From 11b0df80b91977dc84903ee8b64ddba18e17ffd1 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Thu, 27 May 2010 13:21:12 +0000
Subject: [PATCH] SE-251 only primary proteins are showed in GUI
SVN: 16170
---
.../server/dataaccess/IProteinQueryDAO.java | 16 ++++++++--------
1 file changed, 8 insertions(+), 8 deletions(-)
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java
index 3eb157ccf0c..4b87704e51c 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java
@@ -49,7 +49,7 @@ public interface IProteinQueryDAO extends BaseQuery
+ "left join identified_proteins as ip on ip.sequ_id = s.id "
+ "left join proteins as p on ip.prot_id = p.id "
+ "left join data_sets as d on p.dase_id = d.id "
- + "left join experiments as e on d.expe_id = e.id where e.perm_id = ?{1}")
+ + "left join experiments as e on d.expe_id = e.id where e.perm_id = ?{1} and ip.is_primary = 't'")
public DataSet<ProteinReferenceWithProtein> listProteinReferencesByExperiment(
String experimentPermID);
@@ -65,7 +65,7 @@ public interface IProteinQueryDAO extends BaseQuery
+ "left join peptides as pe on pe.prot_id = p.id "
+ "left join data_sets as d on p.dase_id = d.id "
+ "left join experiments as e on d.expe_id = e.id "
- + "where e.perm_id = ?{1} ")
+ + "where e.perm_id = ?{1} and ip.is_primary = 't'")
public DataSet<ProteinReferenceWithProbabilityAndPeptide> listProteinsWithProbabilityAndPeptidesByExperiment(
String experimentPermID);
@@ -89,11 +89,11 @@ public interface IProteinQueryDAO extends BaseQuery
+ "probability, count(pe.id) as peptide_count, amino_acid_sequence, s.db_id, name_and_version "
+ "from data_sets as ds join experiments as e on ds.expe_id = e.id "
+ " join proteins as p on p.dase_id = ds.id "
- + " join identified_proteins as i on i.prot_id = p.id "
- + " join sequences as s on i.sequ_id = s.id "
+ + " join identified_proteins as ip on ip.prot_id = p.id "
+ + " join sequences as s on ip.sequ_id = s.id "
+ " join databases as db on s.db_id = db.id "
+ " left join peptides as pe on pe.prot_id = p.id "
- + "where s.prre_id = ?{2} and e.perm_id = ?{1} "
+ + "where s.prre_id = ?{2} and e.perm_id = ?{1} and ip.is_primary = 't' "
+ "group by data_set_id, data_set_perm_id, protein_id, probability, "
+ " amino_acid_sequence, s.db_id, name_and_version order by data_set_perm_id")
public DataSet<IdentifiedProtein> listProteinsByProteinReferenceAndExperiment(
@@ -106,10 +106,10 @@ public interface IProteinQueryDAO extends BaseQuery
+ "from abundances as a left join proteins as p on a.prot_id = p.id "
+ " left join data_sets as d on p.dase_id = d.id "
+ " left join experiments as e on d.expe_id = e.id "
- + " left join identified_proteins as i on i.prot_id = p.id "
- + " left join sequences as s on i.sequ_id = s.id "
+ + " left join identified_proteins as ip on ip.prot_id = p.id "
+ + " left join sequences as s on ip.sequ_id = s.id "
+ " left join samples on a.samp_id = samples.id "
- + "where e.perm_id = ?{1} and s.prre_id = ?{2}")
+ + "where e.perm_id = ?{1} and s.prre_id = ?{2} and ip.is_primary = 't'")
public DataSet<SampleAbundance> listSampleAbundanceByProtein(String experimentPermID,
long proteinReferenceID);
--
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