diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java
index 6de611e8956eecb99e1662edfd52e4bddf00f60b..f0c30e2f1965268ea3dc76ddae956e65767ec195 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java
@@ -204,7 +204,7 @@ public class ProteinViewer extends AbstractViewer<IEntityInformationHolder> impl
String accessionNumber = info.getAccessionNumber();
TabItem item = new TabItem(accessionNumber);
item.setLayout(new FitLayout());
- PropertyGrid propertyGrid = new PropertyGrid(viewContext, 3);
+ PropertyGrid propertyGrid = new PropertyGrid(viewContext, 4);
final Map<String, Object> properties = new LinkedHashMap<String, Object>();
properties.put(viewContext.getMessage(Dict.ACCESSION_NUMBER), info);
propertyGrid.registerPropertyValueRenderer(IndistinguishableProteinInfo.class,
@@ -213,6 +213,7 @@ public class ProteinViewer extends AbstractViewer<IEntityInformationHolder> impl
.getDescription());
String markedSequence = markPeptides(info.getSequence(), peptides);
properties.put(viewContext.getMessage(Dict.SEQUENCE_NAME), markedSequence);
+ properties.put(viewContext.getMessage(Dict.COVERAGE), info.getCoverage());
propertyGrid.setProperties(properties);
ContentPanel contentPanel = new ContentPanel();
contentPanel.setHeight("100%");
@@ -300,6 +301,8 @@ public class ProteinViewer extends AbstractViewer<IEntityInformationHolder> impl
String markedSequence =
markPeptides(proteinDetails.getSequence(), proteinDetails.getPeptides());
properties.put(viewContext.getMessage(Dict.SEQUENCE_NAME), markedSequence);
+
+ properties.put(viewContext.getMessage(Dict.COVERAGE), proteinDetails.getCoverage());
propertyGrid.registerPropertyValueRenderer(Peptide.class, PropertyValueRenderers
.createPeptideRenderer(viewContext));
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinDetailsBO.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinDetailsBO.java
index 9f7092acc194e7ebe4c6e641bff847393be02ead..25a8e021224cb2e3fe66f1498a07fba9deaf7bbf 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinDetailsBO.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinDetailsBO.java
@@ -71,6 +71,7 @@ class ProteinDetailsBO extends AbstractBusinessObject implements IProteinDetails
details.setSequence(protein.getSequence());
details.setDatabaseNameAndVersion(protein.getDatabaseNameAndVersion());
details.setProbability(protein.getProbability());
+ details.setCoverage(100 * protein.getCoverage());
details.setFalseDiscoveryRate(protein.getFalseDiscoveryRate());
String dataSetPermID = protein.getDataSetPermID();
details.setDataSetPermID(dataSetPermID);
@@ -108,6 +109,7 @@ class ProteinDetailsBO extends AbstractBusinessObject implements IProteinDetails
info.setAccessionNumberType(builder.getTypeOrNull());
info.setDescription(protein.getDescription());
info.setSequence(protein.getSequence());
+ info.setCoverage(100 * protein.getCoverage());
infos.add(info);
}
return infos;
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 2888433b7adb6ca0addab2fc34fe4c5db3bc2b63..0bbed1dc0b756ac020d9360fe8c9274595a8eadc 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
@@ -87,7 +87,7 @@ public interface IProteinQueryDAO extends BaseQuery
public DataSet<Sequence> listProteinSequencesByProteinReference(long proteinReferenceID);
@Select("select ds.id as data_set_id, ds.perm_id as data_set_perm_id, p.id as protein_id, "
- + "probability, count(pe.id) as peptide_count, amino_acid_sequence, s.db_id, name_and_version "
+ + "probability, coverage, 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 ip on ip.prot_id = p.id "
@@ -95,7 +95,7 @@ public interface IProteinQueryDAO extends BaseQuery
+ " 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} and ip.is_primary = 't' "
- + "group by data_set_id, data_set_perm_id, protein_id, probability, "
+ + "group by data_set_id, data_set_perm_id, protein_id, probability, coverage, "
+ " amino_acid_sequence, s.db_id, name_and_version order by data_set_perm_id")
public DataSet<IdentifiedProtein> listProteinsByProteinReferenceAndExperiment(
String experimentPermID, long proteinReferenceID);
@@ -103,7 +103,7 @@ public interface IProteinQueryDAO extends BaseQuery
@Select("select * from peptides where prot_id = ?{1}")
public DataSet<IdentifiedPeptide> listIdentifiedPeptidesByProtein(long proteinID);
- @Select("select accession_number, description, amino_acid_sequence "
+ @Select("select accession_number, description, amino_acid_sequence, coverage "
+ "from identified_proteins as ip join sequences as s on ip.sequ_id = s.id "
+ " join protein_references as pr on s.prre_id = pr.id "
+ "where ip.prot_id = ?{1} and ip.is_primary = 'f'")
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/IndistinguishableProteinInfo.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/IndistinguishableProteinInfo.java
index e96a36e187772781ecb45f10536f6bf22abac21b..508b79e529d4bc01563d27008dfc69bc45547f45 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/IndistinguishableProteinInfo.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/IndistinguishableProteinInfo.java
@@ -31,6 +31,8 @@ public class IndistinguishableProteinInfo extends AccessionNumberProvider
private String description;
+ private double coverage;
+
public final String getSequence()
{
return sequence;
@@ -50,4 +52,14 @@ public class IndistinguishableProteinInfo extends AccessionNumberProvider
{
this.description = description;
}
+
+ public void setCoverage(double coverage)
+ {
+ this.coverage = coverage;
+ }
+
+ public double getCoverage()
+ {
+ return coverage;
+ }
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinDetails.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinDetails.java
index aa306a7c62763caf53595b4084ca2b6a9f2a5f16..694f6d867a14499d1a743190dd8f7ebc5e8b8a3b 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinDetails.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinDetails.java
@@ -36,6 +36,8 @@ public class ProteinDetails implements IsSerializable, Serializable
private String databaseNameAndVersion;
private double probability;
+
+ private double coverage;
private double falseDiscoveryRate;
@@ -86,6 +88,16 @@ public class ProteinDetails implements IsSerializable, Serializable
this.probability = probability;
}
+ public void setCoverage(double coverage)
+ {
+ this.coverage = coverage;
+ }
+
+ public double getCoverage()
+ {
+ return coverage;
+ }
+
public void setFalseDiscoveryRate(double falseDiscoveryRate)
{
this.falseDiscoveryRate = falseDiscoveryRate;
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IdentifiedProtein.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IdentifiedProtein.java
index 10ffe5044197ccf0ab58aa1f81fa9bad46449716..58f3d7a7ae4e376a9f43f99359a70946de1f2ade 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IdentifiedProtein.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IdentifiedProtein.java
@@ -51,6 +51,9 @@ public class IdentifiedProtein extends AbstractDTOWithID
@ResultColumn("probability")
private double probability;
+ @ResultColumn("coverage")
+ private double coverage;
+
private double falseDiscoveryRate;
public final String getDataSetPermID()
@@ -113,6 +116,16 @@ public class IdentifiedProtein extends AbstractDTOWithID
this.probability = probability;
}
+ public void setCoverage(double coverage)
+ {
+ this.coverage = coverage;
+ }
+
+ public double getCoverage()
+ {
+ return coverage;
+ }
+
public final double getFalseDiscoveryRate()
{
return falseDiscoveryRate;
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IndistinguishableProtein.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IndistinguishableProtein.java
index 05aaac1a08afc8f2978303e9bddd7aeb66ecb381..8414b778160daac28085b5ea51a48642796b486e 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IndistinguishableProtein.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IndistinguishableProtein.java
@@ -30,6 +30,9 @@ public class IndistinguishableProtein extends ProteinReference
@ResultColumn("amino_acid_sequence")
private String sequence;
+ @ResultColumn("coverage")
+ private double coverage;
+
public void setSequence(String sequence)
{
this.sequence = sequence;
@@ -40,4 +43,14 @@ public class IndistinguishableProtein extends ProteinReference
return sequence;
}
+ public void setCoverage(double coverage)
+ {
+ this.coverage = coverage;
+ }
+
+ public double getCoverage()
+ {
+ return coverage;
+ }
+
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithProtein.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithProtein.java
index 2eb03624586a83ea8f5e8f8343520f3a216508b4..65db03747b8ea14e84cd49ebaa830d3c1c629273 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithProtein.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithProtein.java
@@ -81,5 +81,4 @@ public class ProteinReferenceWithProtein extends ProteinReference implements Ser
return coverage;
}
-
}