From 95a8a1bcfd2bc3e98e779ddc0b703fd49195d4ea Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Fri, 1 Sep 2006 09:27:53 +0000
Subject: [PATCH] rename some chado table objects
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@4680 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
artemis_sqlmap/Cvterm.xml | 13 +-
artemis_sqlmap/Dbxref.xml | 48 +++---
artemis_sqlmap/Feature.xml | 86 +++++-----
artemis_sqlmap/Synonym.xml | 20 +--
uk/ac/sanger/artemis/chado/ChadoDAO.java | 8 +-
uk/ac/sanger/artemis/chado/ChadoDemo.java | 24 +--
.../artemis/chado/ChadoTransaction.java | 3 -
.../chado/ChadoTransactionManager.java | 106 ++++++-------
.../chado/{Cvterm.java => CvTerm.java} | 24 +--
.../chado/{Dbxref.java => DbXRef.java} | 12 +-
uk/ac/sanger/artemis/chado/Feature.java | 101 ++++++------
...{FeatureDbxref.java => FeatureDbXRef.java} | 27 ++--
uk/ac/sanger/artemis/chado/FeatureProp.java | 14 +-
.../artemis/chado/FeatureRelationship.java | 14 +-
uk/ac/sanger/artemis/chado/IBatisDAO.java | 87 +++++-----
uk/ac/sanger/artemis/chado/JdbcDAO.java | 150 +++++++++---------
uk/ac/sanger/artemis/chado/Synonym.java | 10 +-
.../genebuilder/GeneViewerPanel.java | 17 +-
.../sanger/artemis/util/DatabaseDocument.java | 81 +++++-----
19 files changed, 426 insertions(+), 419 deletions(-)
rename uk/ac/sanger/artemis/chado/{Cvterm.java => CvTerm.java} (89%)
rename uk/ac/sanger/artemis/chado/{Dbxref.java => DbXRef.java} (90%)
rename uk/ac/sanger/artemis/chado/{FeatureDbxref.java => FeatureDbXRef.java} (79%)
diff --git a/artemis_sqlmap/Cvterm.xml b/artemis_sqlmap/Cvterm.xml
index 0fe20fb9b..09344b66c 100644
--- a/artemis_sqlmap/Cvterm.xml
+++ b/artemis_sqlmap/Cvterm.xml
@@ -6,18 +6,21 @@
<sqlMap namespace="Cvterm">
+
+ <typeAlias alias="CvTerm"
+ type="uk.ac.sanger.artemis.chado.CvTerm"/>
- <resultMap id="select-cvterm-names-result" class="uk.ac.sanger.artemis.chado.Cvterm">
- <result property="cvtermId" column="cvterm_id"/>
+ <resultMap id="select-cvterm-names-result" class="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.Cvterm">
- <result property="cvtermId" column="cvterm_id"/>
+ <resultMap id="lazy-cvterm" class="CvTerm">
+ <result property="cvTermId" column="cvterm_id"/>
<result property="name" column="name"/>
<result property="definition" column="definition"/>
- <result property="dbxref" column="dbxref_id" select="selectDbxref"/>
+ <result property="dbXRef" column="dbxref_id" select="selectDbXRef"/>
<result property="isObsolete" column="is_obsolete"/>
<result property="isRelationshiptype" column="is_relationshiptype"/>
</resultMap>
diff --git a/artemis_sqlmap/Dbxref.xml b/artemis_sqlmap/Dbxref.xml
index 435a4d09b..1638e050f 100644
--- a/artemis_sqlmap/Dbxref.xml
+++ b/artemis_sqlmap/Dbxref.xml
@@ -5,26 +5,26 @@
"http://ibatis.apache.org/dtd/sql-map-2.dtd">
-<sqlMap namespace="Dbxref">
+<sqlMap namespace="DbXRef">
- <typeAlias alias="FeatureDbxref"
- type="uk.ac.sanger.artemis.chado.FeatureDbxref"/>
+ <typeAlias alias="FeatureDbXRef"
+ type="uk.ac.sanger.artemis.chado.FeatureDbXRef"/>
- <typeAlias alias="Dbxref"
- type="uk.ac.sanger.artemis.chado.Dbxref"/>
+ <typeAlias alias="DbXRef"
+ type="uk.ac.sanger.artemis.chado.DbXRef"/>
<typeAlias alias="Db"
type="uk.ac.sanger.artemis.chado.Db"/>
<resultMap id="select-feature-dbxref"
- class="FeatureDbxref">
+ class="FeatureDbXRef">
<result property="feature.id" column="feature_id"/>
- <result property="dbxref.db.name" column="name"/>
- <result property="dbxref.accession" column="accession"/>
- <result property="dbxref.version" column="version"/>
+ <result property="dbXRef.db.name" column="name"/>
+ <result property="dbXRef.accession" column="accession"/>
+ <result property="dbXRef.version" column="version"/>
</resultMap>
- <select id="getFeatureDbxref"
+ <select id="getFeatureDbXRef"
parameterClass="uk.ac.sanger.artemis.chado.Feature"
resultMap="select-feature-dbxref">
SELECT db.name, dbx.accession, dbx.version, dbx_f.feature_id
@@ -32,8 +32,8 @@
LEFT JOIN dbxref dbx ON dbx.dbxref_id=dbx_f.dbxref_id
LEFT JOIN db ON db.db_id=dbx.db_id
LEFT JOIN feature f ON dbx_f.feature_id=f.feature_id
- <isNotNull property="uniquename">
- WHERE f.uniquename=#uniquename#
+ <isNotNull property="uniqueName">
+ WHERE f.uniquename=#uniqueName#
</isNotNull>
<isGreaterThan property="id" compareValue="0">
WHERE dbx_f.feature_id=$id$
@@ -46,40 +46,40 @@
SELECT db_id FROM db WHERE name=#name#
</select>
- <select id="getDbxrefId" parameterClass="Dbxref"
+ <select id="getDbXRefId" parameterClass="DbXRef"
resultClass="java.lang.Integer">
SELECT dbxref_id FROM dbxref WHERE accession=#accession#
- AND db_id=$db_id$;
+ AND db_id=$dbXRefId$;
</select>
- <select id="selectDbxref" resultClass="Dbxref">
- SELECT * FROM dbxref WHERE dbxref_id=$dbxref_id$
+ <select id="selectDbXRef" resultClass="DbXRef">
+ SELECT * FROM dbxref WHERE dbxref_id=$dbXRefId$
</select>
<!-- WRITE BACK -->
- <delete id="deleteFeatureDbxref" parameterClass="FeatureDbxref">
+ <delete id="deleteFeatureDbXRef" parameterClass="FeatureDbXRef">
DELETE FROM feature_dbxref
WHERE dbxref_id=
- (SELECT dbxref_id FROM dbxref WHERE accession=#dbxref.accession#
- AND db_id=(SELECT db_id FROM db WHERE name=#dbxref.db.name#))
+ (SELECT dbxref_id FROM dbxref WHERE accession=#dbXRef.accession#
+ AND db_id=(SELECT db_id FROM db WHERE name=#dbXRef.db.name#))
AND feature_id=
- (SELECT feature_id FROM feature WHERE uniquename=#feature.uniquename#)
+ (SELECT feature_id FROM feature WHERE uniquename=#feature.uniqueName#)
</delete>
- <insert id="insertFeatureDbxref" parameterClass="FeatureDbxref">
+ <insert id="insertFeatureDbXRef" parameterClass="FeatureDbXRef">
INSERT INTO feature_dbxref
(feature_id, dbxref_id, is_current)
VALUES
- ($feature.id$, $dbxref_id$, $current$)
+ ($feature.id$, $dbXRef.dbXRefId$, $current$)
</insert>
- <insert id="insertDbxref" parameterClass="Dbxref">
+ <insert id="insertDbXRef" parameterClass="DbXRef">
INSERT INTO dbxref ( db_id, accession )
- VALUES ($db_id$, #accession#)
+ VALUES ($dbXRefId$, #accession#)
</insert>
</sqlMap>
diff --git a/artemis_sqlmap/Feature.xml b/artemis_sqlmap/Feature.xml
index 89c416c3b..726052cbe 100644
--- a/artemis_sqlmap/Feature.xml
+++ b/artemis_sqlmap/Feature.xml
@@ -22,7 +22,7 @@
<parameterMap id="schema-cvlist"
class="Feature">
<parameter property="schema" javaType="java.lang.String"/>
- <parameter property="featureCvterms" javaType="java.util.List"/>
+ <parameter property="featureCvTerms" javaType="java.util.List"/>
</parameterMap>
<resultMap id="select-feature"
@@ -30,15 +30,15 @@
<result property="timelastmodified" column="timelastmodified"/>
<result property="id" column="id"/>
<result property="feature_relationship.object.id" column="object_id"/>
- <result property="feature_relationship.cvterm.cvtermId" column="relation_type_id"/>
+ <result property="feature_relationship.cvTerm.cvTermId" column="relation_type_id"/>
<result property="feature_relationship.rank" column="rank"/>
<result property="featureloc.strand" column="strand" nullValue="0"/>
<result property="featureloc.fmin" column="fmin" nullValue="-1"/>
<result property="featureloc.fmax" column="fmax" nullValue="0"/>
<result property="featureloc.phase" column="phase" nullValue="10"/>
- <result property="uniquename" column="uniquename"/>
- <result property="cvterm.cvtermId" column="type_id"/>
- <result property="featureprop.cvterm.cvtermId" column="prop_type_id" nullValue="0"/>
+ <result property="uniqueName" column="uniquename"/>
+ <result property="cvTerm.cvTermId" column="type_id"/>
+ <result property="featureprop.cvTerm.cvTermId" column="prop_type_id" nullValue="0"/>
<result property="featureprop.value" column="value"/>
<result property="featureprop.rank" column="prop_rank" nullValue="0"/>
</resultMap>
@@ -49,22 +49,22 @@
class="Feature">
<result property="timelastmodified" column="timelastmodified"/>
<result property="id" column="id"/>
- <result property="uniquename" column="uniquename"/>
+ <result property="uniqueName" column="uniquename"/>
<result property="name" column="name"/>
<result property="length" column="length" nullValue="-999" />
<result property="residues" column="residues" />
- <result property="cvterm" column="type_id" select="selectCvterm" />
+ <result property="cvTerm" column="type_id" select="selectCvterm" />
<result property="featurelocsForFeatureId" column="{id=id}"
select="getFeatureLoc" />
<result property="featurepropList" column="{feature_id=id}"
select="selectFeatureProp" />
- <result property="featureDbxrefs" column="{id=id}"
- select="getFeatureDbxref" />
+ <result property="featureDbXRefs" column="{id=id}"
+ select="getFeatureDbXRef" />
<result property="featureRelationshipsForObjectId" column="{object_id=id}"
select="getFeatureRelationship" />
<result property="featureRelationshipsForSubjectId" column="{subject_id=id}"
select="getFeatureRelationship" />
- <result property="featureSynonymsForFeatureId" column="{feature.uniquename=uniquename}"
+ <result property="featureSynonymsForFeatureId" column="{feature.uniqueName=uniqueName}"
select="getLazyFeatureSynonymsByUniquename" />
<result property="organism" column="organism_id" select="getOrganism" />
</resultMap>
@@ -74,16 +74,16 @@
class="Feature">
<result property="organism.abbreviation" column="abbreviation"/>
<result property="name" column="name"/>
- <result property="uniquename" column="uniquename"/>
+ <result property="uniqueName" column="uniquename"/>
<result property="id" column="feature_id"/>
- <result property="cvterm.cvtermId" column="type_id"/>
+ <result property="cvTerm.cvTermId" column="type_id"/>
</resultMap>
<resultMap id="select-featureprop"
class="FeatureProp">
<result property="value" column="value" />
<result property="rank" column="rank" />
- <result property="cvterm" column="type_id" select="selectCvterm" />
+ <result property="cvTerm" column="type_id" select="selectCvterm" />
</resultMap>
<resultMap id="select-relationship"
@@ -92,7 +92,7 @@
<result property="object.id" column="object_id" />
<result property="value" column="value" />
<result property="rank" column="rank" />
- <result property="cvterm" column="type_id" select="selectCvterm" />
+ <result property="cvTerm" column="type_id" select="selectCvterm" />
</resultMap>
<resultMap id="select-location"
@@ -168,8 +168,8 @@
<isGreaterThan property="featureloc.srcfeature_id" compareValue="0">
srcfeature_id=$featureloc.srcfeature_id$
</isGreaterThan>
- <isNotNull property="uniquename">
- uniquename LIKE #uniquename#
+ <isNotNull property="uniqueName">
+ uniquename LIKE #uniqueName#
</isNotNull>
</dynamic>
ORDER BY f.type_id, uniquename
@@ -193,17 +193,17 @@
f.feature_id=$id$ AND
</isGreaterThan>
- <isNotNull property="uniquename">
+ <isNotNull property="uniqueName">
<isNotNull property="featureSynonymsForFeatureId">
<iterate property="featureSynonymsForFeatureId" conjunction="OR" open="(" close=") OR">
f.feature_id=#featureSynonymsForFeatureId[].feature.id#
</iterate>
</isNotNull>
- uniquename LIKE #uniquename# OR name LIKE #uniquename# AND
+ uniquename LIKE #uniqueName# OR name LIKE #uniqueName# AND
</isNotNull>
- <isGreaterThan property="cvterm.cvtermId" compareValue="0">
- feature.type_id=$cvterm.cvtermId$ AND
+ <isGreaterThan property="cvTerm.cvTermId" compareValue="0">
+ feature.type_id=$cvTerm.cvTermId$ AND
</isGreaterThan>
</dynamic>
f.feature_id > 0
@@ -233,8 +233,8 @@
FROM organism, $schema$.feature WHERE
organism.organism_id=$schema$.feature.organism_id AND
residues notnull
- <iterate prepend="AND" property="featureCvterms" conjunction="OR" open="(" close=")">
- type_id=#featureCvterms[]#
+ <iterate prepend="AND" property="featureCvTerms" conjunction="OR" open="(" close=")">
+ type_id=#featureCvTerms[]#
</iterate>
ORDER BY abbreviation
</select>
@@ -261,17 +261,17 @@
UPDATE featureloc
SET fmin=$fmin$, fmax=$fmax$, rank=$rank$, strand=$strand$, phase=$phase$
WHERE
- <isNotNull property="feature.uniquename">
- feature_id=(SELECT feature_id FROM feature WHERE uniquename=#feature.uniquename#)
+ <isNotNull property="feature.uniqueName">
+ feature_id=(SELECT feature_id FROM feature WHERE uniquename=#feature.uniqueName#)
</isNotNull>
</update>
<update id="updateFeature"
parameterClass="Feature">
UPDATE feature
- SET uniquename=#uniquename#
- <isNotNull property="cvterm.cvtermId">
- , type_id=$cvterm.cvtermId$
+ SET uniquename=#uniqueName#
+ <isNotNull property="cvTerm.cvTermId">
+ , type_id=$cvTerm.cvTermId$
</isNotNull>
<isNotNull property="timelastmodified">
, timelastmodified=#timelastmodified#
@@ -283,19 +283,19 @@
parameterClass="FeatureProp">
UPDATE featureprop
SET value=#value#
- WHERE rank=$rank$ AND type_id=$cvterm.cvtermId$ AND
- feature_id=(SELECT feature_id FROM feature WHERE uniquename=#feature.uniquename#)
+ WHERE rank=$rank$ AND type_id=$cvTerm.cvTermId$ AND
+ feature_id=(SELECT feature_id FROM feature WHERE uniquename=#feature.uniqueName#)
</update>
<update id="updateFeatureRelationshipsForSubjectId"
parameterClass="FeatureRelationship">
UPDATE feature_relationship
SET
- rank=$rank$, type_id=$cvterm.cvtermId$
+ rank=$rank$, type_id=$cvTerm.cvTermId$
WHERE subject_id=
- ( SELECT feature_id FROM feature WHERE uniquename=#subject.uniquename# )
+ ( SELECT feature_id FROM feature WHERE uniquename=#subject.uniqueName# )
AND object_id=
- ( SELECT feature_id FROM feature WHERE uniquename=#object.uniquename# )
+ ( SELECT feature_id FROM feature WHERE uniquename=#object.uniqueName# )
</update>
<!-- INSERT -->
@@ -304,8 +304,8 @@
INSERT INTO featureprop
( feature_id, type_id, value, rank )
VALUES
- ( (SELECT feature_id FROM feature WHERE uniquename=#feature.uniquename#),
- $cvterm.cvtermId$, #value#, $rank$ )
+ ( (SELECT feature_id FROM feature WHERE uniquename=#feature.uniqueName#),
+ $cvTerm.cvTermId$, #value#, $rank$ )
</insert>
<insert id="insertFeature"
@@ -316,8 +316,8 @@
( nextval('feature_feature_id_seq'),
$organism.id$,
#name#,
- #uniquename#,
- $cvterm.cvtermId$ )
+ #uniqueName#,
+ $cvTerm.cvTermId$ )
</insert>
<insert id="insertFeatureLoc"
@@ -339,9 +339,9 @@
INSERT INTO feature_relationship
( subject_id, object_id, type_id )
VALUES
- ( (SELECT feature_id FROM feature WHERE uniquename=#subject.uniquename#),
- (SELECT feature_id FROM feature WHERE uniquename=#object.uniquename#),
- $cvterm.cvtermId$ )
+ ( (SELECT feature_id FROM feature WHERE uniquename=#subject.uniqueName#),
+ (SELECT feature_id FROM feature WHERE uniquename=#object.uniqueName#),
+ $cvTerm.cvTermId$ )
</insert>
@@ -351,9 +351,9 @@
parameterClass="FeatureProp">
DELETE FROM featureprop
WHERE
- <isNotNull property="feature.uniquename">
+ <isNotNull property="feature.uniqueName">
feature_id=
- (SELECT feature_id FROM feature WHERE uniquename=#feature.uniquename#)
+ (SELECT feature_id FROM feature WHERE uniquename=#feature.uniqueName#)
AND
</isNotNull>
<isGreaterThan property="rank" compareValue="-1">
@@ -362,13 +362,13 @@
<isNotNull property="value">
value=#value# AND
</isNotNull>
- type_id=$cvterm.cvtermId$
+ type_id=$cvTerm.cvTermId$
</delete>
<delete id="deleteFeature"
parameterClass="Feature">
DELETE FROM feature
- WHERE uniquename=#uniquename#
+ WHERE uniquename=#uniqueName#
</delete>
diff --git a/artemis_sqlmap/Synonym.xml b/artemis_sqlmap/Synonym.xml
index 0d73c2745..4e6d27363 100644
--- a/artemis_sqlmap/Synonym.xml
+++ b/artemis_sqlmap/Synonym.xml
@@ -23,7 +23,7 @@
<result property="synonym.synonym_id" column="synonym_id"/>
<result property="synonym.name" column="name"/>
<result property="synonym.synonym_sgml" column="synonym_sgml"/>
- <result property="synonym.cvterm.cvtermId" column="type_id" />
+ <result property="synonym.cvTerm.cvTermId" column="type_id" />
</resultMap>
<resultMap id="select-alias-part-lazy"
@@ -50,7 +50,7 @@
<result property="synonym_id" column="synonym_id"/>
<result property="name" column="name"/>
<result property="synonym_sgml" column="synonym_sgml"/>
- <result property="cvterm" column="type_id" select="selectCvterm"/>
+ <result property="cvTerm" column="type_id" select="selectCvterm"/>
</resultMap>
@@ -62,7 +62,7 @@
FROM feature_synonym fs
LEFT JOIN feature f ON f.feature_id=fs.feature_id
LEFT JOIN synonym s ON fs.synonym_id=s.synonym_id
- <isNotNull property="uniquename">
+ <isNotNull property="uniqueName">
WHERE uniquename=#uniquename#
</isNotNull>
</select>
@@ -72,8 +72,8 @@
SELECT fs.*
FROM feature_synonym fs
LEFT JOIN feature f ON f.feature_id=fs.feature_id
- <isNotNull property="feature.uniquename">
- WHERE uniquename=#feature.uniquename#
+ <isNotNull property="feature.uniqueName">
+ WHERE uniquename=#feature.uniqueName#
</isNotNull>
</select>
@@ -91,8 +91,8 @@
<isNotNull property="name">
name=#name# AND
</isNotNull>
- <isNotNull property="cvterm">
- type_id=$cvterm.cvtermId$ AND
+ <isNotNull property="cvTerm">
+ type_id=$cvTerm.cvTermId$ AND
</isNotNull>
synonym_id > 0
</select>
@@ -108,13 +108,13 @@
DELETE FROM feature_synonym WHERE
synonym_id=$synonym_id$ AND
feature_id=(SELECT feature_id FROM feature WHERE
- uniquename=#feature.uniquename#)
+ uniquename=#feature.uniqueName#)
</delete>
<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=#feature.uniquename#),
+ (SELECT feature_id FROM feature WHERE uniquename=#feature.uniqueName#),
1)
</insert>
@@ -124,7 +124,7 @@
<insert id="insertAlias" parameterClass="FeatureSynonym">
INSERT INTO synonym ( name, type_id, synonym_sgml )
- VALUES ( #synonym.name#, $synonym.cvterm.cvtermId$, #synonym.name# )
+ VALUES ( #synonym.name#, $synonym.cvTerm.cvTermId$, #synonym.name# )
</insert>
</sqlMap>
\ No newline at end of file
diff --git a/uk/ac/sanger/artemis/chado/ChadoDAO.java b/uk/ac/sanger/artemis/chado/ChadoDAO.java
index fdcabc445..4e10aafb0 100644
--- a/uk/ac/sanger/artemis/chado/ChadoDAO.java
+++ b/uk/ac/sanger/artemis/chado/ChadoDAO.java
@@ -105,10 +105,10 @@ public interface ChadoDAO
public List getSchema();
/**
- * Get the all the <code>Cvterm</code> objects as a<code>List</code>.
+ * Get the all the <code>CvTerm</code> objects as a<code>List</code>.
* @return the full list of cvterm_id and name
*/
- public List getCvterm();
+ public List getCvTerm();
/**
@@ -117,7 +117,7 @@ public interface ChadoDAO
* all <code>FeatureDbxref</code> are returned.
* @return a <code>List</code> of feature_dbxrefs.
*/
- public List getFeatureDbxrefByUniquename(final String uniquename);
+ public List getFeatureDbXRefByUniquename(final String uniquename);
/**
* Return a list of FeatureSynonyms for a uniquename
@@ -134,7 +134,7 @@ public interface ChadoDAO
* @param type the type of the Synonym
* @return a Synonym, or null
*/
- public Synonym getSynonymByNameAndCvTerm(String name, Cvterm type);
+ public Synonym getSynonymByNameAndCvTerm(String name, CvTerm type);
/**
diff --git a/uk/ac/sanger/artemis/chado/ChadoDemo.java b/uk/ac/sanger/artemis/chado/ChadoDemo.java
index 2dd5fe0a9..0348fa0b1 100644
--- a/uk/ac/sanger/artemis/chado/ChadoDemo.java
+++ b/uk/ac/sanger/artemis/chado/ChadoDemo.java
@@ -251,22 +251,22 @@ public class ChadoDemo
int row = result_table.getSelectedRow();
StringBuffer attr_buff = new StringBuffer();
Feature chado_feature = (Feature)featureList.get(row);
- List attributes = chado_feature.getFeaturepropList();
- List dbxrefs = chado_feature.getFeatureDbxrefs();
+ List attributes = (List)chado_feature.getFeaturepropList();
+ List dbxrefs = (List)chado_feature.getFeatureDbXRefs();
if(dbxrefs.size() > 0)
{
attr_buff.append("/Dbxref=");
for(int i = 0; i < dbxrefs.size(); i++)
{
- FeatureDbxref dbxref = (FeatureDbxref) dbxrefs.get(i);
- attr_buff.append(dbxref.getDbxref().getDb().getName() + ":"
- + dbxref.getDbxref().getAccession() + "; ");
+ FeatureDbXRef dbxref = (FeatureDbXRef) dbxrefs.get(i);
+ attr_buff.append(dbxref.getDbXRef().getDb().getName() + ":"
+ + dbxref.getDbXRef().getAccession() + "; ");
}
attr_buff.append("\n");
}
- List synonyms = chado_feature.getFeatureSynonymsForFeatureId();
+ List synonyms = (List)chado_feature.getFeatureSynonymsForFeatureId();
// append synonyms
if(synonyms.size() > 0)
@@ -277,7 +277,7 @@ public class ChadoDemo
{
alias = (FeatureSynonym) synonyms.get(i);
attr_buff.append("/");
- attr_buff.append(alias.getSynonym().getCvterm().getName() + "=");
+ attr_buff.append(alias.getSynonym().getCvTerm().getName() + "=");
attr_buff.append(alias.getSynonym().getName());
attr_buff.append(";");
@@ -290,7 +290,7 @@ public class ChadoDemo
{
FeatureProp featprop = (FeatureProp) attributes.get(i);
- attr_buff.append("/" + featprop.getCvterm().getName() + "="
+ attr_buff.append("/" + featprop.getCvTerm().getName() + "="
+ GFFStreamFeature.decode(featprop.getValue()) + "\n");
}
@@ -332,7 +332,7 @@ public class ChadoDemo
feature = (Feature) featureList.get(i);
// assume only one featureloc
- List locs = feature.getFeaturelocsForFeatureId();
+ List locs = (List)feature.getFeaturelocsForFeatureId();
if(locs.size() > 0)
{
@@ -348,10 +348,10 @@ public class ChadoDemo
if(ind > 0)
schema = schema.substring(0,ind)+schema.substring(ind+1);
- System.out.println("get featur type_id.......");
+ System.out.println("get feature type_id.......");
rowData[i][0] = schema;
- rowData[i][1] = feature.getUniquename();
- rowData[i][2] = feature.getCvterm().getName();
+ rowData[i][1] = feature.getUniqueName();
+ rowData[i][2] = feature.getCvTerm().getName();
//rowData[i][2] = (String)cvterm.get(new Long(feature.getType_id()));
rowData[i][3] = Integer.toString(feature.getId());
rowData[i][6] = feature.getTimelastmodified().toString();
diff --git a/uk/ac/sanger/artemis/chado/ChadoTransaction.java b/uk/ac/sanger/artemis/chado/ChadoTransaction.java
index 2b1f8564d..f295226e2 100644
--- a/uk/ac/sanger/artemis/chado/ChadoTransaction.java
+++ b/uk/ac/sanger/artemis/chado/ChadoTransaction.java
@@ -24,9 +24,6 @@
package uk.ac.sanger.artemis.chado;
-import java.util.List;
-import java.util.Vector;
-import java.util.StringTokenizer;
import java.sql.Timestamp;
import uk.ac.sanger.artemis.io.GFFStreamFeature;
diff --git a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
index b44abe55e..1fa1ff26b 100644
--- a/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
+++ b/uk/ac/sanger/artemis/chado/ChadoTransactionManager.java
@@ -382,7 +382,7 @@ public class ChadoTransactionManager
uk.ac.sanger.artemis.chado.Feature chado_feature =
new uk.ac.sanger.artemis.chado.Feature();
- chado_feature.setUniquename(seq_id);
+ chado_feature.setUniqueName(seq_id);
List featureRelationshipsForSubjectId = null;
if(qualifier_relation != null)
@@ -395,15 +395,15 @@ public class ChadoTransactionManager
{
uk.ac.sanger.artemis.chado.Feature parent =
new uk.ac.sanger.artemis.chado.Feature();
- parent.setUniquename((String)parents.get(i));
+ parent.setUniqueName((String)parents.get(i));
FeatureRelationship feature_relationship =
new FeatureRelationship();
- Cvterm cvterm = new Cvterm();
- cvterm.setCvtermId(DatabaseDocument.getCvtermID("part_of").longValue());
+ CvTerm cvterm = new CvTerm();
+ cvterm.setCvTermId(DatabaseDocument.getCvtermID("part_of").longValue());
feature_relationship.setObject(parent);
feature_relationship.setSubject(chado_feature);
- feature_relationship.setCvterm(cvterm);
+ feature_relationship.setCvTerm(cvterm);
feature_relationship.setRank(rank);
featureRelationshipsForSubjectId.add(feature_relationship);
@@ -496,15 +496,15 @@ public class ChadoTransactionManager
{
uk.ac.sanger.artemis.chado.Feature parent =
new uk.ac.sanger.artemis.chado.Feature();
- parent.setUniquename((String)parents.get(i));
+ parent.setUniqueName((String)parents.get(i));
FeatureRelationship feature_relationship =
new FeatureRelationship();
- Cvterm cvterm = new Cvterm();
- cvterm.setCvtermId(DatabaseDocument.getCvtermID("part_of").longValue());
+ CvTerm cvterm = new CvTerm();
+ cvterm.setCvTermId(DatabaseDocument.getCvtermID("part_of").longValue());
feature_relationship.setObject(parent);
feature_relationship.setSubject(chado_feature);
- feature_relationship.setCvterm(cvterm);
+ feature_relationship.setCvTerm(cvterm);
featureRelationshipsForSubjectId.add(feature_relationship);
}
}
@@ -520,15 +520,15 @@ public class ChadoTransactionManager
{
uk.ac.sanger.artemis.chado.Feature parent =
new uk.ac.sanger.artemis.chado.Feature();
- parent.setUniquename((String) derives.get(i));
+ parent.setUniqueName((String) derives.get(i));
FeatureRelationship feature_relationship = new FeatureRelationship();
- Cvterm cvterm = new Cvterm();
- cvterm.setCvtermId(DatabaseDocument.getCvtermID("derives_from")
+ CvTerm cvterm = new CvTerm();
+ cvterm.setCvTermId(DatabaseDocument.getCvtermID("derives_from")
.longValue());
feature_relationship.setObject(parent);
feature_relationship.setSubject(chado_feature);
- feature_relationship.setCvterm(cvterm);
+ feature_relationship.setCvTerm(cvterm);
featureRelationshipsForSubjectId.add(feature_relationship);
}
}
@@ -544,14 +544,14 @@ public class ChadoTransactionManager
featureloc.setFmin(feature.getRawFirstBase()-1);
featureloc.setFmax(feature.getRawLastBase());
- chado_feature.setUniquename(feature_uniquename);
+ chado_feature.setUniqueName(feature_uniquename);
chado_feature.setName(feature_uniquename);
String key = feature.getKey().toString();
- Cvterm cvterm = new Cvterm();
- cvterm.setCvtermId(DatabaseDocument.getCvtermID(key).longValue());
- chado_feature.setCvterm(cvterm);
+ CvTerm cvterm = new CvTerm();
+ cvterm.setCvTermId(DatabaseDocument.getCvtermID(key).longValue());
+ chado_feature.setCvTerm(cvterm);
addQualifiers(feature.getQualifiers(), chado_feature);
// create transaction object
@@ -609,15 +609,15 @@ public class ChadoTransactionManager
{
uk.ac.sanger.artemis.chado.Feature parent =
new uk.ac.sanger.artemis.chado.Feature();
- parent.setUniquename((String)parents.get(i));
+ parent.setUniqueName((String)parents.get(i));
FeatureRelationship feature_relationship =
new FeatureRelationship();
- Cvterm cvterm = new Cvterm();
- cvterm.setCvtermId(DatabaseDocument.getCvtermID("part_of").longValue());
+ CvTerm cvterm = new CvTerm();
+ cvterm.setCvTermId(DatabaseDocument.getCvtermID("part_of").longValue());
feature_relationship.setObject(parent);
feature_relationship.setSubject(chado_feature);
- feature_relationship.setCvterm(cvterm);
+ feature_relationship.setCvTerm(cvterm);
featureRelationshipsForSubjectId.add(feature_relationship);
}
}
@@ -633,15 +633,15 @@ public class ChadoTransactionManager
{
uk.ac.sanger.artemis.chado.Feature parent =
new uk.ac.sanger.artemis.chado.Feature();
- parent.setUniquename((String) derives.get(i));
+ parent.setUniqueName((String) derives.get(i));
FeatureRelationship feature_relationship = new FeatureRelationship();
- Cvterm cvterm = new Cvterm();
- cvterm.setCvtermId(DatabaseDocument.getCvtermID("derives_from")
+ CvTerm cvterm = new CvTerm();
+ cvterm.setCvTermId(DatabaseDocument.getCvtermID("derives_from")
.longValue());
feature_relationship.setObject(parent);
feature_relationship.setSubject(chado_feature);
- feature_relationship.setCvterm(cvterm);
+ feature_relationship.setCvTerm(cvterm);
featureRelationshipsForSubjectId.add(feature_relationship);
}
}
@@ -652,14 +652,14 @@ public class ChadoTransactionManager
featureloc.setFmin(segment.getRawRange().getStart()-1);
featureloc.setFmax(segment.getRawRange().getEnd());
- chado_feature.setUniquename(segment_uniquename);
+ chado_feature.setUniqueName(segment_uniquename);
chado_feature.setName(segment_uniquename);
String key = feature.getKey().toString();
- Cvterm cvterm = new Cvterm();
- cvterm.setCvtermId(DatabaseDocument.getCvtermID(key).longValue());
- chado_feature.setCvterm(cvterm);
+ CvTerm cvterm = new CvTerm();
+ cvterm.setCvTermId(DatabaseDocument.getCvtermID(key).longValue());
+ chado_feature.setCvTerm(cvterm);
//addQualifiers(feature.getQualifiers(), chado_feature);
// create transaction object
@@ -678,7 +678,7 @@ public class ChadoTransactionManager
{
uk.ac.sanger.artemis.chado.Feature chado_feature =
new uk.ac.sanger.artemis.chado.Feature();
- chado_feature.setUniquename(uniquename);
+ chado_feature.setUniqueName(uniquename);
ChadoTransaction tsn = new ChadoTransaction(ChadoTransaction.DELETE,
chado_feature,
@@ -798,11 +798,11 @@ public class ChadoTransactionManager
{
uk.ac.sanger.artemis.chado.Feature chado_feature =
new uk.ac.sanger.artemis.chado.Feature();
- Cvterm cvterm = new Cvterm();
- cvterm.setCvtermId( lcvterm_id.longValue() );
+ CvTerm cvterm = new CvTerm();
+ cvterm.setCvTermId( lcvterm_id.longValue() );
- chado_feature.setCvterm(cvterm);
- chado_feature.setUniquename(uniquename);
+ chado_feature.setCvTerm(cvterm);
+ chado_feature.setUniqueName(uniquename);
tsn = new ChadoTransaction(ChadoTransaction.UPDATE,
chado_feature,
@@ -1093,7 +1093,7 @@ public class ChadoTransactionManager
uk.ac.sanger.artemis.chado.Feature chado_feature =
new uk.ac.sanger.artemis.chado.Feature();
- chado_feature.setUniquename((String)new_qualifier.getValues().get(0));
+ chado_feature.setUniqueName((String)new_qualifier.getValues().get(0));
ChadoTransaction tsn = new ChadoTransaction(ChadoTransaction.UPDATE,
chado_feature,
@@ -1123,16 +1123,16 @@ public class ChadoTransactionManager
System.out.println(uniquename+" in handleReservedTags() DELETE db="+
qualifier_string.substring(0,index)+" acc="+qualifier_string.substring(index+1));
- FeatureDbxref old_dbxref = new FeatureDbxref();
+ FeatureDbXRef old_dbxref = new FeatureDbXRef();
uk.ac.sanger.artemis.chado.Feature chado_feature =
new uk.ac.sanger.artemis.chado.Feature();
- Dbxref dbxref = new Dbxref();
+ 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);
- chado_feature.setUniquename(uniquename);
- old_dbxref.setDbxref(dbxref);
+ chado_feature.setUniqueName(uniquename);
+ old_dbxref.setDbXRef(dbxref);
old_dbxref.setFeature(chado_feature);
tsn = new ChadoTransaction(ChadoTransaction.DELETE,
@@ -1147,7 +1147,7 @@ public class ChadoTransactionManager
FeatureSynonym alias = new FeatureSynonym();
uk.ac.sanger.artemis.chado.Feature chado_feature =
new uk.ac.sanger.artemis.chado.Feature();
- chado_feature.setUniquename(uniquename);
+ chado_feature.setUniqueName(uniquename);
Synonym synonym = new Synonym();
synonym.setName(qualifier_string);
@@ -1180,16 +1180,16 @@ public class ChadoTransactionManager
System.out.println(uniquename+" in handleReservedTags() INSERT db="+
qualifier_string.substring(0,index)+" acc="+qualifier_string.substring(index+1));
- FeatureDbxref new_dbxref = new FeatureDbxref();
- Dbxref dbxref = new Dbxref();
+ 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));
- new_dbxref.setDbxref(dbxref);
+ new_dbxref.setDbXRef(dbxref);
uk.ac.sanger.artemis.chado.Feature feat =
new uk.ac.sanger.artemis.chado.Feature();
- feat.setUniquename(uniquename);
+ feat.setUniqueName(uniquename);
new_dbxref.setFeature(feat);
tsn = new ChadoTransaction(ChadoTransaction.INSERT,
@@ -1204,13 +1204,13 @@ public class ChadoTransactionManager
FeatureSynonym alias = new FeatureSynonym();
uk.ac.sanger.artemis.chado.Feature chado_feature =
new uk.ac.sanger.artemis.chado.Feature();
- chado_feature.setUniquename(uniquename);
+ chado_feature.setUniqueName(uniquename);
Synonym synonym = new Synonym();
- Cvterm cvterm = new Cvterm();
- cvterm.setCvtermId(lcvterm_id.longValue());
+ CvTerm cvterm = new CvTerm();
+ cvterm.setCvTermId(lcvterm_id.longValue());
synonym.setName(qualifier_string);
- synonym.setCvterm(cvterm);
+ synonym.setCvTerm(cvterm);
alias.setSynonym(synonym);
alias.setFeature(chado_feature);
@@ -1255,7 +1255,7 @@ public class ChadoTransactionManager
FeatureLoc featureloc = new FeatureLoc();
uk.ac.sanger.artemis.chado.Feature chado_feature =
new uk.ac.sanger.artemis.chado.Feature();
- chado_feature.setUniquename(seg_id);
+ chado_feature.setUniqueName(seg_id);
featureloc.setFeature(chado_feature);
featureloc.setFmax(range_new.getEnd());
@@ -1305,12 +1305,12 @@ public class ChadoTransactionManager
FeatureProp featureprop = new FeatureProp();
uk.ac.sanger.artemis.chado.Feature chado_feature =
new uk.ac.sanger.artemis.chado.Feature();
- chado_feature.setUniquename(uniquename);
- Cvterm cvterm = new Cvterm();
- cvterm.setCvtermId(lcvterm_id.longValue());
+ chado_feature.setUniqueName(uniquename);
+ CvTerm cvterm = new CvTerm();
+ cvterm.setCvTermId(lcvterm_id.longValue());
featureprop.setValue(stripQuotes(qualifier_string));
featureprop.setRank(rank);
- featureprop.setCvterm(cvterm);
+ featureprop.setCvTerm(cvterm);
featureprop.setFeature(chado_feature);
return featureprop;
}
diff --git a/uk/ac/sanger/artemis/chado/Cvterm.java b/uk/ac/sanger/artemis/chado/CvTerm.java
similarity index 89%
rename from uk/ac/sanger/artemis/chado/Cvterm.java
rename to uk/ac/sanger/artemis/chado/CvTerm.java
index f3a53247f..d2f13c58b 100644
--- a/uk/ac/sanger/artemis/chado/Cvterm.java
+++ b/uk/ac/sanger/artemis/chado/CvTerm.java
@@ -1,4 +1,4 @@
-/* Cvterm.java
+/* CvTerm.java
*
* created: 2005
*
@@ -28,24 +28,24 @@ package uk.ac.sanger.artemis.chado;
/**
* Representation of cvterm table.
*/
-public class Cvterm
+public class CvTerm
{
- private long cvtermId;
+ private long cvTermId;
private String name;
private Cv cv;
- private Dbxref dbxref;
+ private DbXRef dbXRef;
private String definition;
private int isObsolete;
private int isRelationshiptype;
- public long getCvtermId()
+ public long getCvTermId()
{
- return cvtermId;
+ return cvTermId;
}
- public void setCvtermId(long cvtermId)
+ public void setCvTermId(long cvTermId)
{
- this.cvtermId = cvtermId;
+ this.cvTermId = cvTermId;
}
/**
@@ -53,9 +53,9 @@ public class Cvterm
* Note that a cvterm may have multiple secondary dbxrefs.
* @return
*/
- public Dbxref getDbxref()
+ public DbXRef getDbXRef()
{
- return dbxref;
+ return dbXRef;
}
/**
@@ -63,9 +63,9 @@ public class Cvterm
* Note that a cvterm may have multiple secondary dbxrefs.
* @param dbxref
*/
- public void setDbxref(Dbxref dbxref)
+ public void setDbXRef(DbXRef dbXRef)
{
- this.dbxref = dbxref;
+ this.dbXRef = dbXRef;
}
public Cv getCv()
diff --git a/uk/ac/sanger/artemis/chado/Dbxref.java b/uk/ac/sanger/artemis/chado/DbXRef.java
similarity index 90%
rename from uk/ac/sanger/artemis/chado/Dbxref.java
rename to uk/ac/sanger/artemis/chado/DbXRef.java
index 299707267..a617b0349 100644
--- a/uk/ac/sanger/artemis/chado/Dbxref.java
+++ b/uk/ac/sanger/artemis/chado/DbXRef.java
@@ -27,9 +27,9 @@ package uk.ac.sanger.artemis.chado;
/**
* Representation of the chado dbxref table.
*/
-public class Dbxref
+public class DbXRef
{
- private int db_id;
+ private int dbXRefId;
private String accession;
private String version;
private String description;
@@ -55,14 +55,14 @@ public class Dbxref
this.db = db;
}
- public int getDb_id()
+ public int getDbXRefId()
{
- return db_id;
+ return dbXRefId;
}
- public void setDb_id(int db_id)
+ public void setDbXRefId(int dbXRefId)
{
- this.db_id = db_id;
+ this.dbXRefId = dbXRefId;
}
public String getDescription()
diff --git a/uk/ac/sanger/artemis/chado/Feature.java b/uk/ac/sanger/artemis/chado/Feature.java
index 165dbbb45..a76cce10e 100644
--- a/uk/ac/sanger/artemis/chado/Feature.java
+++ b/uk/ac/sanger/artemis/chado/Feature.java
@@ -29,6 +29,7 @@ import java.sql.Timestamp;
import java.util.Hashtable;
import java.util.Vector;
import java.util.List;
+import java.util.Collection;
/**
@@ -47,7 +48,7 @@ public class Feature
/** sequence length */
private int length;
/** features unique name */
- private String uniquename = null;
+ private String uniqueName = null;
/** features name */
private String name;
/** features residues */
@@ -56,8 +57,8 @@ public class Feature
private boolean analysis;
/** whether this feature has been obsoleted */
private boolean obsolete;
- /** feature cvterm */
- private Cvterm cvterm;
+ /** feature cvTerm */
+ private CvTerm cvTerm;
/** feature property */
private FeatureProp featureprop;
/** feature location (for a given srcfeature) */
@@ -67,23 +68,23 @@ public class Feature
/** feature organism */
private Organism organism;
/** optional primary public stable identifier */
- private FeatureDbxref feature_dbxref;
+ private FeatureDbXRef featureDbXRef;
/** merged featureprops */
private Hashtable qualifiers;
/** list of FeatureProp */
- private List featurepropList;
+ private Collection featurepropList;
/** list of FeatureRelationship children */
- private List featureRelationshipsForObjectId;
+ private Collection featureRelationshipsForObjectId;
/** list of FeatureRelationship parent */
- private List featureRelationshipsForSubjectId;
+ private Collection featureRelationshipsForSubjectId;
/** list of feature dbxrefs (FeatureDbxref) */
- private List featureDbxrefs;
+ private Collection featureDbXRefs;
/** list of feature locations for a feature_id */
- private List featurelocsForFeatureId;
+ private Collection featurelocsForFeatureId;
/** used by getResidueFeatures */
- private List featureCvterms;
+ private Collection featureCvTerms;
/** list of feature synonyms */
- private List featureSynonymsForFeatureId;
+ private Collection featureSynonymsForFeatureId;
@@ -165,9 +166,9 @@ public class Feature
* must be unique for this type of feature within this organism.
* @return the unique name for a feature.
*/
- public String getUniquename()
+ public String getUniqueName()
{
- return uniquename;
+ return uniqueName;
}
/**
@@ -176,9 +177,9 @@ public class Feature
* must be unique for this type of feature within this organism.
* @param uniquename the unique name for a feature.
*/
- public void setUniquename(String uniquename)
+ public void setUniqueName(String uniqueName)
{
- this.uniquename = uniquename;
+ this.uniqueName = uniqueName;
}
/**
@@ -258,23 +259,23 @@ public class Feature
}
/**
- * A reference to a table:cvterm giving the feature type.
+ * A reference to a table:cvTerm giving the feature type.
* This will typically be a Sequence Ontology identifier.
- * @return the feature SO cvterm
+ * @return the feature SO cvTerm
*/
- public Cvterm getCvterm()
+ public CvTerm getCvTerm()
{
- return cvterm;
+ return cvTerm;
}
/**
- * A reference to a table:cvterm giving the feature type.
+ * A reference to a table:cvTerm giving the feature type.
* This will typically be a Sequence Ontology identifier.
- * @param cvterm the feature SO cvterm
+ * @param cvTerm the feature SO cvTerm
*/
- public void setCvterm(Cvterm cvterm)
+ public void setCvTerm(CvTerm cvTerm)
{
- this.cvterm = cvterm;
+ this.cvTerm = cvTerm;
}
/**
@@ -358,9 +359,9 @@ public class Feature
* Secondary identifiers and external dbxrefs go in table:feature_dbxref
* @return
*/
- public FeatureDbxref getFeature_dbxref()
+ public FeatureDbXRef getFeatureDbXRef()
{
- return feature_dbxref;
+ return featureDbXRef;
}
/**
@@ -368,19 +369,19 @@ public class Feature
* Secondary identifiers and external dbxrefs go in table:feature_dbxref
* @param dbxref
*/
- public void setFeature_dbxref(FeatureDbxref feature_dbxref)
+ public void setFeatureDbXRef(FeatureDbXRef featureDbXRef)
{
- this.feature_dbxref = feature_dbxref;
+ this.featureDbXRef = featureDbXRef;
}
- public List getFeatureCvterms()
+ public Collection getFeatureCvTerms()
{
- return featureCvterms;
+ return featureCvTerms;
}
- public void setFeatureCvterms(List featureCvterms)
+ public void setFeatureCvTerms(Collection featureCvTerms)
{
- this.featureCvterms = featureCvterms;
+ this.featureCvTerms = featureCvTerms;
}
/**
@@ -388,7 +389,7 @@ public class Feature
* @return featurepropList a <code>List</code> of featureprop's
* for a feature.
*/
- public List getFeaturepropList()
+ public Collection getFeaturepropList()
{
return featurepropList;
}
@@ -398,14 +399,14 @@ public class Feature
* @param featurepropList a <code>List</code> of featureprop's
* for a feature.
*/
- public void setFeaturepropList(List featurepropList)
+ public void setFeaturepropList(Collection featurepropList)
{
this.featurepropList = featurepropList;
for(int i=0; i<featurepropList.size(); i++)
{
- FeatureProp featureprop = (FeatureProp)featurepropList.get(i);
- addQualifier(featureprop.getCvterm().getCvtermId(), featureprop);
+ FeatureProp featureprop = (FeatureProp)(((List)featurepropList).get(i));
+ addQualifier(featureprop.getCvTerm().getCvTermId(), featureprop);
}
}
@@ -413,7 +414,7 @@ public class Feature
* Get a list of <code>FeatureRelationship</code> children
* @return
*/
- public List getFeatureRelationshipsForObjectId()
+ public Collection getFeatureRelationshipsForObjectId()
{
return featureRelationshipsForObjectId;
}
@@ -423,7 +424,7 @@ public class Feature
* @param featureRelationshipsForObjectId
*/
public void setFeatureRelationshipsForObjectId(
- List featureRelationshipsForObjectId)
+ Collection featureRelationshipsForObjectId)
{
this.featureRelationshipsForObjectId = featureRelationshipsForObjectId;
}
@@ -432,7 +433,7 @@ public class Feature
* Get a list of <code>FeatureRelationship</code> parent
* @return
*/
- public List getFeatureRelationshipsForSubjectId()
+ public Collection getFeatureRelationshipsForSubjectId()
{
return featureRelationshipsForSubjectId;
}
@@ -442,7 +443,7 @@ public class Feature
* @param featureRelationshipsForSubjectId
*/
public void setFeatureRelationshipsForSubjectId(
- List featureRelationshipsForSubjectId)
+ Collection featureRelationshipsForSubjectId)
{
this.featureRelationshipsForSubjectId = featureRelationshipsForSubjectId;
}
@@ -451,25 +452,25 @@ public class Feature
* Get a list of feature dbxrefs (<code>FeatureDbxref</code>)
* @return
*/
- public List getFeatureDbxrefs()
+ public Collection getFeatureDbXRefs()
{
- return featureDbxrefs;
+ return featureDbXRefs;
}
/**
* Set a list of feature dbxrefs (<code>FeatureDbxref</code>)
* @param featureDbxrefs
*/
- public void setFeatureDbxrefs(List featureDbxrefs)
+ public void setFeatureDbXRefs(Collection featureDbXRefs)
{
- this.featureDbxrefs = featureDbxrefs;
+ this.featureDbXRefs = featureDbXRefs;
}
/**
* Get list of feature locations for a feature_id
* @return
*/
- public List getFeaturelocsForFeatureId()
+ public Collection getFeaturelocsForFeatureId()
{
return featurelocsForFeatureId;
}
@@ -478,17 +479,17 @@ public class Feature
* Set a list of feature locations for a feature_id
* @param featurelocsForFeatureId
*/
- public void setFeaturelocsForFeatureId(List featurelocsForFeatureId)
+ public void setFeaturelocsForFeatureId(Collection featurelocsForFeatureId)
{
this.featurelocsForFeatureId = featurelocsForFeatureId;
}
- public List getFeatureSynonymsForFeatureId()
+ public Collection getFeatureSynonymsForFeatureId()
{
return featureSynonymsForFeatureId;
}
- public void setFeatureSynonymsForFeatureId(List featureSynonymsForFeatureId)
+ public void setFeatureSynonymsForFeatureId(Collection featureSynonymsForFeatureId)
{
this.featureSynonymsForFeatureId = featureSynonymsForFeatureId;
}
@@ -497,9 +498,9 @@ public class Feature
/**
* Used in merging the qualifiers to store them as a <code>Hashtable</code> of
- * the cvterm type_id (of the property name) and the property values as a
+ * the cvTerm type_id (of the property name) and the property values as a
* <code>Vector</code>.
- * @param the cvterm type_id of the property name
+ * @param the cvTerm type_id of the property name
* @param the property value
*/
public void addQualifier(long prop_type_id, FeatureProp featprop)
@@ -523,7 +524,7 @@ public class Feature
}
/**
- * Get the qualifiers which are stored as a <code>Hashtable</code> of cvterm
+ * Get the qualifiers which are stored as a <code>Hashtable</code> of cvTerm
* type_id (of the property name) and the property values as a <code>Vector</code>.
* @return the qualifiers as a <code>Hashtable</code>
*/
diff --git a/uk/ac/sanger/artemis/chado/FeatureDbxref.java b/uk/ac/sanger/artemis/chado/FeatureDbXRef.java
similarity index 79%
rename from uk/ac/sanger/artemis/chado/FeatureDbxref.java
rename to uk/ac/sanger/artemis/chado/FeatureDbXRef.java
index 54b5576dd..f5a95b75f 100644
--- a/uk/ac/sanger/artemis/chado/FeatureDbxref.java
+++ b/uk/ac/sanger/artemis/chado/FeatureDbXRef.java
@@ -27,13 +27,13 @@ package uk.ac.sanger.artemis.chado;
/**
* Representation of the chado feature_dbxref.
*/
-public class FeatureDbxref
+public class FeatureDbXRef
{
/** feature_dbxref */
private Feature feature;
- private int dbxref_id;
+ private int featureDbXRefId;
private boolean current = true;
- private Dbxref dbxref;
+ private DbXRef dbXRef;
public Feature getFeature()
{
@@ -54,26 +54,25 @@ public class FeatureDbxref
{
this.current = current;
}
-
-
- public int getDbxref_id()
+
+ public DbXRef getDbXRef()
{
- return dbxref_id;
+ return dbXRef;
}
- public void setDbxref_id(int dbxref_id)
+ public void setDbXRef(DbXRef dbXRef)
{
- this.dbxref_id = dbxref_id;
+ this.dbXRef = dbXRef;
}
-
- public Dbxref getDbxref()
+
+ public int getFeatureDbXRefId()
{
- return dbxref;
+ return featureDbXRefId;
}
- public void setDbxref(Dbxref dbxref)
+ public void setFeatureDbXRefId(int featureDbXRefId)
{
- this.dbxref = dbxref;
+ this.featureDbXRefId = featureDbXRefId;
}
}
diff --git a/uk/ac/sanger/artemis/chado/FeatureProp.java b/uk/ac/sanger/artemis/chado/FeatureProp.java
index 121787a98..0fc7b0ac9 100644
--- a/uk/ac/sanger/artemis/chado/FeatureProp.java
+++ b/uk/ac/sanger/artemis/chado/FeatureProp.java
@@ -30,26 +30,26 @@ package uk.ac.sanger.artemis.chado;
public class FeatureProp
{
public Feature feature;
- public Cvterm cvterm;
+ public CvTerm cvTerm;
public String value;
public int rank;
/**
* Get the cv term
- * @return cvterm
+ * @return cvTerm
*/
- public Cvterm getCvterm()
+ public CvTerm getCvTerm()
{
- return cvterm;
+ return cvTerm;
}
/**
* Set the cv term
- * @param cvterm
+ * @param cvTerm
*/
- public void setCvterm(Cvterm cvterm)
+ public void setCvTerm(CvTerm cvTerm)
{
- this.cvterm = cvterm;
+ this.cvTerm = cvTerm;
}
/**
diff --git a/uk/ac/sanger/artemis/chado/FeatureRelationship.java b/uk/ac/sanger/artemis/chado/FeatureRelationship.java
index 47c86993d..2fa8c0344 100644
--- a/uk/ac/sanger/artemis/chado/FeatureRelationship.java
+++ b/uk/ac/sanger/artemis/chado/FeatureRelationship.java
@@ -34,7 +34,7 @@ public class FeatureRelationship
/** id of the parent feature */
public Feature object;
/** cv term of feature relationship (e.g. part_of) */
- public Cvterm cvterm;
+ public CvTerm cvTerm;
/** Additional notes/comments */
public String value;
/** ordering of subject features */
@@ -43,21 +43,21 @@ public class FeatureRelationship
/**
* Get the cv term for the relationship type between
* subject and object (e.g. part_of).
- * @return cvterm
+ * @return cvTerm
*/
- public Cvterm getCvterm()
+ public CvTerm getCvTerm()
{
- return cvterm;
+ return cvTerm;
}
/**
* Set the cv term for the relationship type between
* subject and object (e.g. part_of).
- * @param cvterm
+ * @param cvTerm
*/
- public void setCvterm(Cvterm cvterm)
+ public void setCvTerm(CvTerm cvTerm)
{
- this.cvterm = cvterm;
+ this.cvTerm = cvTerm;
}
/**
diff --git a/uk/ac/sanger/artemis/chado/IBatisDAO.java b/uk/ac/sanger/artemis/chado/IBatisDAO.java
index 7132a78d2..f3df5dd63 100644
--- a/uk/ac/sanger/artemis/chado/IBatisDAO.java
+++ b/uk/ac/sanger/artemis/chado/IBatisDAO.java
@@ -75,7 +75,7 @@ public class IBatisDAO implements ChadoDAO
public Feature getFeatureByUniqueName(String uniquename)
{
Feature feature = new Feature();
- feature.setUniquename(uniquename);
+ feature.setUniqueName(uniquename);
return getLazyFeature(feature);
}
@@ -109,7 +109,7 @@ public class IBatisDAO implements ChadoDAO
sqlMap.queryForList("getFeatureSynonymsByName", alias);
Feature feature = new Feature();
- feature.setUniquename(name);
+ feature.setUniqueName(name);
feature.setFeatureSynonymsForFeatureId(feature_synonym_list);
List features = sqlMap.queryForList("getLazyFeature", feature);
@@ -153,7 +153,7 @@ public class IBatisDAO implements ChadoDAO
{
Feature feature = new Feature();
feature.setSchema(schema);
- feature.setFeatureCvterms(cvterm_ids);
+ feature.setFeatureCvTerms(cvterm_ids);
return sqlMap.queryForList("getResidueFeatures",
feature);
@@ -184,10 +184,10 @@ public class IBatisDAO implements ChadoDAO
/**
* Get the full list of cvterm_id and name as a <code>List</code> of
- * <code>Cvterm</code> objects.
+ * <code>CvTerm</code> objects.
* @return the full list of cvterm_id and name
*/
- public List getCvterm()
+ public List getCvTerm()
{
return sqlMap.queryForList("getCvterm", null);
}
@@ -196,15 +196,15 @@ public class IBatisDAO implements ChadoDAO
/**
* Get dbxref for a feature.
* @param uniquename the unique name for the feature. If set to NULL
- * all <code>FeatureDbxref</code> are returned.
+ * all <code>FeatureDbXRef</code> are returned.
* @return a <code>List</code> of feature_dbxrefs.
*/
- public List getFeatureDbxrefByUniquename(final String uniquename)
+ public List getFeatureDbXRefByUniquename(final String uniquename)
{
Feature feature = new Feature();
- feature.setUniquename(uniquename);
+ feature.setUniqueName(uniquename);
- return sqlMap.queryForList("getFeatureDbxref", feature);
+ return sqlMap.queryForList("getFeatureDbXRef", feature);
}
/**
@@ -216,7 +216,7 @@ public class IBatisDAO implements ChadoDAO
public List getFeatureSynonymsByUniquename(final String uniquename)
{
Feature feature = new Feature();
- feature.setUniquename(uniquename);
+ feature.setUniqueName(uniquename);
return sqlMap.queryForList("getFeatureSynonymsByUniquename", feature);
}
@@ -228,11 +228,11 @@ public class IBatisDAO implements ChadoDAO
* @return a Synonym, or null
*/
public Synonym getSynonymByNameAndCvTerm(
- String name, Cvterm type)
+ String name, CvTerm type)
{
Synonym synonym = new Synonym();
synonym.setName(name);
- synonym.setCvterm(type);
+ synonym.setCvTerm(type);
return (Synonym)sqlMap.queryForObject("getSynonymByNameAndType",
synonym);
@@ -259,15 +259,15 @@ public class IBatisDAO implements ChadoDAO
* @param name cvterm name
* @param cv_name ontology name (e.g. gene, sequence)
*/
- public Cvterm getCvtermID(String name, String cv_name)
+ public CvTerm getCvtermID(String name, String cv_name)
{
- Cvterm cvterm = new Cvterm();
+ CvTerm cvterm = new CvTerm();
Cv cv = new Cv();
cv.setName(cv_name);
cvterm.setCv(cv);
cvterm.setName(name);
- return (Cvterm)sqlMap.queryForObject("getCvterm", cvterm);
+ return (CvTerm)sqlMap.queryForObject("getCvterm", cvterm);
}
//
@@ -308,8 +308,8 @@ public class IBatisDAO implements ChadoDAO
sqlMap.insert("insertFeatureProp", o);
else if(o instanceof Feature)
insertFeature((Feature)o);
- else if(o instanceof FeatureDbxref)
- insertFeatureDbxref((FeatureDbxref)o);
+ else if(o instanceof FeatureDbXRef)
+ insertFeatureDbXRef((FeatureDbXRef)o);
else if(o instanceof FeatureSynonym)
insertFeatureAlias((FeatureSynonym)o);
}
@@ -328,8 +328,8 @@ public class IBatisDAO implements ChadoDAO
sqlMap.delete("deleteFeature", o);
else if(o instanceof FeatureProp)
sqlMap.delete("deleteFeatureProp", o);
- else if(o instanceof FeatureDbxref)
- sqlMap.delete("deleteFeatureDbxref", o);
+ else if(o instanceof FeatureDbXRef)
+ sqlMap.delete("deleteFeatureDbXRef", o);
else if(o instanceof FeatureSynonym)
deleteFeatureSynonym((FeatureSynonym)o);
}
@@ -364,7 +364,8 @@ public class IBatisDAO implements ChadoDAO
// insert feature relationships
if(feature.getFeatureRelationshipsForSubjectId() != null)
{
- List parents = feature.getFeatureRelationshipsForSubjectId();
+ List parents = new Vector(
+ feature.getFeatureRelationshipsForSubjectId());
for(int i=0; i<parents.size(); i++)
{
@@ -377,43 +378,45 @@ public class IBatisDAO implements ChadoDAO
/**
* Insert a feature_dbxref for a feature.
- * @param feature_dbxref the <code>FeatureDbxref</code>
+ * @param feature_dbxref the <code>FeatureDbXRef</code>
*/
- private void insertFeatureDbxref(final FeatureDbxref feature_dbxref)
+ private void insertFeatureDbXRef(final FeatureDbXRef feature_dbxref)
{
Integer db_id = (Integer)sqlMap.queryForObject("getDbId",
- feature_dbxref.getDbxref().getDb());
+ feature_dbxref.getDbXRef().getDb());
System.out.print(db_id.intValue());
if(db_id == null)
throw new RuntimeException("No database called "+
- feature_dbxref.getDbxref().getDb().getName()+" found (for "+
- feature_dbxref.getFeature().getUniquename()+
+ feature_dbxref.getDbXRef().getDb().getName()+" found (for "+
+ feature_dbxref.getFeature().getUniqueName()+
") check the spelling!");
- feature_dbxref.getDbxref().setDb_id(db_id.intValue());
+ feature_dbxref.getDbXRef().setDbXRefId(db_id.intValue());
Integer dbxref_id =
- (Integer)sqlMap.queryForObject("getDbxrefId", feature_dbxref.getDbxref());
+ (Integer)sqlMap.queryForObject("getDbXRefId", feature_dbxref.getDbXRef());
if(dbxref_id == null)
{
// create a new accession entry in dbxref
- sqlMap.insert("insertDbxref", feature_dbxref.getDbxref());
+ sqlMap.insert("insertDbXRef", feature_dbxref.getDbXRef());
// now get the new dbxref_id
- dbxref_id = (Integer)sqlMap.queryForObject("getDbxrefId",
- feature_dbxref.getDbxref());
+ dbxref_id = (Integer)sqlMap.queryForObject("getDbXRefId",
+ feature_dbxref.getDbXRef());
}
- feature_dbxref.setDbxref_id(dbxref_id.intValue());
+ DbXRef dbXRef = new DbXRef();
+ dbXRef.setDbXRefId(dbxref_id.intValue());
+ feature_dbxref.setDbXRef(dbXRef);
// get the feature id's
Feature feature = getFeatureByUniqueName(
- feature_dbxref.getFeature().getUniquename());
+ feature_dbxref.getFeature().getUniqueName());
feature_dbxref.getFeature().setId( feature.getId() );
- sqlMap.insert("insertFeatureDbxref", feature_dbxref);
+ sqlMap.insert("insertFeatureDbXRef", feature_dbxref);
}
@@ -494,9 +497,9 @@ public class IBatisDAO implements ChadoDAO
for(int i = 0; i < feature_size; i++)
{
Feature feat = (Feature)list.get(i);
- String name = feat.getUniquename();
+ String name = feat.getUniqueName();
- feat.addQualifier(feat.getFeatureprop().getCvterm().getCvtermId(),
+ feat.addQualifier(feat.getFeatureprop().getCvTerm().getCvTermId(),
feat.getFeatureprop());
if(i < feature_size - 1)
@@ -505,9 +508,9 @@ public class IBatisDAO implements ChadoDAO
featNext = null;
// merge next line if part of the same feature
- while(featNext != null && featNext.getUniquename().equals(name))
+ while(featNext != null && featNext.getUniqueName().equals(name))
{
- feat.addQualifier(featNext.getFeatureprop().getCvterm().getCvtermId(),
+ feat.addQualifier(featNext.getFeatureprop().getCvTerm().getCvTermId(),
featNext.getFeatureprop());
i++;
@@ -526,18 +529,18 @@ public class IBatisDAO implements ChadoDAO
/**
* Takes a list and creates a <code>Hashtable</code> with the keys
* being the feature_id and the value a <code>Vector</code> of the dbxrefs.
- * @param list a <code>List</code> of <code>Dbxref</code> objects.
+ * @param list a <code>List</code> of <code>DbXRef</code> objects.
* @return a <code>Hashtable</code> of dbxrefs.
*/
- public static Hashtable mergeDbxref(final List list)
+ public static Hashtable mergeDbXRef(final List list)
{
Hashtable dbxrefHash = new Hashtable();
for(int i = 0; i < list.size(); i++)
{
- FeatureDbxref dbxref = (FeatureDbxref)list.get(i);
+ FeatureDbXRef dbxref = (FeatureDbXRef)list.get(i);
Integer feature_id = new Integer(dbxref.getFeature().getId());
- String value = dbxref.getDbxref().getDb().getName() + ":" +
- dbxref.getDbxref().getAccession();
+ String value = dbxref.getDbXRef().getDb().getName() + ":" +
+ dbxref.getDbXRef().getAccession();
if(dbxrefHash.containsKey(feature_id))
{
Vector v = (Vector)dbxrefHash.get(feature_id);
diff --git a/uk/ac/sanger/artemis/chado/JdbcDAO.java b/uk/ac/sanger/artemis/chado/JdbcDAO.java
index 541e67b48..0b0fb3b22 100644
--- a/uk/ac/sanger/artemis/chado/JdbcDAO.java
+++ b/uk/ac/sanger/artemis/chado/JdbcDAO.java
@@ -88,7 +88,7 @@ public class JdbcDAO
public Feature getFeatureByUniqueName(String uniquename)
{
Feature feature = new Feature();
- feature.setUniquename(uniquename);
+ feature.setUniqueName(uniquename);
feature.setId(-1);
return getLazyFeature(feature);
}
@@ -116,7 +116,7 @@ public class JdbcDAO
public List getFeaturesByAnyCurrentName(String name)
{
Feature feature = new Feature();
- feature.setUniquename(name);
+ feature.setUniqueName(name);
return getFeatureQuery(name, -1, -1);
}
@@ -138,7 +138,7 @@ public class JdbcDAO
*/
private Feature getLazyFeature(final Feature feature)
{
- List list = getFeatureQuery(feature.getUniquename(),
+ List list = getFeatureQuery(feature.getUniqueName(),
-1, feature.getId());
return (Feature)list.get(0);
}
@@ -204,26 +204,26 @@ public class JdbcDAO
feature.setResidues(rs.getBytes("residues"));
feature.setFeatureloc(featureloc);
- feature.setCvterm(new Cvterm());
- feature.getCvterm().setCvtermId(rs.getLong("type_id"));
+ feature.setCvTerm(new CvTerm());
+ feature.getCvTerm().setCvTermId(rs.getLong("type_id"));
// feature properties
FeatureProp featureprop = new FeatureProp();
- Cvterm cvterm = new Cvterm();
- cvterm.setCvtermId(rs.getLong("prop_type_id"));
- featureprop.setCvterm(cvterm);
+ CvTerm cvterm = new CvTerm();
+ cvterm.setCvTermId(rs.getLong("prop_type_id"));
+ featureprop.setCvTerm(cvterm);
featureprop.setValue(rs.getString("value"));
feature.setFeatureprop(featureprop);
- feature.setUniquename(rs.getString("uniquename"));
+ feature.setUniqueName(rs.getString("uniquename"));
feature.setTimelastmodified(rs.getTimestamp("timelastmodified"));
feature.setId(rs.getInt("feature_id"));
// feature relationship
FeatureRelationship feature_relationship = new FeatureRelationship();
- cvterm = new Cvterm();
- cvterm.setCvtermId(rs.getLong("relation_type_id"));
- feature_relationship.setCvterm(cvterm);
+ cvterm = new CvTerm();
+ cvterm.setCvTermId(rs.getLong("relation_type_id"));
+ feature_relationship.setCvTerm(cvterm);
Feature object = new Feature();
object.setId(rs.getInt("object_id"));
@@ -297,9 +297,9 @@ public class JdbcDAO
feature.setOrganism(organism);
feature.setId(rs.getInt("feature_id"));
feature.setName(rs.getString("name"));
- feature.setUniquename(rs.getString("uniquename"));
- feature.setCvterm(new Cvterm());
- feature.getCvterm().setCvtermId(rs.getLong("type_id"));
+ feature.setUniqueName(rs.getString("uniquename"));
+ feature.setCvTerm(new CvTerm());
+ feature.getCvTerm().setCvTermId(rs.getLong("type_id"));
list.add(feature);
}
@@ -372,10 +372,10 @@ public class JdbcDAO
/**
* Get the full list of cvterm_id and name as a <code>List</code> of
- * <code>Cvterm</code> objects.
+ * <code>CvTerm</code> objects.
* @return the full list of cvterm_id and name
*/
- public List getCvterm()
+ public List getCvTerm()
{
String sql = "SELECT cvterm.cvterm_id, cvterm.name " +
"FROM cvterm, cv WHERE cv.cv_id = cvterm.cv_id";
@@ -390,8 +390,8 @@ public class JdbcDAO
while(rs.next())
{
- Cvterm cvterm = new Cvterm();
- cvterm.setCvtermId(rs.getLong("cvterm_id"));
+ CvTerm cvterm = new CvTerm();
+ cvterm.setCvTermId(rs.getLong("cvterm_id"));
cvterm.setName(rs.getString("name"));
cvterms.add(cvterm);
}
@@ -407,10 +407,10 @@ public class JdbcDAO
/**
* Get dbxref for a feature.
* @param uniquename the unique name for the feature. If set to NULL
- * all <code>FeatureDbxref</code> are returned.
+ * all <code>FeatureDbXRef</code> are returned.
* @return a <code>List</code> of feature_dbxrefs.
*/
- public List getFeatureDbxrefByUniquename(final String uniquename)
+ public List getFeatureDbXRefByUniquename(final String uniquename)
{
String sql = "SELECT db.name, dbx.accession, f.feature_id FROM "+
"feature_dbxref dbx_f "+
@@ -431,15 +431,15 @@ public class JdbcDAO
while(rs.next())
{
- FeatureDbxref feature_dbxref = new FeatureDbxref();
- Dbxref dbxref = new Dbxref();
+ 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);
Feature feat = new Feature();
feat.setId(rs.getInt("feature_id"));
- feature_dbxref.setDbxref(dbxref);
+ feature_dbxref.setDbXRef(dbxref);
feature_dbxref.setFeature(feat);
dbxrefs.add(feature_dbxref);
}
@@ -480,11 +480,11 @@ public class JdbcDAO
while(rs.next())
{
alias = new FeatureSynonym();
- Cvterm cvterm = new Cvterm();
- cvterm.setCvtermId(rs.getLong("type_id"));
+ CvTerm cvterm = new CvTerm();
+ cvterm.setCvTermId(rs.getLong("type_id"));
Synonym syn = new Synonym();
syn.setName(rs.getString("name"));
- syn.setCvterm(cvterm);
+ syn.setCvTerm(cvterm);
Feature feat = new Feature();
feat.setId(rs.getInt("feature_id"));
@@ -512,7 +512,7 @@ public class JdbcDAO
public Synonym getSynonymByNameAndCvTerm(
- String name, Cvterm type)
+ String name, CvTerm type)
{
return null;
}
@@ -554,8 +554,8 @@ public class JdbcDAO
insertFeatureProp((FeatureProp)o);
else if(o instanceof Feature)
insertFeature((Feature)o);
- else if(o instanceof FeatureDbxref)
- insertFeatureDbxref((FeatureDbxref)o);
+ else if(o instanceof FeatureDbXRef)
+ insertFeatureDbXRef((FeatureDbXRef)o);
else if(o instanceof FeatureSynonym)
insertFeatureAlias((FeatureSynonym)o);
}
@@ -573,8 +573,8 @@ public class JdbcDAO
deleteFeature((Feature)o);
else if(o instanceof FeatureProp)
deleteFeatureProp((FeatureProp)o);
- else if(o instanceof FeatureDbxref)
- deleteFeatureDbxref((FeatureDbxref)o);
+ else if(o instanceof FeatureDbXRef)
+ deleteFeatureDbXRef((FeatureDbXRef)o);
else if(o instanceof FeatureSynonym)
deleteFeatureSynonym((FeatureSynonym)o);
}
@@ -597,7 +597,7 @@ public class JdbcDAO
pstmt.setInt(3, featureloc.getRank());
pstmt.setInt(4, featureloc.getStrand());
pstmt.setInt(5, featureloc.getPhase());
- pstmt.setString(6, featureloc.getFeature().getUniquename());
+ pstmt.setString(6, featureloc.getFeature().getUniqueName());
appendToLogFile(sql, sqlLog);
pstmt.executeUpdate();
@@ -616,7 +616,7 @@ public class JdbcDAO
{
String sql = "UPDATE feature SET uniquename=?";
- if(feature.getCvterm() != null)
+ if(feature.getCvTerm() != null)
sql = sql+", type_id=?";
if(feature.getTimelastmodified() != null)
@@ -627,11 +627,11 @@ public class JdbcDAO
try
{
PreparedStatement pstmt = conn.prepareStatement(sql);
- pstmt.setString(1, feature.getUniquename());
+ pstmt.setString(1, feature.getUniqueName());
int param = 2;
- if(feature.getCvterm() != null)
+ if(feature.getCvTerm() != null)
{
- pstmt.setLong(param, feature.getCvterm().getCvtermId());
+ pstmt.setLong(param, feature.getCvTerm().getCvTermId());
param++;
}
@@ -666,8 +666,8 @@ public class JdbcDAO
PreparedStatement pstmt = conn.prepareStatement(sql);
pstmt.setString(1, featureprop.getValue());
pstmt.setInt(2, featureprop.getRank());
- pstmt.setLong(3, featureprop.getCvterm().getCvtermId());
- pstmt.setString(4, featureprop.getFeature().getUniquename());
+ pstmt.setLong(3, featureprop.getCvTerm().getCvTermId());
+ pstmt.setString(4, featureprop.getFeature().getUniqueName());
appendToLogFile(sql, sqlLog);
pstmt.executeUpdate();
@@ -693,8 +693,8 @@ public class JdbcDAO
sqlBuff.append("VALUES ");
sqlBuff.append("((SELECT feature_id FROM feature WHERE uniquename=");
- sqlBuff.append("'"+ featureprop.getFeature().getUniquename()+"')," );
- sqlBuff.append(featureprop.getCvterm().getCvtermId()+", ");
+ sqlBuff.append("'"+ featureprop.getFeature().getUniqueName()+"')," );
+ sqlBuff.append(featureprop.getCvTerm().getCvTermId()+", ");
sqlBuff.append(featureprop.getValue()+",");
sqlBuff.append(featureprop.getRank());
@@ -720,7 +720,7 @@ public class JdbcDAO
(final FeatureProp featureprop)
{
StringBuffer sqlBuff = new StringBuffer();
- String uniquename = featureprop.getFeature().getUniquename();
+ String uniquename = featureprop.getFeature().getUniqueName();
sqlBuff.append("DELETE FROM featureprop WHERE ");
@@ -735,7 +735,7 @@ public class JdbcDAO
if(featureprop.getValue() != null)
sqlBuff.append("value="+featureprop.getValue()+" AND ");
- sqlBuff.append("type_id="+featureprop.getCvterm().getCvtermId());
+ sqlBuff.append("type_id="+featureprop.getCvTerm().getCvTermId());
appendToLogFile(new String(sqlBuff), sqlLog);
@@ -785,8 +785,8 @@ public class JdbcDAO
sql_buff.append("nextval('feature_feature_id_seq') , ");
sql_buff.append(organism_id + " , ");
sql_buff.append("'" + feature.getName() + "'" + " , ");
- sql_buff.append("'" + feature.getUniquename() + "'" + " , ");
- sql_buff.append(Long.toString(feature.getCvterm().getCvtermId()));
+ sql_buff.append("'" + feature.getUniqueName() + "'" + " , ");
+ sql_buff.append(Long.toString(feature.getCvTerm().getCvTermId()));
sql_buff.append(" )");
sql = new String(sql_buff);
@@ -832,7 +832,7 @@ public class JdbcDAO
// insert feature relationships
if(feature.getFeatureRelationshipsForSubjectId() != null)
{
- List parents = feature.getFeatureRelationshipsForSubjectId();
+ List parents = (List)feature.getFeatureRelationshipsForSubjectId();
for(int i = 0; i < parents.size(); i++)
{
// insert feature_relationship
@@ -845,12 +845,12 @@ public class JdbcDAO
sql_buff.append("VALUES ");
sql_buff
.append("( (SELECT feature_id FROM feature WHERE uniquename='");
- sql_buff.append(feature_relationship.getSubject().getUniquename()
+ sql_buff.append(feature_relationship.getSubject().getUniqueName()
+ "'), ");
sql_buff.append("(SELECT feature_id FROM feature WHERE uniquename='");
- sql_buff.append(feature_relationship.getObject().getUniquename()
+ sql_buff.append(feature_relationship.getObject().getUniqueName()
+ "'), ");
- sql_buff.append(feature_relationship.getCvterm().getCvtermId() + ")");
+ sql_buff.append(feature_relationship.getCvTerm().getCvTermId() + ")");
sql = new String(sql_buff);
appendToLogFile(sql, sqlLog);
@@ -878,7 +878,7 @@ public class JdbcDAO
try
{
String sql = "DELETE FROM feature WHERE uniquename='"
- + feature.getUniquename() + "'";
+ + feature.getUniqueName() + "'";
appendToLogFile(sql, sqlLog);
Statement st = conn.createStatement();
@@ -892,13 +892,13 @@ public class JdbcDAO
/**
* Insert a feature_dbxref for a feature.
- * @param feature_dbxref the new <code>FeatureDbxref</code>
+ * @param feature_dbxref the new <code>FeatureDbXRef</code>
*/
- private void insertFeatureDbxref(final FeatureDbxref feature_dbxref)
+ private void insertFeatureDbXRef(final FeatureDbXRef feature_dbxref)
{
// find database id
String sql = "SELECT db_id FROM db WHERE name='"+
- feature_dbxref.getDbxref().getDb().getName()+"'";
+ feature_dbxref.getDbXRef().getDb().getName()+"'";
try
{
@@ -908,31 +908,31 @@ public class JdbcDAO
if(!exists)
throw new SQLException("No database called "
- + feature_dbxref.getDbxref().getDb().getName() + " found (for "
- + feature_dbxref.getFeature().getUniquename()
+ + feature_dbxref.getDbXRef().getDb().getName() + " found (for "
+ + feature_dbxref.getFeature().getUniqueName()
+ ") check the spelling!");
final int db_id = rs.getInt("db_id");
// find if accession exists already
- String sqlDbxrefId = "SELECT dbxref_id FROM dbxref WHERE accession='"
- + feature_dbxref.getDbxref().getAccession() + "' AND db_id=" + db_id;
+ String sqlDbXRefId = "SELECT dbxref_id FROM dbxref WHERE accession='"
+ + feature_dbxref.getDbXRef().getAccession() + "' AND db_id=" + db_id;
- appendToLogFile(sqlDbxrefId, sqlLog);
- rs = st.executeQuery(sqlDbxrefId);
+ appendToLogFile(sqlDbXRefId, sqlLog);
+ rs = st.executeQuery(sqlDbXRefId);
exists = rs.next();
if(!exists)
{
// create a new accession entry in dbxref
sql = "INSERT INTO dbxref ( db_id, accession ) " + "VALUES (" + db_id
- + ", '" + feature_dbxref.getDbxref().getAccession() + "' )";
+ + ", '" + feature_dbxref.getDbXRef().getAccession() + "' )";
appendToLogFile(sql, sqlLog);
int rowCount = st.executeUpdate(new String(sql));
// now get the new dbxref_id
- appendToLogFile(sqlDbxrefId, sqlLog);
- rs = st.executeQuery(sqlDbxrefId);
+ appendToLogFile(sqlDbXRefId, sqlLog);
+ rs = st.executeQuery(sqlDbXRefId);
rs.next();
}
@@ -940,7 +940,7 @@ public class JdbcDAO
sql = "INSERT INTO feature_dbxref "
+ "(feature_id, dbxref_id, is_current)" + " VALUES "
+ "( (SELECT feature_id FROM " + "feature WHERE uniquename='"
- + feature_dbxref.getFeature().getUniquename() + "'), " + dbxref_id
+ + feature_dbxref.getFeature().getUniqueName() + "'), " + dbxref_id
+ ", " + Boolean.toString(feature_dbxref.isCurrent()) + ")";
System.out.println(sql);
appendToLogFile(sql, sqlLog);
@@ -954,19 +954,19 @@ public class JdbcDAO
/**
* Delete a feature_dbxref for a feature.
- * @param feature_dbxref the new <code>FeatureDbxref</code>
+ * @param feature_dbxref the new <code>FeatureDbXRef</code>
*/
- private void deleteFeatureDbxref(final FeatureDbxref feature_dbxref)
+ private void deleteFeatureDbXRef(final FeatureDbXRef feature_dbxref)
{
- final String uniquename = feature_dbxref.getFeature().getUniquename();
+ final String uniquename = feature_dbxref.getFeature().getUniqueName();
final String sql =
"DELETE FROM feature_dbxref "+
"WHERE dbxref_id="+
"(SELECT dbxref_id FROM dbxref WHERE accession='"+
- feature_dbxref.getDbxref().getAccession()+"' "+
+ feature_dbxref.getDbXRef().getAccession()+"' "+
"AND db_id=(SELECT db_id FROM db WHERE name='"+
- feature_dbxref.getDbxref().getDb().getName()+"'))"+
+ feature_dbxref.getDbXRef().getDb().getName()+"'))"+
"AND feature_id=(SELECT feature_id FROM "+
"feature WHERE uniquename='"+uniquename+"')";
@@ -987,7 +987,7 @@ public class JdbcDAO
*/
private void insertFeatureAlias(final FeatureSynonym feature_synonym)
{
- final String uniquename = feature_synonym.getFeature().getUniquename();
+ final String uniquename = feature_synonym.getFeature().getUniqueName();
final String synonym_name = feature_synonym.getSynonym().getName();
String sql;
@@ -1007,8 +1007,8 @@ public class JdbcDAO
if(!exists)
{
// create a new synonym name
- String type_id = Long.toString(feature_synonym.getSynonym().getCvterm()
- .getCvtermId());
+ String type_id = Long.toString(feature_synonym.getSynonym().getCvTerm()
+ .getCvTermId());
sql = "INSERT INTO "
+ "synonym (name, type_id, synonym_sgml) values ( '" + synonym_name
@@ -1044,7 +1044,7 @@ public class JdbcDAO
*/
private void deleteFeatureSynonym(final FeatureSynonym feature_synonym)
{
- final String uniquename = feature_synonym.getFeature().getUniquename();
+ final String uniquename = feature_synonym.getFeature().getUniqueName();
final String synonym_name = feature_synonym.getSynonym().getName();
String sql = "SELECT synonym_id FROM synonym WHERE "+
"synonym.name='"+synonym_name+"'";
@@ -1091,15 +1091,15 @@ public class JdbcDAO
sqlBuff.append("UPDATE feature_relationship ");
sqlBuff.append(" SET ");
sqlBuff.append(" rank="+feature_relationship.getRank()+", ");
- sqlBuff.append(" type_id="+feature_relationship.getCvterm().getCvtermId());
+ sqlBuff.append(" type_id="+feature_relationship.getCvTerm().getCvTermId());
sqlBuff.append(" WHERE ");
sqlBuff.append("subject_id=");
sqlBuff.append("( SELECT feature_id FROM feature WHERE uniquename='");
- sqlBuff.append(feature_relationship.getSubject().getUniquename()+"' ) ");
+ sqlBuff.append(feature_relationship.getSubject().getUniqueName()+"' ) ");
sqlBuff.append("AND ");
sqlBuff.append("object_id=");
sqlBuff.append("( SELECT feature_id FROM feature WHERE uniquename='");
- sqlBuff.append(feature_relationship.getObject().getUniquename()+"' ) ");
+ sqlBuff.append(feature_relationship.getObject().getUniqueName()+"' ) ");
String sql = sqlBuff.toString();
diff --git a/uk/ac/sanger/artemis/chado/Synonym.java b/uk/ac/sanger/artemis/chado/Synonym.java
index 3c8eee486..accdfde2e 100644
--- a/uk/ac/sanger/artemis/chado/Synonym.java
+++ b/uk/ac/sanger/artemis/chado/Synonym.java
@@ -33,7 +33,7 @@ public class Synonym
// synonym
private Integer synonym_id;
private String name;
- private Cvterm cvterm;
+ private CvTerm cvTerm;
private String synonym_sgml;
public Integer getSynonym_id()
@@ -56,14 +56,14 @@ public class Synonym
this.name = name;
}
- public Cvterm getCvterm()
+ public CvTerm getCvTerm()
{
- return cvterm;
+ return cvTerm;
}
- public void setCvterm(Cvterm cvterm)
+ public void setCvTerm(CvTerm cvTerm)
{
- this.cvterm = cvterm;
+ this.cvTerm = cvTerm;
}
public String getSynonym_sgml()
diff --git a/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java b/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java
index ee4978908..e7c6ac275 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 1.28 2006-08-31 12:41:57 tjc Exp $
+ * $Header: //tmp/pathsoft/artemis/uk/ac/sanger/artemis/components/genebuilder/GeneViewerPanel.java,v 1.29 2006-09-01 09:27:38 tjc Exp $
*/
package uk.ac.sanger.artemis.components.genebuilder;
@@ -30,6 +30,7 @@ import javax.swing.*;
import java.awt.*;
import java.awt.event.*;
import java.util.List;
+import java.util.Vector;
import java.util.Collections;
import java.util.Hashtable;
import java.util.Set;
@@ -696,12 +697,12 @@ public class GeneViewerPanel extends JPanel
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());
+ new Vector(start_exon.getFeaturelocsForFeatureId()), chado_gene.getSrcfeature_id());
if(loc.getStrand() == -1)
{
FeatureLoc loc_last = uk.ac.sanger.artemis.chado.Feature.getFeatureLoc(
- ((uk.ac.sanger.artemis.chado.Feature)exons.get(exons.size()-1)).getFeaturelocsForFeatureId(),
+ new Vector(((uk.ac.sanger.artemis.chado.Feature)exons.get(exons.size()-1)).getFeaturelocsForFeatureId()),
chado_gene.getSrcfeature_id());
if(loc.getFmin() < loc_last.getFmin())
@@ -713,7 +714,7 @@ public class GeneViewerPanel extends JPanel
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());
+ new Vector(exon.getFeaturelocsForFeatureId()), chado_gene.getSrcfeature_id());
int ex_start = border+(int)((loc.getFmin()+1-start)*fraction);
int ex_end = border+(int)((loc.getFmax()-start)*fraction);
@@ -1080,13 +1081,13 @@ public class GeneViewerPanel extends JPanel
*/
private Color getColorFromAttributes(uk.ac.sanger.artemis.chado.Feature feature)
{
- List properties = feature.getFeaturepropList();
+ List properties = new Vector(feature.getFeaturepropList());
for(int i=0; i<properties.size(); i++)
{
FeatureProp property = (FeatureProp)properties.get(i);
- if(property.getCvterm().getName().equals("colour") ||
- property.getCvterm().getName().equals("color") )
+ if(property.getCvTerm().getName().equals("colour") ||
+ property.getCvTerm().getName().equals("color") )
return Options.getOptions().getColorFromColourNumber(Integer.parseInt(property.getValue()));
}
return Color.CYAN;
@@ -1164,7 +1165,7 @@ public class GeneViewerPanel extends JPanel
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());
+ new Vector(this_feature.getFeaturelocsForFeatureId()), chado_gene.getSrcfeature_id());
int this_direction;
if(featureLoc.getStrand() == 1)
diff --git a/uk/ac/sanger/artemis/util/DatabaseDocument.java b/uk/ac/sanger/artemis/util/DatabaseDocument.java
index 0c86bafb3..88a7edc44 100644
--- a/uk/ac/sanger/artemis/util/DatabaseDocument.java
+++ b/uk/ac/sanger/artemis/util/DatabaseDocument.java
@@ -39,6 +39,7 @@ import java.util.Hashtable;
import java.util.Vector;
import java.util.Enumeration;
import java.util.List;
+import java.util.Collection;
import java.util.Iterator;
import javax.swing.JOptionPane;
import javax.swing.JPasswordField;
@@ -455,15 +456,15 @@ public class DatabaseDocument extends Document
for(int i = 0; i < feature_size; i++)
{
Feature feat = (Feature)featList.get(i);
- String name = feat.getUniquename();
+ String name = feat.getUniqueName();
String feature_id = Integer.toString(feat.getId());
id_store.put(feature_id, name);
}
// get all dbrefs & synonyms
- Hashtable dbxrefs = IBatisDAO.mergeDbxref(
- dao.getFeatureDbxrefByUniquename(null));
+ Hashtable dbxrefs = IBatisDAO.mergeDbXRef(
+ dao.getFeatureDbXRefByUniquename(null));
Hashtable synonym = getAllFeatureSynonyms(dao, null);
// create gff byte stream
@@ -471,7 +472,7 @@ public class DatabaseDocument extends Document
{
// select buffer based on feature type
Feature feat = (Feature)featList.get(i);
- long type_id = feat.getCvterm().getCvtermId();
+ long type_id = feat.getCvTerm().getCvTermId();
String typeName = getCvtermName(type_id, dao);
this_buff = buffers[types.length];
for(int j = 0; j < types.length; j++)
@@ -481,14 +482,14 @@ public class DatabaseDocument extends Document
}
- chadoToGFF(feat, parentFeature.getUniquename(),
+ chadoToGFF(feat, parentFeature.getUniqueName(),
dbxrefs, synonym,
id_store, dao,
feat.getFeatureloc(), this_buff);
if( i%10 == 0 || i == feature_size-1)
progress_listener.progressMade("Read from database: " +
- feat.getUniquename());
+ feat.getUniqueName());
}
return buffers;
@@ -551,9 +552,9 @@ public class DatabaseDocument extends Document
Feature feature = dao.getFeatureByUniqueName(search_gene);
ChadoCanonicalGene chado_gene = new ChadoCanonicalGene();
- id_store.put(Integer.toString(feature.getId()), feature.getUniquename());
+ id_store.put(Integer.toString(feature.getId()), feature.getUniqueName());
- List featurelocs = feature.getFeaturelocsForFeatureId();
+ List featurelocs = new Vector(feature.getFeaturelocsForFeatureId());
FeatureLoc featureloc = (FeatureLoc) featurelocs.get(0);
int src_id = featureloc.getSrcfeature_id();
@@ -571,7 +572,7 @@ public class DatabaseDocument extends Document
featureloc, buff);
// get children of gene
- List relations = feature.getFeatureRelationshipsForObjectId();
+ List relations = new Vector(feature.getFeatureRelationshipsForObjectId());
for(int i = 0; i < relations.size(); i++)
{
@@ -581,16 +582,17 @@ public class DatabaseDocument extends Document
//transcript.setId(id);
Feature transcript = dao.getFeatureById(id); //.getLazyFeature(transcript);
- id_store.put(Integer.toString(transcript.getId()), transcript
- .getUniquename());
+ id_store.put(Integer.toString(transcript.getId()),
+ transcript.getUniqueName());
- FeatureLoc loc = Feature.getFeatureLoc(transcript
- .getFeaturelocsForFeatureId(), src_id);
- chadoToGFF(transcript, feature.getUniquename(), null,
+ FeatureLoc loc = Feature.getFeatureLoc(new Vector(
+ transcript.getFeaturelocsForFeatureId()), src_id);
+ chadoToGFF(transcript, feature.getUniqueName(), null,
null, id_store, dao, loc, buff);
// get children of transcript - exons and pp
- List transcipt_relations = transcript.getFeatureRelationshipsForObjectId();
+ List transcipt_relations = new Vector(
+ transcript.getFeatureRelationshipsForObjectId());
for(int j = 0; j < transcipt_relations.size(); j++)
{
@@ -600,10 +602,11 @@ public class DatabaseDocument extends Document
// .getSubject_id());
Feature child = dao.getFeatureById(id); //dao.getLazyFeature(child);
- id_store.put(Integer.toString(child.getId()), child.getUniquename());
+ id_store.put(Integer.toString(child.getId()), child.getUniqueName());
- loc = Feature.getFeatureLoc(child.getFeaturelocsForFeatureId(),src_id);
- chadoToGFF(child, transcript.getUniquename(), null,
+ loc = Feature.getFeatureLoc(
+ new Vector(child.getFeaturelocsForFeatureId()),src_id);
+ chadoToGFF(child, transcript.getUniqueName(), null,
null, id_store, dao, loc, buff);
}
}
@@ -635,10 +638,10 @@ public class DatabaseDocument extends Document
int fmin = featureloc.getFmin() + 1;
int fmax = featureloc.getFmax();
- long type_id = feat.getCvterm().getCvtermId();
+ long type_id = feat.getCvTerm().getCvTermId();
int strand = featureloc.getStrand();
int phase = featureloc.getPhase();
- String name = feat.getUniquename();
+ String name = feat.getUniqueName();
String typeName = getCvtermName(type_id, dao);
String timelastmodified = Long.toString(feat.getTimelastmodified().getTime());
@@ -651,9 +654,9 @@ public class DatabaseDocument extends Document
{
FeatureRelationship feat_relationship = feat.getFeature_relationship();
parent_id = Integer.toString(feat_relationship.getObject().getId());
- long parent_type_id = feat_relationship.getCvterm().getCvtermId();
+ long parent_type_id = feat_relationship.getCvTerm().getCvTermId();
- parent_relationship = feat_relationship.getCvterm().getName();
+ parent_relationship = feat_relationship.getCvTerm().getName();
rank= feat_relationship.getRank();
if(parent_relationship == null)
@@ -661,15 +664,15 @@ public class DatabaseDocument extends Document
}
else if(feat.getFeatureRelationshipsForSubjectId() != null)
{
- List relations = feat.getFeatureRelationshipsForSubjectId();
+ List relations = new Vector(feat.getFeatureRelationshipsForSubjectId());
for(int i=0; i<relations.size(); i++)
{
FeatureRelationship feat_relationship =
(FeatureRelationship)relations.get(i);
parent_id = Integer.toString(feat_relationship.getObject().getId());
- System.out.println("HERE "+i+" "+feat_relationship.getCvterm().getName()+ " "+
+ System.out.println("HERE "+i+" "+feat_relationship.getCvTerm().getName()+ " "+
feat_relationship.getObject().getId()+" "+feat_relationship.getSubject().getId()+ " parent_id="+ parent_id);
- parent_relationship = feat_relationship.getCvterm().getName();
+ parent_relationship = feat_relationship.getCvTerm().getName();
}
}
@@ -784,7 +787,7 @@ public class DatabaseDocument extends Document
{
alias = (FeatureSynonym)v_synonyms.get(j);
- this_buff.append( getCvtermName(alias.getSynonym().getCvterm().getCvtermId(), dao) + "=" );
+ this_buff.append( getCvtermName(alias.getSynonym().getCvTerm().getCvTermId(), dao) + "=" );
//this_buff.append(alias.getSynonym().getCvterm().getName()+"=");
this_buff.append(alias.getSynonym().getName());
@@ -838,13 +841,13 @@ public class DatabaseDocument extends Document
try
{
- List cvtem_list = dao.getCvterm();
+ List cvtem_list = dao.getCvTerm();
Iterator it = cvtem_list.iterator();
while(it.hasNext())
{
- Cvterm cv = (Cvterm)it.next();
- cvterm.put(new Long(cv.getCvtermId()), cv.getName());
+ CvTerm cv = (CvTerm)it.next();
+ cvterm.put(new Long(cv.getCvTermId()), cv.getName());
}
}
catch(RuntimeException sqle)
@@ -868,7 +871,7 @@ public class DatabaseDocument extends Document
Feature feature = dao.getFeatureById(Integer.parseInt(feature_id));
buff.append("##FASTA\n>");
- buff.append(feature.getUniquename());
+ buff.append(feature.getUniqueName());
buff.append("\n");
buff.append(feature.getResidues());
return buff;
@@ -941,9 +944,9 @@ public class DatabaseDocument extends Document
while(it_residue_features.hasNext())
{
Feature feature = (Feature)it_residue_features.next();
- String typeName = getCvtermName(feature.getCvterm().getCvtermId(), getDAO());
+ String typeName = getCvtermName(feature.getCvTerm().getCvTermId(), getDAO());
- db.put(schema + " - " + typeName + " - " + feature.getUniquename(),
+ db.put(schema + " - " + typeName + " - " + feature.getUniqueName(),
Integer.toString(feature.getId()));
}
}
@@ -1077,19 +1080,19 @@ public class DatabaseDocument extends Document
{
Feature feature = (Feature)tsn.getFeatureObject();
- if(feature.getUniquename() != null)
+ if(feature.getUniqueName() != null)
{
final String uniquename;
if(tsn.getOldUniquename() != null)
uniquename = (String)tsn.getOldUniquename();
else
- uniquename = feature.getUniquename();
+ uniquename = feature.getUniqueName();
Feature old_feature
= dao.getFeatureByUniqueName(uniquename);
feature.setId( old_feature.getId() );
- tsn.setOldUniquename(feature.getUniquename());
+ tsn.setOldUniquename(feature.getUniqueName());
}
}
dao.merge(tsn.getFeatureObject());
@@ -1231,7 +1234,7 @@ public class DatabaseDocument extends Document
dao = new IBatisDAO(src.getPfield());
Feature feature = new Feature();
- feature.setUniquename(args[0]);
+ feature.setUniqueName(args[0]);
List schemas = new Vector();
schemas.add(args[1]);
List featureList = new Vector();
@@ -1242,17 +1245,17 @@ public class DatabaseDocument extends Document
feature = (Feature)featureList.get(i);
String abb = feature.getOrganism().getAbbreviation();
- String type = feature.getCvterm().getName();
+ String type = feature.getCvTerm().getName();
int fmin = feature.getFeatureloc().getFmin() + 1;
int fmax = feature.getFeatureloc().getFmax();
String featprop =
- ((FeatureProp)feature.getFeaturepropList().get(0)).getCvterm().getName();
+ ((FeatureProp)(new Vector(feature.getFeaturepropList()).get(0))).getCvTerm().getName();
System.out.print(fmin+".."+fmax);
System.out.print(" "+type);
System.out.print(" "+featprop);
System.out.print(" "+feature.getFeatureloc().getStrand());
- System.out.print(" "+feature.getUniquename());
+ System.out.print(" "+feature.getUniqueName());
System.out.print(" "+abb);
System.out.println(" "+Integer.toString(feature.getId()));
--
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