SE-251 show protein coverage

SVN: 16282

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));

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;

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'")

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;
+    }
 }

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;

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;

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;
+    }
+    
 }

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;
     }
 
-
 }