From 679f6e5870b31ef923053c314009df5d95774887 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Mon, 17 Nov 2008 13:48:09 +0000
Subject: [PATCH] add getOrganismsContainingSrcFeatures
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@9367 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
uk/ac/sanger/artemis/chado/GmodDAO.java | 1 +
uk/ac/sanger/artemis/chado/IBatisDAO.java | 24 +++++++++++++++++++----
uk/ac/sanger/artemis/chado/JdbcDAO.java | 5 +++++
3 files changed, 26 insertions(+), 4 deletions(-)
diff --git a/uk/ac/sanger/artemis/chado/GmodDAO.java b/uk/ac/sanger/artemis/chado/GmodDAO.java
index 2aca30748..69e733f19 100644
--- a/uk/ac/sanger/artemis/chado/GmodDAO.java
+++ b/uk/ac/sanger/artemis/chado/GmodDAO.java
@@ -49,6 +49,7 @@ public abstract class GmodDAO
implements SequenceDaoI, SchemaDaoI, OrganismDaoI, CvDaoI, PubDaoI, GeneralDaoI
{
+ public abstract List getOrganismsContainingSrcFeatures();
public abstract List getSimilarityMatchesByFeatureIds(final List featureIds);
public abstract List getSimilarityMatches(final Integer srcFeatureId);
public abstract List getClustersByFeatureIds(final List featureIds);
diff --git a/uk/ac/sanger/artemis/chado/IBatisDAO.java b/uk/ac/sanger/artemis/chado/IBatisDAO.java
index c097c5476..1c2e2db46 100644
--- a/uk/ac/sanger/artemis/chado/IBatisDAO.java
+++ b/uk/ac/sanger/artemis/chado/IBatisDAO.java
@@ -118,7 +118,12 @@ public class IBatisDAO extends GmodDAO
public List getResidueFeatures(final Integer organismId)
{
- return sqlMap.queryForList("getResidueFeatures",organismId);
+
+ CvTerm cvTerm = getCvTermByNameAndCvName("top_level_seq", "genedb_misc");
+ if(cvTerm != null)
+ return sqlMap.queryForList("getTopLevelFeatures",organismId);
+ else
+ return sqlMap.queryForList("getResidueFeatures",organismId);
}
public List getResidueFeaturesByOrganismCommonName(final String commonName)
@@ -492,8 +497,6 @@ public class IBatisDAO extends GmodDAO
/**
* Return a list of top-level features
- *
- *
* @return a (possibly empty) List<Feature> of children
*/
public List getTopLevelFeatures()
@@ -570,9 +573,22 @@ public class IBatisDAO extends GmodDAO
*/
public List getResidueFeatures()
{
- return sqlMap.queryForList("getResidueFeatures",null);
+ CvTerm cvTerm = getCvTermByNameAndCvName("top_level_seq", "genedb_misc");
+ if(cvTerm != null)
+ return sqlMap.queryForList("getTopLevelFeatures",null);
+ else
+ return sqlMap.queryForList("getResidueFeatures",null);
}
+ public List getOrganismsContainingSrcFeatures()
+ {
+ CvTerm cvTerm = getCvTermByNameAndCvName("top_level_seq", "genedb_misc");
+ if(cvTerm != null)
+ return sqlMap.queryForList("getTopLevelOrganisms", null);
+ else
+ return sqlMap.queryForList("getOrganismsContainingSrcFeatures", null);
+ }
+
/**
*
* For a schema return the type_id's with residues.
diff --git a/uk/ac/sanger/artemis/chado/JdbcDAO.java b/uk/ac/sanger/artemis/chado/JdbcDAO.java
index 27c549cc9..2d7c4d05e 100644
--- a/uk/ac/sanger/artemis/chado/JdbcDAO.java
+++ b/uk/ac/sanger/artemis/chado/JdbcDAO.java
@@ -101,6 +101,11 @@ public class JdbcDAO extends GmodDAO
//////
//////
+ public List getOrganismsContainingSrcFeatures()
+ {
+ return null;
+ }
+
public Feature getLazyFeatureNoResiduesById(final Integer featureId)
{
return null;
--
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