diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ProteinBrowserColumnIDs.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ProteinBrowserColumnIDs.java
new file mode 100644
index 0000000000000000000000000000000000000000..42c3c4a448de228952e13f387a504b09e63568fd
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ProteinBrowserColumnIDs.java
@@ -0,0 +1,29 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ProteinBrowserColumnIDs
+{
+ public static final String ACCESSION_NUMBER = "ACCESSION_NUMBER";
+ public static final String PROTEIN_DESCRIPTION = "PROTEIN_DESCRIPTION";
+ public static final String COVERAGE = "COVERAGE";
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/resultset/ProteinProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/resultset/ProteinProvider.java
new file mode 100644
index 0000000000000000000000000000000000000000..82bba5bf54260f4265fafdf06cd57d386971cea0
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/resultset/ProteinProvider.java
@@ -0,0 +1,129 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.server.resultset;
+
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ProteinBrowserColumnIDs.ACCESSION_NUMBER;
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ProteinBrowserColumnIDs.COVERAGE;
+import static ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ProteinBrowserColumnIDs.PROTEIN_DESCRIPTION;
+
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+
+import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.AbstractTableModelProvider;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TypedTableModel;
+import ch.systemsx.cisd.openbis.generic.shared.util.IColumn;
+import ch.systemsx.cisd.openbis.generic.shared.util.TypedTableModelBuilder;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IPhosphoNetXServer;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AbundanceColumnDefinition;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AggregateFunction;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinInfo;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.Treatment;
+
+/**
+ * Provider of {@link ProteinInfo} instances.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ProteinProvider extends AbstractTableModelProvider<ProteinInfo>
+{
+ private static final String ABUNDANCE_PROPERTY_KEY = "ABUNDANCE";
+
+ private final IPhosphoNetXServer server;
+ private final String sessionToken;
+ private final TechId experimentID;
+ private final double falseDiscoveryRate;
+ private final AggregateFunction aggregateFunction;
+ private final String treatmentTypeCode;
+ private final boolean aggregateOnOriginal;
+
+ public ProteinProvider(IPhosphoNetXServer server, String sessionToken,
+ TechId experimentID, double falseDiscoveryRate, AggregateFunction function,
+ String treatmentTypeCode, boolean aggregateOnOriginal)
+ {
+ this.server = server;
+ this.sessionToken = sessionToken;
+ this.experimentID = experimentID;
+ this.falseDiscoveryRate = falseDiscoveryRate;
+ this.aggregateFunction = function;
+ this.treatmentTypeCode = treatmentTypeCode;
+ this.aggregateOnOriginal = aggregateOnOriginal;
+ }
+
+ @Override
+ protected TypedTableModel<ProteinInfo> createTableModel()
+ {
+ List<AbundanceColumnDefinition> abundanceColumnDefinitions =
+ server.getAbundanceColumnDefinitionsForProteinByExperiment(sessionToken,
+ experimentID, treatmentTypeCode);
+ List<ProteinInfo> proteins =
+ server.listProteinsByExperiment(sessionToken, experimentID, falseDiscoveryRate,
+ aggregateFunction, treatmentTypeCode, aggregateOnOriginal);
+ TypedTableModelBuilder<ProteinInfo> builder = new TypedTableModelBuilder<ProteinInfo>();
+ builder.addColumn(ACCESSION_NUMBER);
+ builder.addColumn(PROTEIN_DESCRIPTION);
+ builder.addColumn(COVERAGE).withDefaultWidth(100);
+ Map<Long, IColumn> sampleIdToAbundanceColumnMap = new HashMap<Long, IColumn>();
+ for (AbundanceColumnDefinition abundanceColumnDefinition : abundanceColumnDefinitions)
+ {
+ long sampleID = abundanceColumnDefinition.getID();
+ String columnID = "abundance-" + Long.toString(sampleID);
+ builder.addColumn(columnID).withDefaultWidth(100);
+ IColumn column = builder.column(columnID);
+ sampleIdToAbundanceColumnMap.put(sampleID, column);
+ String header = abundanceColumnDefinition.getSampleCode();
+ Map<String, String> properties = new HashMap<String, String>();
+ properties.put(ABUNDANCE_PROPERTY_KEY, header);
+ List<Treatment> treatments = abundanceColumnDefinition.getTreatments();
+ if (treatments.isEmpty() == false)
+ {
+ header = "";
+ String delim = "";
+ for (Treatment treatment : treatments)
+ {
+ header += delim + treatment;
+ delim = ", ";
+ column.property(treatment.getTypeCode(), treatment.getValue());
+ }
+ }
+ column.withTitle(header);
+ }
+ for (ProteinInfo protein : proteins)
+ {
+ builder.addRow(protein);
+ builder.column(ACCESSION_NUMBER).addString(protein.getAccessionNumber());
+ builder.column(PROTEIN_DESCRIPTION).addString(protein.getDescription());
+ builder.column(COVERAGE).addDouble(protein.getCoverage());
+ Map<Long, Double> abundances = protein.getAbundances();
+ Set<Entry<Long, Double>> entrySet = abundances.entrySet();
+ for (Entry<Long, Double> entry : entrySet)
+ {
+ IColumn column = sampleIdToAbundanceColumnMap.get(entry.getKey());
+ if (column != null)
+ {
+ column.addDouble(entry.getValue());
+ }
+ }
+ }
+ return builder.getModel();
+ }
+
+
+}