)
@@ -512,7 +512,7 @@ public class IBatisDAO implements ChadoDAO
sqlMap.insert("insertAlias", alias);
synonym =
- (ChadoSynonym)sqlMap.queryForObject("getSynonymByNameAndType",
+ (Synonym)sqlMap.queryForObject("getSynonymByNameAndType",
alias.getSynonym());
}
@@ -523,20 +523,20 @@ public class IBatisDAO implements ChadoDAO
/**
* Delete a synonym for a feature.
- * @param tsn the <code>ChadoTransaction</code>
+ * @param tsn the <code>Transaction</code>
* @return number of rows changed
* @throws SQLException
*/
public int deleteFeatureAlias(final ChadoTransaction tsn)
throws SQLException
{
- final ChadoFeatureSynonym alias = tsn.getAlias();
+ final FeatureSynonym alias = tsn.getAlias();
List feature_synonym_list =
sqlMap.queryForList("getFeatureSynonymsByName", alias.getSynonym());
- final ChadoFeatureSynonym synonym =
- (ChadoFeatureSynonym)feature_synonym_list.get(0);
+ final FeatureSynonym synonym =
+ (FeatureSynonym)feature_synonym_list.get(0);
alias.setSynonym_id(synonym.getSynonym().getSynonym_id());
// check this name is not used some where else,
@@ -549,7 +549,7 @@ public class IBatisDAO implements ChadoDAO
/**
* Update feature_relationship for a feature.
- * @param tsn the <code>ChadoTransaction</code>
+ * @param tsn the <code>Transaction</code>
* @return number of rows changed
* @throws SQLException
*/
@@ -635,18 +635,18 @@ public class IBatisDAO implements ChadoDAO
// merge same features in the list
int feature_size = list.size();
final List flatten_list = new Vector();
- ChadoFeature featNext = null;
+ Feature featNext = null;
for(int i = 0; i < feature_size; i++)
{
- ChadoFeature feat = (ChadoFeature)list.get(i);
+ Feature feat = (Feature)list.get(i);
String name = feat.getUniquename();
feat.addQualifier(feat.getFeatureprop().getCvterm().getCvtermId(),
feat.getFeatureprop());
if(i < feature_size - 1)
- featNext = (ChadoFeature)list.get(i + 1);
+ featNext = (Feature)list.get(i + 1);
// merge next line if part of the same feature
while(featNext != null && featNext.getUniquename().equals(name))
@@ -656,7 +656,7 @@ public class IBatisDAO implements ChadoDAO
i++;
if(i < feature_size - 1)
- featNext = (ChadoFeature)list.get(i + 1);
+ featNext = (Feature)list.get(i + 1);
else
break;
}
@@ -678,7 +678,7 @@ public class IBatisDAO implements ChadoDAO
Hashtable dbxrefHash = new Hashtable();
for(int i = 0; i < list.size(); i++)
{
- ChadoFeatureDbxref dbxref = (ChadoFeatureDbxref)list.get(i);
+ FeatureDbxref dbxref = (FeatureDbxref)list.get(i);
Integer feature_id = new Integer(dbxref.getFeature_id());
String value = dbxref.getDbxref().getDb().getName() + ":" +
dbxref.getDbxref().getAccession();
diff --git a/uk/ac/sanger/artemis/chado/JdbcDAO.java b/uk/ac/sanger/artemis/chado/JdbcDAO.java
index d4a2d56a61df8fb53c72b08063ace9a3efdfde17..6758a870a76bd62816e6fa35a5ebcfd19ee3836c 100644
--- a/uk/ac/sanger/artemis/chado/JdbcDAO.java
+++ b/uk/ac/sanger/artemis/chado/JdbcDAO.java
@@ -30,7 +30,6 @@ import java.sql.*;
import java.io.*;
import java.util.List;
import java.util.Vector;
-import java.util.Hashtable;
/**
*
@@ -74,10 +73,10 @@ public class JdbcDAO
* @return the Feature, or null
* @throws SQLException
*/
- public ChadoFeature getFeatureById(int id)
+ public Feature getFeatureById(int id)
throws SQLException
{
- ChadoFeature feature = new ChadoFeature();
+ Feature feature = new Feature();
feature.setId(id);
return getLazyFeature(feature);
}
@@ -89,24 +88,25 @@ public class JdbcDAO
* @return the Feature, or null
* @throws SQLException
*/
- public ChadoFeature getFeatureByUniqueName(String uniquename)
+ public Feature getFeatureByUniqueName(String uniquename)
throws SQLException
{
- ChadoFeature feature = new ChadoFeature();
+ Feature feature = new Feature();
feature.setUniquename(uniquename);
+ feature.setId(-1);
return getLazyFeature(feature);
}
/**
* This can be used to get individual features or children.
- * If ChadoFeature.featureloc.srcfeature_id is set this is used
+ * If Feature.featureloc.srcfeature_id is set this is used
* to return the children of that srcfeature_id.
* @param feature the feature to query
- * @return the <code>List</code> of child <code>ChadoFeature</code> objects
+ * @return the <code>List</code> of child <code>Feature</code> objects
* @throws SQLException
*/
- public List getFeaturesByLocatedOnFeature(final ChadoFeature feature)
+ public List getFeaturesByLocatedOnFeature(final Feature feature)
throws SQLException
{
return getFeatureQuery(null,
@@ -123,7 +123,7 @@ public class JdbcDAO
public List getFeaturesByAnyCurrentName(String name)
throws SQLException
{
- ChadoFeature feature = new ChadoFeature();
+ Feature feature = new Feature();
feature.setUniquename(name);
return getFeatureQuery(name, -1, -1);
}
@@ -142,22 +142,22 @@ public class JdbcDAO
/**
* Get the properties of a feature.
* @param uniquename the unique name of the feature
- * @return the <code>List</code> of <code>ChadoFeature</code>
+ * @return the <code>List</code> of <code>Feature</code>
* @throws SQLException
*/
- private ChadoFeature getLazyFeature(final ChadoFeature feature)
+ private Feature getLazyFeature(final Feature feature)
throws SQLException
{
List list = getFeatureQuery(feature.getUniquename(),
-1, feature.getId());
- return (ChadoFeature)list.get(0);
+ return (Feature)list.get(0);
}
/**
* Get the properties of a feature.
* @param uniquename the unique name of the feature
* @param parentFeatureID the id of parent feature to query
- * @return the <code>List</code> of <code>ChadoFeature</code>
+ * @return the <code>List</code> of <code>Feature</code>
* @throws SQLException
*/
private List getFeatureQuery(final String uniquename,
@@ -202,9 +202,9 @@ public class JdbcDAO
final List list = new Vector();
while(rs.next())
{
- ChadoFeature feature = new ChadoFeature();
+ Feature feature = new Feature();
- ChadoFeatureLoc featureloc = new ChadoFeatureLoc();
+ FeatureLoc featureloc = new FeatureLoc();
featureloc.setFmin( rs.getInt("fmin") );
featureloc.setFmax( rs.getInt("fmax") );
featureloc.setStrand( rs.getInt("strand") );
@@ -218,12 +218,12 @@ public class JdbcDAO
feature.setResidues( rs.getBytes("residues") );
feature.setFeatureloc(featureloc);
- feature.setCvterm(new ChadoCvterm());
+ feature.setCvterm(new Cvterm());
feature.getCvterm().setCvtermId( rs.getLong("type_id") );
// feature properties
- ChadoFeatureProp featureprop = new ChadoFeatureProp();
- ChadoCvterm cvterm = new ChadoCvterm();
+ FeatureProp featureprop = new FeatureProp();
+ Cvterm cvterm = new Cvterm();
cvterm.setCvtermId(rs.getLong("prop_type_id"));
featureprop.setCvterm(cvterm);
featureprop.setValue(rs.getString("value"));
@@ -234,15 +234,15 @@ public class JdbcDAO
feature.setId( rs.getInt("feature_id") );
// feature relationship
- ChadoFeatureRelationship feature_relationship = new ChadoFeatureRelationship();
- cvterm = new ChadoCvterm();
+ FeatureRelationship feature_relationship = new FeatureRelationship();
+ cvterm = new Cvterm();
cvterm.setCvtermId(rs.getLong("relation_type_id"));
feature_relationship.setCvterm(cvterm);
feature_relationship.setObject_id( rs.getInt("object_id") );
feature.setFeature_relationship(feature_relationship);
// feature organism
- ChadoOrganism organism = new ChadoOrganism();
+ Organism organism = new Organism();
organism.setAbbreviation(rs.getString("abbreviation"));
organism.setComment(rs.getString("comment"));
organism.setCommon_name(rs.getString("common_name"));
@@ -265,7 +265,7 @@ public class JdbcDAO
* with residues.
* @param cvterm_ids list of cvterm_id/type_id's
* @param schema schema/organism name or null
- * @return the <code>List</code> of <code>ChadoFeature</code> objects
+ * @return the <code>List</code> of <code>Feature</code> objects
* @throws SQLException
*/
public List getResidueFeatures(List cvterm_ids,
@@ -294,15 +294,15 @@ public class JdbcDAO
List list = new Vector();
while(rs.next())
{
- ChadoFeature feature = new ChadoFeature();
- ChadoOrganism organism = new ChadoOrganism();
+ Feature feature = new Feature();
+ Organism organism = new Organism();
organism.setAbbreviation( rs.getString("abbreviation") );
feature.setOrganism(organism);
feature.setId( rs.getInt("feature_id") );
feature.setName( rs.getString("name") );
feature.setUniquename( rs.getString("uniquename") );
- feature.setCvterm(new ChadoCvterm());
+ feature.setCvterm(new Cvterm());
feature.getCvterm().setCvtermId( rs.getLong("type_id") );
list.add(feature);
@@ -378,7 +378,7 @@ public class JdbcDAO
while(rs.next())
{
- ChadoCvterm cvterm = new ChadoCvterm();
+ Cvterm cvterm = new Cvterm();
cvterm.setCvtermId( rs.getLong("cvterm_id") );
cvterm.setName( rs.getString("name") );
cvterms.add(cvterm);
@@ -390,7 +390,7 @@ public class JdbcDAO
/**
* Get dbxref for a feature.
* @param uniquename the unique name for the feature. If set to NULL
- * all <code>ChadoFeatureDbxref</code> are returned.
+ * all <code>FeatureDbxref</code> are returned.
* @return a <code>List</code> of feature_dbxrefs.
* @throws SQLException
*/
@@ -413,9 +413,9 @@ public class JdbcDAO
while(rs.next())
{
- ChadoFeatureDbxref feature_dbxref = new ChadoFeatureDbxref();
- ChadoDbxref dbxref = new ChadoDbxref();
- ChadoDb db = new ChadoDb();
+ FeatureDbxref feature_dbxref = new FeatureDbxref();
+ Dbxref dbxref = new Dbxref();
+ Db db = new Db();
db.setName( rs.getString("name") );
dbxref.setAccession( rs.getString("accession") );
dbxref.setDb(db);
@@ -429,9 +429,9 @@ public class JdbcDAO
/**
- * Return a list of ChadoFeatureSynonyms for a uniquename
+ * Return a list of FeatureSynonyms for a uniquename
* @param uniquename the unique name for the feature. If set to NULL
- * all <code>ChadoFeatureSynonym</code> are returned.
+ * all <code>FeatureSynonym</code> are returned.
* @return
* @throws SQLException
*/
@@ -450,13 +450,13 @@ public class JdbcDAO
Statement st = conn.createStatement();
ResultSet rs = st.executeQuery(sql);
List synonym = new Vector();
- ChadoFeatureSynonym alias;
+ FeatureSynonym alias;
while(rs.next())
{
- alias = new ChadoFeatureSynonym();
- ChadoCvterm cvterm = new ChadoCvterm();
+ alias = new FeatureSynonym();
+ Cvterm cvterm = new Cvterm();
cvterm.setCvtermId(rs.getLong("type_id"));
- ChadoSynonym syn = new ChadoSynonym();
+ Synonym syn = new Synonym();
syn.setName(rs.getString("name"));
syn.setCvterm(cvterm);
@@ -472,14 +472,14 @@ public class JdbcDAO
}
public List getFeatureSynonymsByFeatureAndSynonym(
- ChadoFeature feature, ChadoSynonym synonym)
+ Feature feature, Synonym synonym)
{
return null;
}
- public ChadoSynonym getSynonymByNameAndCvTerm(
- String name, ChadoCvterm type)
+ public Synonym getSynonymByNameAndCvTerm(
+ String name, Cvterm type)
{
return null;
}
@@ -664,7 +664,7 @@ public class JdbcDAO
final int organism_id = rs.getInt("organism_id");
- ChadoFeature chadoFeature = tsn.getChadoFeature();
+ Feature chadoFeature = tsn.getChadoFeature();
// insert new feature into feature table
StringBuffer sql_buff = new StringBuffer();
sql_buff.append("INSERT INTO feature (");
@@ -750,7 +750,7 @@ public class JdbcDAO
public int insertFeatureDbxref(final ChadoTransaction tsn)
throws SQLException
{
- final ChadoFeatureDbxref dbxref = tsn.getFeatureDbxref();
+ final FeatureDbxref dbxref = tsn.getFeatureDbxref();
final String uniquename = tsn.getUniqueName();
// find database id
@@ -812,7 +812,7 @@ public class JdbcDAO
public int deleteFeatureDbxref(final ChadoTransaction tsn)
throws SQLException
{
- final ChadoFeatureDbxref dbxref = tsn.getFeatureDbxref();
+ final FeatureDbxref dbxref = tsn.getFeatureDbxref();
final String uniquename = tsn.getUniqueName();
final String sql =
@@ -836,7 +836,7 @@ public class JdbcDAO
public int insertFeatureAlias(final ChadoTransaction tsn)
throws SQLException
{
- final ChadoFeatureSynonym alias = tsn.getAlias();
+ final FeatureSynonym alias = tsn.getAlias();
final String uniquename = alias.getUniquename();
final String synonym_name = alias.getSynonym().getName();
@@ -889,7 +889,7 @@ public class JdbcDAO
public int deleteFeatureAlias(final ChadoTransaction tsn)
throws SQLException
{
- final ChadoFeatureSynonym alias = tsn.getAlias();
+ final FeatureSynonym alias = tsn.getAlias();
final String uniquename = alias.getUniquename();
final String synonym_name = alias.getSynonym().getName();
String sql = "SELECT synonym_id FROM synonym WHERE "+
@@ -929,7 +929,7 @@ public class JdbcDAO
final ChadoTransaction tsn)
throws SQLException
{
- final ChadoFeature chado_feature = tsn.getChadoFeature();
+ final Feature chado_feature = tsn.getChadoFeature();
final String parent = tsn.getParent_uniquename();
diff --git a/uk/ac/sanger/artemis/chado/ChadoOrganism.java b/uk/ac/sanger/artemis/chado/Organism.java
similarity index 98%
rename from uk/ac/sanger/artemis/chado/ChadoOrganism.java
rename to uk/ac/sanger/artemis/chado/Organism.java
index 8a352a2e549daf354fc87e9ffa608a6f9eace703..17a8c62fa197a8a64816043bac11f38cccf194d6 100644
--- a/uk/ac/sanger/artemis/chado/ChadoOrganism.java
+++ b/uk/ac/sanger/artemis/chado/Organism.java
@@ -27,7 +27,7 @@ package uk.ac.sanger.artemis.chado;
/**
* Representation of the organism table.
*/
-public class ChadoOrganism
+public class Organism
{
/** organism identifier */
diff --git a/uk/ac/sanger/artemis/chado/ChadoSynonym.java b/uk/ac/sanger/artemis/chado/Synonym.java
similarity index 92%
rename from uk/ac/sanger/artemis/chado/ChadoSynonym.java
rename to uk/ac/sanger/artemis/chado/Synonym.java
index 689290b04fa8d76039dc61480345bed14ddb05cd..3c8eee48651bc138aa120b05f405f12e4ad3e8da 100644
--- a/uk/ac/sanger/artemis/chado/ChadoSynonym.java
+++ b/uk/ac/sanger/artemis/chado/Synonym.java
@@ -28,12 +28,12 @@ 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 ChadoSynonym
+public class Synonym
{
// synonym
private Integer synonym_id;
private String name;
- private ChadoCvterm cvterm;
+ private Cvterm cvterm;
private String synonym_sgml;
public Integer getSynonym_id()
@@ -56,12 +56,12 @@ public class ChadoSynonym
this.name = name;
}
- public ChadoCvterm getCvterm()
+ public Cvterm getCvterm()
{
return cvterm;
}
- public void setCvterm(ChadoCvterm cvterm)
+ public void setCvterm(Cvterm cvterm)
{
this.cvterm = cvterm;
}
diff --git a/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java b/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java
index 74e8dacec556f7a7d06288f55ca8949ae7a581bd..5d85a47c8af5746eef51d3b975f7040a63eef6cd 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.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/genebuilder/GeneBuilderFrame.java,v 1.13 2006-08-08 10:20:23 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/GeneBuilderFrame.java,v 1.14 2006-08-22 13:00:57 tjc Exp $
*/
package uk.ac.sanger.artemis.components.genebuilder;
@@ -49,7 +49,6 @@ import uk.ac.sanger.artemis.FeatureChangeEvent;
import uk.ac.sanger.artemis.FeatureChangeListener;
import uk.ac.sanger.artemis.GotoEventSource;
import uk.ac.sanger.artemis.Selection;
-import uk.ac.sanger.artemis.chado.ChadoFeature;
import uk.ac.sanger.artemis.components.FeatureEdit;
import uk.ac.sanger.artemis.io.GFFStreamFeature;
import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
@@ -418,7 +417,7 @@ public class GeneBuilderFrame extends JFrame
if(exons == null)
continue;
- if(exons.get(0) instanceof ChadoFeature)
+ if(exons.get(0) instanceof uk.ac.sanger.artemis.chado.Feature)
return;
for(int j=0; j<exons.size(); j++)
diff --git a/uk/ac/sanger/artemis/components/genebuilder/GeneComponentTree.java b/uk/ac/sanger/artemis/components/genebuilder/GeneComponentTree.java
index e9a5a7d844bf4f6803701bfb66e432ea2b81d083..dd1f669292564c2577ff960687a8c4273bba19a7 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/GeneComponentTree.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/GeneComponentTree.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/genebuilder/GeneComponentTree.java,v 1.12 2006-08-16 14:43:56 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/GeneComponentTree.java,v 1.13 2006-08-22 13:00:57 tjc Exp $
*/
package uk.ac.sanger.artemis.components.genebuilder;
@@ -28,7 +28,6 @@ package uk.ac.sanger.artemis.components.genebuilder;
import uk.ac.sanger.artemis.io.ChadoCanonicalGene;
import uk.ac.sanger.artemis.io.Feature;
import uk.ac.sanger.artemis.io.InvalidRelationException;
-import uk.ac.sanger.artemis.chado.ChadoFeature;
import uk.ac.sanger.artemis.Selection;
import uk.ac.sanger.artemis.FeatureVector;
@@ -185,11 +184,9 @@ public class GeneComponentTree extends JTree
if(protein == null)
continue;
- if(protein instanceof Feature)
- protein_id =
+ protein_id =
(String)((Feature)protein).getQualifierByName("ID").getValues().get(0);
- else
- protein_id = ((ChadoFeature)protein).getUniquename();
+
protein_node = new DefaultMutableTreeNode(protein_id);
diff --git a/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java b/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java
index dd83161a41eb6ea71cf5c81dec8edfc5e870b593..a101782a5bad04ab7baf297cbfcfdcf983957716 100644
--- a/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java
+++ b/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.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/genebuilder/GeneViewerPanel.java,v 1.24 2006-08-17 13:21:38 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java,v 1.25 2006-08-22 13:00:57 tjc Exp $
*/
package uk.ac.sanger.artemis.components.genebuilder;
@@ -44,9 +44,8 @@ import uk.ac.sanger.artemis.LastSegmentException;
import uk.ac.sanger.artemis.Selection;
import uk.ac.sanger.artemis.FeatureVector;
-import uk.ac.sanger.artemis.chado.ChadoFeature;
-import uk.ac.sanger.artemis.chado.ChadoFeatureLoc;
-import uk.ac.sanger.artemis.chado.ChadoFeatureProp;
+import uk.ac.sanger.artemis.chado.FeatureLoc;
+import uk.ac.sanger.artemis.chado.FeatureProp;
import uk.ac.sanger.artemis.io.EntryInformationException;
import uk.ac.sanger.artemis.io.Feature;
import uk.ac.sanger.artemis.io.GFFStreamFeature;
@@ -619,20 +618,21 @@ public class GeneViewerPanel extends JPanel
int offset = 0;
boolean last_segment = false;
- if(exons.get(0) instanceof ChadoFeature)
+ if(exons.get(0) instanceof uk.ac.sanger.artemis.chado.Feature)
{
int last_ex_start = 0;
int last_ex_end = 0;
int last_ypos = 0;
- ChadoFeature start_exon = (ChadoFeature)exons.get(0);
- ChadoFeatureLoc loc = ChadoFeature.getFeatureLoc(
+ uk.ac.sanger.artemis.chado.Feature start_exon =
+ (uk.ac.sanger.artemis.chado.Feature)exons.get(0);
+ FeatureLoc loc = uk.ac.sanger.artemis.chado.Feature.getFeatureLoc(
start_exon.getFeaturelocsForFeatureId(), chado_gene.getSrcfeature_id());
if(loc.getStrand() == -1)
{
- ChadoFeatureLoc loc_last = ChadoFeature.getFeatureLoc(
- ((ChadoFeature)exons.get(exons.size()-1)).getFeaturelocsForFeatureId(),
+ FeatureLoc loc_last = uk.ac.sanger.artemis.chado.Feature.getFeatureLoc(
+ ((uk.ac.sanger.artemis.chado.Feature)exons.get(exons.size()-1)).getFeaturelocsForFeatureId(),
chado_gene.getSrcfeature_id());
if(loc.getFmin() < loc_last.getFmin())
@@ -641,8 +641,9 @@ public class GeneViewerPanel extends JPanel
for(int j=0; j<exons.size(); j++)
{
- ChadoFeature exon = (ChadoFeature)exons.get(j);
- loc = ChadoFeature.getFeatureLoc(
+ uk.ac.sanger.artemis.chado.Feature exon =
+ (uk.ac.sanger.artemis.chado.Feature)exons.get(j);
+ loc = uk.ac.sanger.artemis.chado.Feature.getFeatureLoc(
exon.getFeaturelocsForFeatureId(), chado_gene.getSrcfeature_id());
int ex_start = border+(int)((loc.getFmin()+1-start)*fraction);
@@ -1008,12 +1009,12 @@ public class GeneViewerPanel extends JPanel
* @param feature
* @return
*/
- private Color getColorFromAttributes(ChadoFeature feature)
+ private Color getColorFromAttributes(uk.ac.sanger.artemis.chado.Feature feature)
{
List properties = feature.getFeaturepropList();
for(int i=0; i<properties.size(); i++)
{
- ChadoFeatureProp property = (ChadoFeatureProp)properties.get(i);
+ FeatureProp property = (FeatureProp)properties.get(i);
if(property.getCvterm().getName().equals("colour") ||
property.getCvterm().getName().equals("color") )
@@ -1031,7 +1032,7 @@ public class GeneViewerPanel extends JPanel
* @return frame id
*/
private int getFrameID(ChadoCanonicalGene chado_gene,
- ChadoFeatureLoc loc,
+ FeatureLoc loc,
int nexon, List exons)
{
final int position_on_strand;
@@ -1083,7 +1084,7 @@ public class GeneViewerPanel extends JPanel
**/
private int getFrameShift(int nexon, List exons,
ChadoCanonicalGene chado_gene,
- ChadoFeatureLoc loc)
+ FeatureLoc loc)
{
// find the number of bases in the segments before this one
int base_count = 0;
@@ -1091,8 +1092,9 @@ public class GeneViewerPanel extends JPanel
for(int i = 0; i < exons.size(); ++i)
{
- ChadoFeature this_feature = (ChadoFeature)exons.get(i);
- ChadoFeatureLoc featureLoc = ChadoFeature.getFeatureLoc(
+ uk.ac.sanger.artemis.chado.Feature this_feature =
+ (uk.ac.sanger.artemis.chado.Feature)exons.get(i);
+ FeatureLoc featureLoc = uk.ac.sanger.artemis.chado.Feature.getFeatureLoc(
this_feature.getFeaturelocsForFeatureId(), chado_gene.getSrcfeature_id());
int this_direction;
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index 6e65bff36e29ccda635c5f4dbed001a97eebc73b..a538fbd70f4dab1f6090e9dfdbbf024f97a5c9cb 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -427,9 +427,9 @@ public class DatabaseDocument extends Document
final int srcfeature_id = Integer.parseInt(parentFeatureID);
// build srcfeature object
- ChadoFeatureLoc featureloc = new ChadoFeatureLoc();
+ FeatureLoc featureloc = new FeatureLoc();
featureloc.setSrcfeature_id(srcfeature_id);
- ChadoFeature parent = new ChadoFeature();
+ Feature parent = new Feature();
parent.setFeatureloc(featureloc);
List featList = dao.getFeaturesByLocatedOnFeature(parent);
@@ -438,7 +438,7 @@ public class DatabaseDocument extends Document
for(int i = 0; i < buffers.length; i++)
buffers[i] = new ByteBuffer();
- final ChadoFeature parentFeature = dao.getFeatureById(srcfeature_id);
+ final Feature parentFeature = dao.getFeatureById(srcfeature_id);
ByteBuffer this_buff;
@@ -448,7 +448,7 @@ public class DatabaseDocument extends Document
// build feature name store
for(int i = 0; i < feature_size; i++)
{
- ChadoFeature feat = (ChadoFeature)featList.get(i);
+ Feature feat = (Feature)featList.get(i);
String name = feat.getUniquename();
String feature_id = Integer.toString(feat.getId());
@@ -464,7 +464,7 @@ public class DatabaseDocument extends Document
for(int i = 0; i < feature_size; i++)
{
// select buffer based on feature type
- ChadoFeature feat = (ChadoFeature)featList.get(i);
+ Feature feat = (Feature)featList.get(i);
long type_id = feat.getCvterm().getCvtermId();
String typeName = getCvtermName(type_id, dao);
this_buff = buffers[types.length];
@@ -491,7 +491,8 @@ public class DatabaseDocument extends Document
* @throws SQLException
*
*/
- private Hashtable getAllFeatureSynonyms(final ChadoDAO dao, final String uniquename)
+ private Hashtable getAllFeatureSynonyms(final ChadoDAO dao,
+ final String uniquename)
throws SQLException
{
List list = dao.getFeatureSynonymsByUniquename(uniquename);
@@ -499,11 +500,11 @@ public class DatabaseDocument extends Document
Hashtable synonym = new Hashtable();
Integer feature_id;
Vector value;
- ChadoFeatureSynonym alias;
+ FeatureSynonym alias;
for(int i=0; i<list.size(); i++)
{
- alias = (ChadoFeatureSynonym)list.get(i);
+ alias = (FeatureSynonym)list.get(i);
feature_id = alias.getFeature_id();
if(synonym.containsKey(feature_id))
value = (Vector)synonym.get(feature_id);
@@ -536,21 +537,21 @@ public class DatabaseDocument extends Document
{
Hashtable id_store = new Hashtable();
- //ChadoFeature feature = new ChadoFeature();
+ //Feature feature = new Feature();
//feature.setUniquename(search_gene);
reset((String)getLocation(), (String)schema_search.get(0));
dao = getDAO();
- ChadoFeature feature = dao.getFeatureByUniqueName(search_gene);
+ Feature feature = dao.getFeatureByUniqueName(search_gene);
ChadoCanonicalGene chado_gene = new ChadoCanonicalGene();
id_store.put(Integer.toString(feature.getId()), feature.getUniquename());
List featurelocs = feature.getFeaturelocsForFeatureId();
- ChadoFeatureLoc featureloc = (ChadoFeatureLoc) featurelocs.get(0);
+ FeatureLoc featureloc = (FeatureLoc) featurelocs.get(0);
int src_id = featureloc.getSrcfeature_id();
- ChadoFeature parent = new ChadoFeature();
+ Feature parent = new Feature();
parent.setId(src_id);
parent = dao.getFeatureById(src_id); //.getLazyFeature(parent);
@@ -568,16 +569,16 @@ public class DatabaseDocument extends Document
for(int i = 0; i < relations.size(); i++)
{
- //ChadoFeature transcript = new ChadoFeature();
+ //Feature transcript = new Feature();
- int id = ((ChadoFeatureRelationship) relations.get(i)).getSubject_id();
+ int id = ((FeatureRelationship) relations.get(i)).getSubject_id();
//transcript.setId(id);
- ChadoFeature transcript = dao.getFeatureById(id); //.getLazyFeature(transcript);
+ Feature transcript = dao.getFeatureById(id); //.getLazyFeature(transcript);
id_store.put(Integer.toString(transcript.getId()), transcript
.getUniquename());
- ChadoFeatureLoc loc = ChadoFeature.getFeatureLoc(transcript
+ FeatureLoc loc = Feature.getFeatureLoc(transcript
.getFeaturelocsForFeatureId(), src_id);
chadoToGFF(transcript, feature.getUniquename(), null,
null, id_store, dao, loc, buff);
@@ -587,15 +588,15 @@ public class DatabaseDocument extends Document
for(int j = 0; j < transcipt_relations.size(); j++)
{
- id = ((ChadoFeatureRelationship) transcipt_relations.get(j)).getSubject_id();
- //ChadoFeature child = new ChadoFeature();
- //child.setId(((ChadoFeatureRelationship) transcipt_relations.get(j))
+ id = ((FeatureRelationship) transcipt_relations.get(j)).getSubject_id();
+ //Feature child = new Feature();
+ //child.setId(((FeatureRelationship) transcipt_relations.get(j))
// .getSubject_id());
- ChadoFeature child = dao.getFeatureById(id); //dao.getLazyFeature(child);
+ Feature child = dao.getFeatureById(id); //dao.getLazyFeature(child);
id_store.put(Integer.toString(child.getId()), child.getUniquename());
- loc = ChadoFeature.getFeatureLoc(child.getFeaturelocsForFeatureId(),src_id);
+ loc = Feature.getFeatureLoc(child.getFeaturelocsForFeatureId(),src_id);
chadoToGFF(child, transcript.getUniquename(), null,
null, id_store, dao, loc, buff);
}
@@ -615,13 +616,13 @@ public class DatabaseDocument extends Document
* @param featureloc feature location for this chado feature
* @param this_buff byte buffer of GFF line
*/
- private static void chadoToGFF(final ChadoFeature feat,
+ private static void chadoToGFF(final Feature feat,
final String parentFeature,
final Hashtable dbxrefs,
final Hashtable synonym,
final Hashtable id_store,
final ChadoDAO dao,
- final ChadoFeatureLoc featureloc,
+ final FeatureLoc featureloc,
final ByteBuffer this_buff)
{
String gff_source = null;
@@ -642,7 +643,7 @@ public class DatabaseDocument extends Document
int rank = -1;
if(feat.getFeature_relationship() != null)
{
- ChadoFeatureRelationship feat_relationship = feat.getFeature_relationship();
+ FeatureRelationship feat_relationship = feat.getFeature_relationship();
parent_id = Integer.toString(feat_relationship.getObject_id());
long parent_type_id = feat_relationship.getCvterm().getCvtermId();
@@ -657,8 +658,8 @@ public class DatabaseDocument extends Document
List relations = feat.getFeatureRelationshipsForSubjectId();
for(int i=0; i<relations.size(); i++)
{
- ChadoFeatureRelationship feat_relationship =
- (ChadoFeatureRelationship)relations.get(i);
+ FeatureRelationship feat_relationship =
+ (FeatureRelationship)relations.get(i);
parent_id = Integer.toString(feat_relationship.getObject_id());
System.out.println("HERE "+i+" "+feat_relationship.getCvterm().getName()+ " "+
feat_relationship.getObject_id()+" "+feat_relationship.getSubject_id()+ " parent_id="+ parent_id);
@@ -745,7 +746,7 @@ public class DatabaseDocument extends Document
Vector qualifier_value = (Vector)qualifiers.get(qualifier_type_id);
for(int j=0; j<qualifier_value.size(); j++)
{
- ChadoFeatureProp featprop = (ChadoFeatureProp)qualifier_value.get(j);
+ FeatureProp featprop = (FeatureProp)qualifier_value.get(j);
if(featprop.getValue() != null)
this_buff.append(qualifier_name+ "=" +
@@ -771,11 +772,11 @@ public class DatabaseDocument extends Document
if(synonym != null &&
synonym.containsKey(feature_id))
{
- ChadoFeatureSynonym alias;
+ FeatureSynonym alias;
Vector v_synonyms = (Vector)synonym.get(feature_id);
for(int j=0; j<v_synonyms.size(); j++)
{
- alias = (ChadoFeatureSynonym)v_synonyms.get(j);
+ alias = (FeatureSynonym)v_synonyms.get(j);
this_buff.append( getCvtermName(alias.getSynonym().getCvterm().getCvtermId(), dao) + "=" );
//this_buff.append(alias.getSynonym().getCvterm().getName()+"=");
@@ -836,7 +837,7 @@ public class DatabaseDocument extends Document
while(it.hasNext())
{
- ChadoCvterm cv = (ChadoCvterm)it.next();
+ Cvterm cv = (Cvterm)it.next();
cvterm.put(new Long(cv.getCvtermId()), cv.getName());
}
}
@@ -859,7 +860,7 @@ public class DatabaseDocument extends Document
private ByteBuffer getChadoSequence(ChadoDAO dao, ByteBuffer buff)
throws java.sql.SQLException
{
- ChadoFeature feature = dao.getFeatureById(Integer.parseInt(feature_id));
+ Feature feature = dao.getFeatureById(Integer.parseInt(feature_id));
buff.append("##FASTA\n>");
buff.append(feature.getUniquename());
@@ -934,7 +935,7 @@ public class DatabaseDocument extends Document
Iterator it_residue_features = list_residue_features.iterator();
while(it_residue_features.hasNext())
{
- ChadoFeature feature = (ChadoFeature)it_residue_features.next();
+ Feature feature = (Feature)it_residue_features.next();
String typeName = getCvtermName(feature.getCvterm().getCvtermId(), getDAO());
db.put(schema + " - " + typeName + " - " + feature.getUniquename(),
@@ -1111,7 +1112,7 @@ public class DatabaseDocument extends Document
dao.writeTimeLastModified((String) uniquename.get(k), ts);
- ChadoFeature feature = dao.getFeatureByUniqueName((String) uniquename.get(k));
+ Feature feature = dao.getFeatureByUniqueName((String) uniquename.get(k));
ts2 = feature.getTimelastmodified();
if(ts2 == null)
continue;
@@ -1171,7 +1172,7 @@ public class DatabaseDocument extends Document
final ChadoDAO dao)
throws SQLException
{
- ChadoFeature feature = dao.getFeatureByUniqueName(uniquename);
+ Feature feature = dao.getFeatureByUniqueName(uniquename);
Timestamp now = feature.getTimelastmodified();
if(now != null && timestamp != null)
@@ -1213,7 +1214,7 @@ public class DatabaseDocument extends Document
else
dao = new IBatisDAO(src.getPfield());
- ChadoFeature feature = new ChadoFeature();
+ Feature feature = new Feature();
feature.setUniquename(args[0]);
List schemas = new Vector();
schemas.add(args[1]);
@@ -1222,14 +1223,14 @@ public class DatabaseDocument extends Document
System.out.println("FINISHED getFeature()");
for(int i = 0; i < featureList.size(); i++)
{
- feature = (ChadoFeature)featureList.get(i);
+ feature = (Feature)featureList.get(i);
String abb = feature.getOrganism().getAbbreviation();
String type = feature.getCvterm().getName();
int fmin = feature.getFeatureloc().getFmin() + 1;
int fmax = feature.getFeatureloc().getFmax();
String featprop =
- ((ChadoFeatureProp)feature.getFeaturepropList().get(0)).getCvterm().getName();
+ ((FeatureProp)feature.getFeaturepropList().get(0)).getCvterm().getName();
System.out.print(fmin+".."+fmax);
System.out.print(" "+type);
@@ -1243,7 +1244,7 @@ public class DatabaseDocument extends Document
Vector syns = (Vector)synonyms.get(new Integer(feature.getId()));
for(int j=0; j<syns.size(); j++)
{
- ChadoFeatureSynonym alias = (ChadoFeatureSynonym)syns.get(j);
+ FeatureSynonym alias = (FeatureSynonym)syns.get(j);
System.out.print(" "+alias.getSynonym().getCvterm().getName()+
"="+alias.getSynonym().getName());
}*/