SE-251 fixed bug concerning experiment identifier in protein details view,...

SE-251 fixed bug concerning experiment identifier in protein details view, implementation of section for indistinguishable protein in protein details view

SVN: 16223

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/Dict.java

@@ -59,6 +59,8 @@ public class Dict
 
     public static final String DATABASE_NAME_AND_VERSION = "database_name_and_version";
 
+    public static final String INDISTINGUISHABLE_PROTEINS = "indistinguishable_proteins";
+    
     public static final String SEQUENCE = "sequence";
 
     public static final String SEQUENCES = "sequences";
@@ -80,7 +82,6 @@ public class Dict
     // Protein Detail View
     public static final String PROBABILITY = "protein_probability";
 
-
     // SampleAbundance Browser
 
     public static final String ABUNDANCE = "abundance";
@@ -95,4 +96,5 @@ public class Dict
     public static final String COPY_DATA_SETS_MESSAGE = "copy_data_sets_message";
     public static final String COPY_DATA_SETS_DATA_SET_TYPE_FIELD = "copy_data_sets_data_set_type_field";
 
+
 }

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ExperimentViewer.java

@@ -67,7 +67,7 @@ public class ExperimentViewer extends GenericExperimentViewer
                         protected IDisposableComponent createDisposableContent()
                         {
                             return ProteinByExperimentBrowserGrid.create(specificViewContext,
-                                    experimentType, experimentId);
+                                    experimentType, experiment);
                         }
                     };
         section.setDisplayID(DisplayTypeIDGenerator.PROTEIN_SECTION, displyIdSuffix);

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowerToolBar.java

@@ -38,8 +38,8 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.model.NonH
 import ch.systemsx.cisd.openbis.generic.client.web.client.application.model.VocabularyTermModel;
 import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.VocabularyTermSelectionWidget;
 import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.widget.IDataRefreshCallback;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IIdAndCodeHolder;
 import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
@@ -160,15 +160,15 @@ class ProteinByExperimentBrowerToolBar extends ToolBar
 
     private ProteinByExperimentBrowserGrid browserGrid;
 
-    private IIdAndCodeHolder experimentId;
+    private Experiment experiment;
 
     private ProteinSummaryGrid summaryGrid;
 
     ProteinByExperimentBrowerToolBar(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
-            IIdAndCodeHolder experimentId)
+            Experiment experiment)
     {
         this.viewContext = viewContext;
-        this.experimentId = experimentId;
+        this.experiment = experiment;
         setBorders(true);
         // WORKAROUND to get all elements in the toolbar present independent of the original width
         // of the parent
@@ -275,9 +275,9 @@ class ProteinByExperimentBrowerToolBar extends ToolBar
         return comboBox;
     }
 
-    IIdAndCodeHolder getExperimentOrNull()
+    Experiment getExperimentOrNull()
     {
-        return experimentId;
+        return experiment;
     }
 
     void setBrowserGrid(ProteinByExperimentBrowserGrid browserGrid)
@@ -292,9 +292,9 @@ class ProteinByExperimentBrowerToolBar extends ToolBar
 
     void update()
     {
-        if (experimentId != null)
+        if (experiment != null)
         {
-            final TechId experimentID = TechId.create(experimentId);
+            final TechId experimentID = TechId.create(experiment);
             browserGrid.setLoadMaskImmediately(true);
             browserGrid.setPostRefreshCallback(new IDataRefreshCallback()
                 {

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowserGrid.java

@@ -51,10 +51,10 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ResultSet;
 import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
 import ch.systemsx.cisd.openbis.generic.shared.basic.GridRowModel;
 import ch.systemsx.cisd.openbis.generic.shared.basic.IColumnDefinition;
-import ch.systemsx.cisd.openbis.generic.shared.basic.IIdAndCodeHolder;
 import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BasicEntityType;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind.ObjectKind;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.columns.InternalAbundanceColumnDefinition;
@@ -97,11 +97,11 @@ class ProteinByExperimentBrowserGrid extends AbstractSimpleBrowserGrid<ProteinIn
 
     static IDisposableComponent create(
             final IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
-            BasicEntityType experimentType, IIdAndCodeHolder experimentId)
+            BasicEntityType experimentType, Experiment experiment)
     {
         final IDisposableComponent summaryGrid = ProteinSummaryGrid.create(viewContext);
         ProteinByExperimentBrowserGrid browserGrid =
-                new ProteinByExperimentBrowserGrid(viewContext, experimentId);
+                new ProteinByExperimentBrowserGrid(viewContext, experiment);
         final IDisposableComponent disposableBrowerGrid = browserGrid.asDisposableWithoutToolbar();
         final ProteinByExperimentBrowerToolBar toolBar = browserGrid.toolbar;
         toolBar.setSummaryGrid((ProteinSummaryGrid) summaryGrid.getComponent());
@@ -152,12 +152,12 @@ class ProteinByExperimentBrowserGrid extends AbstractSimpleBrowserGrid<ProteinIn
 
     private ProteinByExperimentBrowserGrid(
             final IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
-            IIdAndCodeHolder experimentId)
+            Experiment experiment)
     {
         super(viewContext.getCommonViewContext(), BROWSER_ID, GRID_ID, false,
                 PhosphoNetXDisplayTypeIDGenerator.PROTEIN_BY_EXPERIMENT_BROWSER_GRID);
         specificViewContext = viewContext;
-        toolbar = new ProteinByExperimentBrowerToolBar(viewContext, experimentId);
+        toolbar = new ProteinByExperimentBrowerToolBar(viewContext, experiment);
         toolbar.setBrowserGrid(this);
         registerLinkClickListenerFor(ProteinColDefKind.ACCESSION_NUMBER.id(),
                 new ICellListener<ProteinInfo>()
@@ -208,9 +208,9 @@ class ProteinByExperimentBrowserGrid extends AbstractSimpleBrowserGrid<ProteinIn
         for (AbundanceColumnDefinition definition : abundanceColumnDefinitions)
         {
             String header = definition.getSampleCode();
-            final long sampleID = definition.getID();
-            List<Treatment> treatments = definition.getTreatments();
             Map<String, String> properties = new HashMap<String, String>();
+            properties.put(ABUNDANCE_PROPERTY_KEY, header);
+            List<Treatment> treatments = definition.getTreatments();
             if (treatments.isEmpty() == false)
             {
                 header = "";
@@ -221,10 +221,8 @@ class ProteinByExperimentBrowserGrid extends AbstractSimpleBrowserGrid<ProteinIn
                     delim = ", ";
                     properties.put(treatment.getTypeCode(), treatment.getValue());
                 }
-            } else
-            {
-                properties.put(ABUNDANCE_PROPERTY_KEY, header);
             }
+            final long sampleID = definition.getID();
             IColumnDefinitionUI<ProteinInfo> columnDefinition =
                     new InternalAbundanceColumnDefinition(header, properties, 100, false, sampleID);
             abundanceColumnIDs.add(columnDefinition.getIdentifier());

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java

@@ -24,9 +24,16 @@ import java.util.Set;
 
 import com.extjs.gxt.ui.client.Style.LayoutRegion;
 import com.extjs.gxt.ui.client.Style.Scroll;
+import com.extjs.gxt.ui.client.util.Margins;
 import com.extjs.gxt.ui.client.widget.ContentPanel;
+import com.extjs.gxt.ui.client.widget.LayoutContainer;
+import com.extjs.gxt.ui.client.widget.TabItem;
+import com.extjs.gxt.ui.client.widget.TabPanel;
 import com.extjs.gxt.ui.client.widget.layout.BorderLayout;
 import com.extjs.gxt.ui.client.widget.layout.BorderLayoutData;
+import com.extjs.gxt.ui.client.widget.layout.FitLayout;
+import com.extjs.gxt.ui.client.widget.layout.RowData;
+import com.extjs.gxt.ui.client.widget.layout.RowLayout;
 
 import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
 import ch.systemsx.cisd.openbis.generic.client.web.client.application.DisposableSectionPanel;
@@ -53,6 +60,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityType;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.IndistinguishableProteinInfo;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.Peptide;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinDetails;
@@ -64,7 +72,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinInfo;
 public class ProteinViewer extends AbstractViewer<IEntityInformationHolder> implements
         IDatabaseModificationObserver
 {
-    private static final int AMINOACIDS_IN_SEQUENCE_PER_LINE = 60;
+    private static final int AMINOACIDS_IN_SEQUENCE_PER_LINE = 90;
 
     private static final int AMINOACIDS_IN_ONE_BLOCK = 10;
 
@@ -74,25 +82,25 @@ public class ProteinViewer extends AbstractViewer<IEntityInformationHolder> impl
 
     static AbstractTabItemFactory createTabItemFactory(
             final IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
-            final IIdAndCodeHolder experimentId, final ProteinInfo proteinInfo)
+            final Experiment experiment, final ProteinInfo proteinInfo)
     {
         return new AbstractTabItemFactory()
             {
                 @Override
                 public String getId()
                 {
-                    return createWidgetID(experimentId, proteinInfo.getId());
+                    return createWidgetID(experiment, proteinInfo.getId());
                 }
 
                 @Override
                 public ITabItem create()
                 {
                     ProteinViewer viewer =
-                            new ProteinViewer(viewContext, experimentId, proteinInfo.getId());
+                            new ProteinViewer(viewContext, experiment, proteinInfo.getId());
                     DatabaseModificationAwareComponent c =
                             new DatabaseModificationAwareComponent(viewer, viewer);
                     String description = getAbbreviatedDescription(proteinInfo);
-                    String identifier = experimentId == null ? "?" : experimentId.getCode();
+                    String identifier = experiment == null ? "?" : experiment.getCode();
                     return DefaultTabItem.create(viewContext.getMessage(
                             Dict.PROTEIN_IN_EXPERIMENT_TAB_LABEL, description, identifier), c,
                             viewContext, false);
@@ -124,27 +132,27 @@ public class ProteinViewer extends AbstractViewer<IEntityInformationHolder> impl
 
     private final IViewContext<IPhosphoNetXClientServiceAsync> viewContext;
 
-    private final IIdAndCodeHolder experimentIdOrNull;
+    private final Experiment experimentOrNull;
 
     private final TechId proteinReferenceID;
 
     private ProteinSamplesSection proteinSamplesSection;
 
     private ProteinViewer(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
-            IIdAndCodeHolder experimentId, TechId proteinReferenceID)
+            Experiment experiment, TechId proteinReferenceID)
     {
-        super(viewContext, "", createWidgetID(experimentId, proteinReferenceID), false);
+        super(viewContext, "", createWidgetID(experiment, proteinReferenceID), false);
         this.viewContext = viewContext;
-        this.experimentIdOrNull = experimentId;
+        this.experimentOrNull = experiment;
         this.proteinReferenceID = proteinReferenceID;
         reloadAllData();
     }
 
     private void reloadAllData()
     {
-        if (experimentIdOrNull != null)
+        if (experimentOrNull != null)
         {
-            viewContext.getService().getProteinByExperiment(new TechId(experimentIdOrNull.getId()),
+            viewContext.getService().getProteinByExperiment(new TechId(experimentOrNull.getId()),
                     proteinReferenceID, new ProteinByExperimentCallback(viewContext, this));
         }
     }
@@ -156,18 +164,74 @@ public class ProteinViewer extends AbstractViewer<IEntityInformationHolder> impl
         setScrollMode(Scroll.AUTO);
         ContentPanel propertyPanel = createPropertyPanel(protein);
 
-        if (protein.getDetails() == null)
+        ProteinDetails details = protein.getDetails();
+        if (details == null)
         {
             recreateUIWithDatasetTable(protein, propertyPanel);
         } else
         {
-            add(propertyPanel, createBorderLayoutData(LayoutRegion.CENTER));
+            List<IndistinguishableProteinInfo> indistinguishableProteins =
+                    details.getIndistinguishableProteinInfos();
+            LayoutContainer southPanel = new LayoutContainer();
+            RowLayoutManager rowDataManager = new RowLayoutManager(southPanel, new RowLayout());
+            add(southPanel, bld(LayoutRegion.CENTER));
+            rowDataManager.addToContainer(propertyPanel, new RowData(1, 0.5f));
+            if (indistinguishableProteins.isEmpty() == false)
+            {
+                List<Peptide> peptides = details.getPeptides();
+                ContentPanel panel =
+                        createIndistinguishableProteinsSection(indistinguishableProteins, peptides);
+                rowDataManager.addToContainer(panel, new RowData(1, 0.3f));
+            }
             proteinSamplesSection =
-                    new ProteinSamplesSection(viewContext, proteinReferenceID, experimentIdOrNull);
-            add(proteinSamplesSection, createBorderLayoutData(LayoutRegion.SOUTH));
+                    new ProteinSamplesSection(viewContext, proteinReferenceID, experimentOrNull);
+            rowDataManager.addToContainer(proteinSamplesSection, new RowData(1, 0.2f));
             layout();
         }
     }
+    
+    private ContentPanel createIndistinguishableProteinsSection(
+            List<IndistinguishableProteinInfo> indistinguishableProteins, List<Peptide> peptides)
+    {
+        ContentPanel panel = new ContentPanel(new RowLayout());
+        panel.setHeading(viewContext.getMessage(Dict.INDISTINGUISHABLE_PROTEINS));
+        panel.setCollapsible(true);
+        panel.setHeight("100%");
+        TabPanel tabPanel = new TabPanel();
+        tabPanel.setTabScroll(true);
+        for (IndistinguishableProteinInfo info : indistinguishableProteins)
+        {
+            String accessionNumber = info.getAccessionNumber();
+            TabItem item = new TabItem(accessionNumber);
+            item.setLayout(new FitLayout());
+            PropertyGrid propertyGrid = new PropertyGrid(viewContext, 3);
+            final Map<String, Object> properties = new LinkedHashMap<String, Object>();
+            properties.put(viewContext.getMessage(Dict.ACCESSION_NUMBER), accessionNumber);
+            properties.put(viewContext.getMessage(Dict.PROTEIN_DESCRIPTION), info
+                    .getDescription());
+            String markedSequence = markPeptides(info.getSequence(), peptides);
+            properties.put(viewContext.getMessage(Dict.SEQUENCE_NAME), markedSequence);
+            propertyGrid.setProperties(properties);
+            ContentPanel contentPanel = new ContentPanel();
+            contentPanel.setHeight("100%");
+            contentPanel.setScrollMode(Scroll.AUTO);
+            contentPanel.add(propertyGrid);
+            item.add(contentPanel);
+            tabPanel.add(item);
+        }
+        
+        panel.add(tabPanel, new RowData(1, 1));
+        return panel;
+    }
+    
+    private BorderLayoutData bld(LayoutRegion region)
+    {
+        BorderLayoutData data = new BorderLayoutData(region);
+        data.setSplit(true);
+        data.setCollapsible(true);
+        data.setMargins(new Margins(2));
+        return data;
+    }
 
     private void recreateUIWithDatasetTable(ProteinByExperiment protein, ContentPanel propertyPanel)
     {
@@ -193,7 +257,7 @@ public class ProteinViewer extends AbstractViewer<IEntityInformationHolder> impl
                         protected IDisposableComponent createDisposableContent()
                         {
                             return DataSetProteinGrid.create(ProteinViewer.this.viewContext,
-                                    experimentIdOrNull, proteinReferenceID);
+                                    experimentOrNull, proteinReferenceID);
                         }
                     };
         add(proteinsSection, createBorderLayoutData(LayoutRegion.SOUTH));
@@ -205,6 +269,7 @@ public class ProteinViewer extends AbstractViewer<IEntityInformationHolder> impl
         PropertyGrid propertyGrid = createPropertyGrid(protein);
         ContentPanel contentPanel = new ContentPanel();
         contentPanel.setScrollMode(Scroll.AUTO);
+        contentPanel.setCollapsible(true);
         contentPanel.add(propertyGrid);
         return contentPanel;
     }
@@ -213,9 +278,9 @@ public class ProteinViewer extends AbstractViewer<IEntityInformationHolder> impl
     {
         final Map<String, Object> properties = new LinkedHashMap<String, Object>();
         PropertyGrid propertyGrid = new PropertyGrid(viewContext, 0);
-        if (experimentIdOrNull != null)
+        if (experimentOrNull != null)
         {
-            properties.put(viewContext.getMessage(Dict.EXPERIMENT_LABEL), experimentIdOrNull);
+            properties.put(viewContext.getMessage(Dict.EXPERIMENT_LABEL), experimentOrNull);
             propertyGrid.registerPropertyValueRenderer(Experiment.class, PropertyValueRenderers
                     .createExperimentPropertyValueRenderer(viewContext));
         }

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/RowLayoutManager.java

+/*
+ * Copyright 2010 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.application;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import com.extjs.gxt.ui.client.Style.Orientation;
+import com.extjs.gxt.ui.client.event.BaseEvent;
+import com.extjs.gxt.ui.client.event.Events;
+import com.extjs.gxt.ui.client.event.Listener;
+import com.extjs.gxt.ui.client.widget.ContentPanel;
+import com.extjs.gxt.ui.client.widget.LayoutContainer;
+import com.extjs.gxt.ui.client.widget.layout.RowData;
+import com.extjs.gxt.ui.client.widget.layout.RowLayout;
+
+/**
+ * Helper class for doing {@link RowLayout} of a {@link LayoutContainer} with instances of
+ * {@link ContentPanel} in a dynamic way. Collapsed row components lead to a resize of the
+ * non-collapsed components if the row size is defined by a positive value <= 1.
+ * 
+ * @author Franz-Josef Elmer
+ */
+public class RowLayoutManager
+{
+    private static interface IManipulator
+    {
+        double getFor(RowData rowData);
+        void setFor(RowData rowData, double newValue);
+        int getFrameSizeFor(ContentPanel panel);
+    }
+    
+    private static final class DynamicRowData
+    {
+        private RowData rowData;
+        private double originalValue;
+        private ContentPanel panel;
+    }
+    
+    private static final IManipulator HEIGHT_MANIPULATOR = new IManipulator()
+    {
+        public void setFor(RowData rowData, double newValue)
+        {
+            rowData.setHeight(newValue);
+        }
+
+        public double getFor(RowData rowData)
+        {
+            return rowData.getHeight();
+        }
+
+        public int getFrameSizeFor(ContentPanel panel)
+        {
+            return panel.isRendered() ? panel.getFrameHeight() : 0;
+        }
+    };
+    
+    private static final IManipulator WIDTH_MANIPULATOR = new IManipulator()
+    {
+        public void setFor(RowData rowData, double newValue)
+        {
+            rowData.setWidth(newValue);
+        }
+
+        public double getFor(RowData rowData)
+        {
+            return rowData.getWidth();
+        }
+
+        public int getFrameSizeFor(ContentPanel panel)
+        {
+            return panel.isRendered() ? panel.getFrameWidth() : 0;
+        }
+    };
+    
+    private final LayoutContainer container;
+    private final IManipulator manipulator;
+    private final List<DynamicRowData> dynamicRowDatas = new ArrayList<DynamicRowData>();
+
+    /**
+     * Creates an instance for the specified container and apply the specified layout.
+     */
+    public RowLayoutManager(LayoutContainer container, RowLayout rowLayout)
+    {
+        this.container = container;
+        container.setLayout(rowLayout);
+        Orientation orientation = rowLayout.getOrientation();
+        if (orientation.equals(Orientation.VERTICAL))
+        {
+            manipulator = HEIGHT_MANIPULATOR;
+        } else
+        {
+            manipulator = WIDTH_MANIPULATOR;
+        }
+    }
+
+    /**
+     * Adds the specified panel to the container in accordance to the specified row data.
+     */
+    public void addToContainer(ContentPanel contentPanel, RowData rowData)
+    {
+        container.add(contentPanel, rowData);
+        double value = manipulator.getFor(rowData);
+        if (value < 0 || value > 1)
+        {
+            return;
+        }
+        DynamicRowData dynamicRowData = new DynamicRowData();
+        dynamicRowData.rowData = rowData;
+        dynamicRowData.originalValue = value;
+        dynamicRowData.panel = contentPanel;
+        dynamicRowDatas.add(dynamicRowData);
+        adjustRelative();
+        Listener<BaseEvent> listener = new Listener<BaseEvent>()
+            {
+                public void handleEvent(BaseEvent event)
+                {
+                    adjustRelative();
+                }
+            };
+        contentPanel.addListener(Events.Collapse, listener);
+        contentPanel.addListener(Events.Expand, listener);
+    }
+
+    private void adjustRelative()
+    {
+        double sum = 0;
+        for (DynamicRowData data : dynamicRowDatas)
+        {
+            if (data.panel.isCollapsed() == false)
+            {
+                sum += data.originalValue;
+            }
+        }
+        for (DynamicRowData data : dynamicRowDatas)
+        {
+            double value;
+            if (data.panel.isCollapsed())
+            {
+                value = manipulator.getFrameSizeFor(data.panel);
+            }
+            else
+            {
+                value = data.originalValue / sum;
+            }
+            manipulator.setFor(data.rowData, value);
+        }
+        container.layout(true);
+    }
+}
\ No newline at end of file

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/public/phosphonetx-dictionary.js

@@ -22,6 +22,7 @@ var phosphonetx = {
   protein_browser: "Proteins",
   protein_summary: "Protein/Peptide Counts",
   database_name_and_version: "Database",
+  indistinguishable_proteins: "Indistinguishable Proteins",
   sequence: "Amino Acid Sequence",
   sequences: "Amino Acid Sequences",
   data_set_proteins: "Data Sets",

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinDetailsBO.java

@@ -28,10 +28,12 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
 import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IPhosphoNetXDAOFactory;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IProteinQueryDAO;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.IndistinguishableProteinInfo;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.Peptide;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinDetails;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.IdentifiedPeptide;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.IdentifiedProtein;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.IndistinguishableProtein;
 
 /**
  * @author Franz-Josef Elmer
@@ -79,29 +81,60 @@ class ProteinDetailsBO extends AbstractBusinessObject implements IProteinDetails
                     details.setDataSetTypeCode(ds.getDataSetType().getCode());
                 }
                 details.setPeptides(loadPeptides(protein));
-                details.setProteinID(new TechId(protein.getProteinID()));
+                long proteinID = protein.getProteinID();
+                details.setProteinID(new TechId(proteinID));
+                details.setIndistinguishableProteinInfos(loadIndistinguishableProteinInfos(proteinID));
             }
         } finally
         {
             proteins.close();
         }
     }
+    
+    private List<IndistinguishableProteinInfo> loadIndistinguishableProteinInfos(long proteinID)
+    {
+        IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAO();
+        DataSet<IndistinguishableProtein> proteins =
+                proteinQueryDAO.listIndistinguishableProteinsByProteinID(proteinID);
+        try
+        {
+            List<IndistinguishableProteinInfo> infos =
+                    new ArrayList<IndistinguishableProteinInfo>();
+            for (IndistinguishableProtein protein : proteins)
+            {
+                IndistinguishableProteinInfo info = new IndistinguishableProteinInfo();
+                info.setAccessionNumber(protein.getAccessionNumber());
+                info.setDescription(protein.getDescription());
+                info.setSequence(protein.getSequence());
+                infos.add(info);
+            }
+            return infos;
+        } finally
+        {
+            proteins.close();
+        }
+    }
 
     private List<Peptide> loadPeptides(IdentifiedProtein protein)
     {
         IProteinQueryDAO proteinQueryDAO = getSpecificDAOFactory().getProteinQueryDAO();
         DataSet<IdentifiedPeptide> identifiedPeptides =
                 proteinQueryDAO.listIdentifiedPeptidesByProtein(protein.getProteinID());
-        List<Peptide> peptides = new ArrayList<Peptide>();
-        for (IdentifiedPeptide identifiedPeptide : identifiedPeptides)
+        try
+        {
+            List<Peptide> peptides = new ArrayList<Peptide>();
+            for (IdentifiedPeptide identifiedPeptide : identifiedPeptides)
+            {
+                Peptide peptide = new Peptide();
+                peptide.setSequence(identifiedPeptide.getSequence());
+                peptide.setCharge(identifiedPeptide.getCharge());
+                peptides.add(peptide);
+            }
+            return peptides;
+        } finally
         {
-            Peptide peptide = new Peptide();
-            peptide.setSequence(identifiedPeptide.getSequence());
-            peptide.setCharge(identifiedPeptide.getCharge());
-            peptides.add(peptide);
+            identifiedPeptides.close();
         }
-        identifiedPeptides.close();
-        return peptides;
     }
 
     private String getExperimentPermIDFor(TechId experimentId)

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java

@@ -25,6 +25,7 @@ import net.lemnik.eodsql.Select;
 import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.LongSetMapper;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.IdentifiedPeptide;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.IdentifiedProtein;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.IndistinguishableProtein;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProbabilityFDRMapping;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinAbundance;
 import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReference;
@@ -98,10 +99,16 @@ public interface IProteinQueryDAO extends BaseQuery
             + "         amino_acid_sequence, s.db_id, name_and_version order by data_set_perm_id")
     public DataSet<IdentifiedProtein> listProteinsByProteinReferenceAndExperiment(
             String experimentPermID, long proteinReferenceID);
-
+    
     @Select("select * from peptides where prot_id = ?{1}")
     public DataSet<IdentifiedPeptide> listIdentifiedPeptidesByProtein(long proteinID);
     
+    @Select("select accession_number, description, amino_acid_sequence "
+            + "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'")
+    public DataSet<IndistinguishableProtein> listIndistinguishableProteinsByProteinID(long proteinID);
+    
     @Select("select distinct a.id, samples.perm_id, value "
             + "from abundances as a left join proteins as p on a.prot_id = p.id "
             + "                     left join data_sets as d on p.dase_id = d.id "

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/IndistinguishableProteinInfo.java

+/*
+ * Copyright 2010 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.shared.basic.dto;
+
+import java.io.Serializable;
+
+import com.google.gwt.user.client.rpc.IsSerializable;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
+
+/**
+ * 
+ *
+ * @author Franz-Josef Elmer
+ */
+public class IndistinguishableProteinInfo implements IsSerializable, Serializable
+{
+    private static final long serialVersionUID = ServiceVersionHolder.VERSION;
+
+    private String sequence;
+    
+    private String accessionNumber;
+    
+    private String description;
+
+    public final String getSequence()
+    {
+        return sequence;
+    }
+
+    public final void setSequence(String sequence)
+    {
+        this.sequence = sequence;
+    }
+
+    public final String getAccessionNumber()
+    {
+        return accessionNumber;
+    }
+
+    public final void setAccessionNumber(String accessionNumber)
+    {
+        this.accessionNumber = accessionNumber;
+    }
+
+    public final String getDescription()
+    {
+        return description;
+    }
+
+    public final void setDescription(String description)
+    {
+        this.description = description;
+    }
+}

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinDetails.java

@@ -48,6 +48,8 @@ public class ProteinDetails implements IsSerializable, Serializable
     private TechId proteinID;
 
     private List<Peptide> peptides;
+    
+    private List<IndistinguishableProteinInfo> indistinguishableProteinInfos;
 
     public String getSequence()
     {
@@ -138,4 +140,14 @@ public class ProteinDetails implements IsSerializable, Serializable
     {
         this.dataSetTypeCode = dataSetTypeCode;
     }
+
+    public void setIndistinguishableProteinInfos(List<IndistinguishableProteinInfo> indistinguishableProteinInfos)
+    {
+        this.indistinguishableProteinInfos = indistinguishableProteinInfos;
+    }
+
+    public List<IndistinguishableProteinInfo> getIndistinguishableProteinInfos()
+    {
+        return indistinguishableProteinInfos;
+    }
 }

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IndistinguishableProtein.java

+/*
+ * Copyright 2010 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.shared.dto;
+
+import net.lemnik.eodsql.ResultColumn;
+
+/**
+ * 
+ *
+ * @author Franz-Josef Elmer
+ */
+public class IndistinguishableProtein extends ProteinReference
+{
+    private static final long serialVersionUID = 1L;
+
+    @ResultColumn("amino_acid_sequence")
+    private String sequence;
+
+    public void setSequence(String sequence)
+    {
+        this.sequence = sequence;
+    }
+
+    public String getSequence()
+    {
+        return sequence;
+    }
+
+}