Refactoring ProteinByExperimentBrowserGrid to TypedTableGrid part I.

SVN: 22960

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ProteinBrowserColumnIDs.java

+/*
+ * 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";
+}

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/resultset/ProteinProvider.java

+/*
+ * 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();
+    }
+    
+
+}