diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/Dict.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/Dict.java index 8ce60800da90df12737a0eae71d0a0979475de15..ac98705d842fe6200751afbfbb4c4a9d54e1866f 100644 --- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/Dict.java +++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/Dict.java @@ -74,6 +74,10 @@ public class Dict public static final String SEQUENCE_NAME = "sequence_name"; public static final String FDR = "false_discovery_rate_column"; + + // Protein Detail View + public static final String PROBABILITY = "protein_probability"; + // SampleAbundance Browser 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 8c3e4d8b01dfe5800ba8f5bd0464b91519529011..edbdfcf35728791fc1dad1924eefd70020561b81 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 @@ -219,6 +219,7 @@ public class ProteinViewer extends AbstractViewer<IEntityInformationHolder> impl properties.put(viewContext.getMessage(Dict.PEPTIDES, proteinDetails.getPeptides().size()), proteinDetails.getPeptides().toArray()); + properties.put(viewContext.getMessage(Dict.PROBABILITY), proteinDetails.getProbability()); properties.put(viewContext.getMessage(Dict.FDR), proteinDetails.getFalseDiscoveryRate()); DatasetInformationHolder dataset = new DatasetInformationHolder(proteinDetails); diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/public/phosphonetx-dictionary.js b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/public/phosphonetx-dictionary.js index 5e331e3847f48c61d3bc66a799aaee7f043744f6..9c8e3e50ea26a954327903346bcbbdd1ecda1554 100644 --- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/public/phosphonetx-dictionary.js +++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/public/phosphonetx-dictionary.js @@ -31,6 +31,7 @@ var phosphonetx = { peptides: "Peptides ({0})", sequence_name: "Sequence", false_discovery_rate_column: "FDR (Protein Prophet)", + protein_probability: "Probability (Protein Prophet)", // SampleAbudndance Browser abundance: "Abundance", 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 20ce913bf626b2844e2624175b0e527c4d2f8a09..53f16b3c145087bd2fe4fd61ae98e34e897c4f19 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 @@ -68,6 +68,7 @@ class ProteinDetailsBO extends AbstractBusinessObject implements IProteinDetails details = new ProteinDetails(); details.setSequence(protein.getSequence()); details.setDatabaseNameAndVersion(protein.getDatabaseNameAndVersion()); + details.setProbability(protein.getProbability()); details.setFalseDiscoveryRate(protein.getFalseDiscoveryRate()); String dataSetPermID = protein.getDataSetPermID(); details.setDataSetPermID(dataSetPermID); 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 ec33394741ae084f956aee9b1b366bd5966b10ab..8495c70c047b9b7195a8be099e7d7db0da8337b2 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 @@ -34,6 +34,8 @@ public class ProteinDetails implements IsSerializable, Serializable private String sequence; private String databaseNameAndVersion; + + private double probability; private double falseDiscoveryRate; @@ -72,6 +74,16 @@ public class ProteinDetails implements IsSerializable, Serializable return falseDiscoveryRate; } + public double getProbability() + { + return probability; + } + + public void setProbability(double probability) + { + this.probability = probability; + } + public void setFalseDiscoveryRate(double falseDiscoveryRate) { this.falseDiscoveryRate = falseDiscoveryRate;