From ec1918f6fc03cd377f2afa1f250fbfc374cc32a4 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 24 Nov 2009 10:03:00 +0000
Subject: [PATCH] SE-163 Protein/Peptide Counts table implemented. Tests
missing.
SVN: 13480
---
.../web/client/IPhosphoNetXClientService.java | 8 ++
.../IPhosphoNetXClientServiceAsync.java | 11 ++
.../client/web/client/application/Dict.java | 7 +
.../PhosphoNetXDisplayTypeIDGenerator.java | 2 +
.../ProteinByExperimentBrowerToolBar.java | 17 ++-
.../ProteinByExperimentBrowserGrid.java | 60 ++++++++-
.../application/ProteinSummaryGrid.java | 111 ++++++++++++++++
.../columns/ProteinSummaryColDefKind.java | 91 +++++++++++++
...istProteinSummaryByExperimentCriteria.java | 45 +++++++
.../web/public/phosphonetx-dictionary.js | 5 +-
.../server/ListProteinSummaryProvider.java | 51 +++++++
.../web/server/PhosphoNetXClientService.java | 15 +++
.../phosphonetx/server/PhosphoNetXServer.java | 11 ++
.../server/PhosphoNetXServerLogger.java | 9 ++
.../business/BusinessObjectFactory.java | 5 +
.../server/business/ErrorModel.java | 14 +-
.../business/IBusinessObjectFactory.java | 2 +
.../server/business/IProteinSummaryTable.java | 36 +++++
.../server/business/ProteinSummaryTable.java | 124 ++++++++++++++++++
.../server/dataaccess/IProteinQueryDAO.java | 11 ++
.../shared/IPhosphoNetXServer.java | 8 ++
.../shared/basic/dto/ProteinInfo.java | 16 ---
.../shared/basic/dto/ProteinSummary.java | 69 ++++++++++
.../ProteinReferenceWithPeptideSequence.java | 14 ++
...einReferenceWithProbabilityAndPeptide.java | 41 ++++++
25 files changed, 756 insertions(+), 27 deletions(-)
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinSummaryGrid.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/ProteinSummaryColDefKind.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ListProteinSummaryByExperimentCriteria.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/ListProteinSummaryProvider.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IProteinSummaryTable.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinSummaryTable.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinSummary.java
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithProbabilityAndPeptide.java
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientService.java
index a5c9d0585ac..ca845babddb 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientService.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientService.java
@@ -27,12 +27,14 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentAndReferenceCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinSequenceCriteria;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinSummaryByExperimentCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListSampleAbundanceByProteinCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AbundanceColumnDefinition;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.DataSetProtein;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinInfo;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSequence;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSummary;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.SampleWithPropertiesAndAbundance;
/**
@@ -53,6 +55,12 @@ public interface IPhosphoNetXClientService extends IClientService
public String prepareExportProteins(TableExportCriteria<ProteinInfo> exportCriteria)
throws UserFailureException;
+ public ResultSet<ProteinSummary> listProteinSummariesByExperiment(
+ ListProteinSummaryByExperimentCriteria criteria) throws UserFailureException;
+
+ public String prepareExportProteinSummary(TableExportCriteria<ProteinSummary> exportCriteria)
+ throws UserFailureException;
+
public ProteinByExperiment getProteinByExperiment(TechId experimentID, TechId proteinReferenceID)
throws UserFailureException;
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientServiceAsync.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientServiceAsync.java
index 4c50cb062db..5d6370d3470 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientServiceAsync.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/IPhosphoNetXClientServiceAsync.java
@@ -23,17 +23,20 @@ import com.google.gwt.user.client.rpc.AsyncCallback;
import ch.systemsx.cisd.openbis.generic.client.web.client.IClientServiceAsync;
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.client.web.client.exception.UserFailureException;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentAndReferenceCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinSequenceCriteria;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinSummaryByExperimentCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListSampleAbundanceByProteinCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.AbundanceColumnDefinition;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.DataSetProtein;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinInfo;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSequence;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSummary;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.SampleWithPropertiesAndAbundance;
/**
@@ -60,6 +63,14 @@ public interface IPhosphoNetXClientServiceAsync extends IClientServiceAsync
public void prepareExportProteins(TableExportCriteria<ProteinInfo> exportCriteria,
AsyncCallback<String> callback);
+ /** @see IPhosphoNetXClientService#listProteinSummariesByExperiment(ListProteinSummaryByExperimentCriteria) */
+ public void listProteinSummariesByExperiment(ListProteinSummaryByExperimentCriteria criteria,
+ AsyncCallback<ResultSet<ProteinSummary>> callback);
+
+ /** @see IPhosphoNetXClientService#prepareExportProteinSummary(TableExportCriteria) */
+ public void prepareExportProteinSummary(TableExportCriteria<ProteinSummary> exportCriteria,
+ AsyncCallback<String> callback);
+
/** @see IPhosphoNetXClientService#getProteinByExperiment(TechId, TechId) */
public void getProteinByExperiment(TechId experimentID, TechId proteinReferenceID,
AsyncCallback<ProteinByExperiment> callback);
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 92d022f3ec1..0e2904ddc8f 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
@@ -42,6 +42,11 @@ public class Dict
public static final String FALSE_DISCOVERY_RATE = "false_discovery_rate";
public static final String DATA_SET = "data_set";
+
+ public static final String PROTEIN_BROWSER = "protein_browser";
+
+ public static final String PROTEIN_SUMMARY = "protein_summary";
+
// Protein Viewer
public static final String PROTEIN_IN_EXPERIMENT_TAB_LABEL = "protein_in_experiment_tab_label";
@@ -60,6 +65,8 @@ public class Dict
public static final String DATA_SET_PERM_ID = "data_set_perm_id";
+ public static final String PROTEIN_COUNT = "protein_count";
+
public static final String PEPTIDE_COUNT = "peptide_count";
public static final String PEPTIDES = "peptides";
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/PhosphoNetXDisplayTypeIDGenerator.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/PhosphoNetXDisplayTypeIDGenerator.java
index d5c2e90be58..72097342ead 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/PhosphoNetXDisplayTypeIDGenerator.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/PhosphoNetXDisplayTypeIDGenerator.java
@@ -26,6 +26,8 @@ public enum PhosphoNetXDisplayTypeIDGenerator implements IDisplayTypeIDGenerator
PROTEIN_BY_EXPERIMENT_BROWSER_GRID("protein-by-experiment-browser-grid"),
PROTEIN_SEQUENCE_BROWSER_GRID("protein-sequence-browser-grid"),
+
+ PROTEIN_SUMMARY_BROWSER_GRID("protein-summary-browser-grid"),
DATA_SET_PROTEIN_BROWSER_GRID("data-set-protein-browser-grid"), ;
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowerToolBar.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowerToolBar.java
index 3569f638e96..73dbdb7f616 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowerToolBar.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowerToolBar.java
@@ -24,6 +24,7 @@ import com.extjs.gxt.ui.client.event.Listener;
import com.extjs.gxt.ui.client.event.SelectionChangedEvent;
import com.extjs.gxt.ui.client.event.SelectionChangedListener;
import com.extjs.gxt.ui.client.store.ListStore;
+import com.extjs.gxt.ui.client.widget.form.CheckBox;
import com.extjs.gxt.ui.client.widget.form.ComboBox;
import com.extjs.gxt.ui.client.widget.toolbar.LabelToolItem;
import com.extjs.gxt.ui.client.widget.toolbar.ToolBar;
@@ -34,7 +35,6 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.GenericCon
import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.model.NonHierarchicalBaseModelData;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.model.VocabularyTermModel;
-import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.CheckBoxField;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.ExperimentChooserField;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.IChosenEntityListener;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.field.VocabularyTermSelectionWidget;
@@ -159,12 +159,14 @@ class ProteinByExperimentBrowerToolBar extends ToolBar
private final VocabularyTermSelectionWidget treatmentTypeComboBox;
- private final CheckBoxField aggregateOriginalCheckBox;
+ private final CheckBox aggregateOriginalCheckBox;
private ProteinByExperimentBrowserGrid browserGrid;
private Experiment experiment;
+ private ProteinSummaryGrid summaryGrid;
+
ProteinByExperimentBrowerToolBar(IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
{
this.viewContext = viewContext;
@@ -232,7 +234,7 @@ class ProteinByExperimentBrowerToolBar extends ToolBar
add(treatmentTypeComboBox);
add(new LabelToolItem(viewContext.getMessage(Dict.AGGREGATE_ORIGINAL_LABEL)
+ GenericConstants.LABEL_SEPARATOR));
- aggregateOriginalCheckBox = new CheckBoxField("aggregateOriginal", false);
+ aggregateOriginalCheckBox = new CheckBox();
aggregateOriginalCheckBox.addListener(Events.Change, new Listener<BaseEvent>()
{
@@ -297,16 +299,23 @@ class ProteinByExperimentBrowerToolBar extends ToolBar
{
this.browserGrid = browserGrid;
}
+
+ void setSummaryGrid(ProteinSummaryGrid summaryGrid)
+ {
+ this.summaryGrid = summaryGrid;
+ }
void update()
{
if (experiment != null)
{
+ TechId experimentID = TechId.create(experiment);
+ summaryGrid.setLoadMaskImmediately(true);
+ summaryGrid.update(experimentID);
browserGrid.setLoadMaskImmediately(true);
double falseDiscoveryRate = getSelection(fdrComboBox, 0.0);
AggregateFunction aggregateFunction =
getSelection(aggregateFunctionComboBox, DEFAULT_AGGREGATE_FUNCTION);
- TechId experimentID = TechId.create(experiment);
VocabularyTermModel value = treatmentTypeComboBox.getValue();
String treatmentTypeCode = value == null ? null : value.getTerm().getCode();
AsyncCallback<List<AbundanceColumnDefinition>> callback =
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowserGrid.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowserGrid.java
index aaeb5d72c1d..6c159e592c5 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowserGrid.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinByExperimentBrowserGrid.java
@@ -22,6 +22,14 @@ import java.util.List;
import java.util.Map;
import java.util.Set;
+import com.extjs.gxt.ui.client.widget.Component;
+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.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.GenericConstants;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
@@ -34,6 +42,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.Ab
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.ColumnDefsAndConfigs;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.ICellListener;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.IDisposableComponent;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.util.IMessageProvider;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.ResultSet;
import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteria;
@@ -71,15 +80,60 @@ class ProteinByExperimentBrowserGrid extends AbstractSimpleBrowserGrid<ProteinIn
private ListProteinByExperimentCriteria criteria;
private List<AbundanceColumnDefinition> abundanceColumnDefinitions;
-
+
static IDisposableComponent create(
final IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
{
- final ProteinByExperimentBrowserGrid browserGrid =
+ final IDisposableComponent summaryGrid = ProteinSummaryGrid.create(viewContext);
+ ProteinByExperimentBrowserGrid browserGrid =
new ProteinByExperimentBrowserGrid(viewContext);
- return browserGrid.asDisposableWithToolbar(browserGrid.toolbar);
+ final IDisposableComponent disposableBrowerGrid = browserGrid.asDisposableWithoutToolbar();
+ ProteinByExperimentBrowerToolBar toolBar = browserGrid.toolbar;
+ toolBar.setSummaryGrid((ProteinSummaryGrid) summaryGrid.getComponent());
+ final LayoutContainer container = new LayoutContainer();
+ container.setLayout(new RowLayout());
+ container.add(toolBar);
+ TabPanel tabPanel = new TabPanel();
+ tabPanel.add(createTab(disposableBrowerGrid, viewContext, Dict.PROTEIN_BROWSER));
+ tabPanel.add(createTab(summaryGrid, viewContext, Dict.PROTEIN_SUMMARY));
+ container.add(tabPanel, new RowData(1, 1));
+ return new IDisposableComponent()
+ {
+ public void update(Set<DatabaseModificationKind> observedModifications)
+ {
+ disposableBrowerGrid.update(observedModifications);
+ summaryGrid.update(observedModifications);
+ }
+
+ public DatabaseModificationKind[] getRelevantModifications()
+ {
+ return disposableBrowerGrid.getRelevantModifications();
+ }
+
+ public Component getComponent()
+ {
+ return container;
+ }
+
+ public void dispose()
+ {
+ disposableBrowerGrid.dispose();
+ summaryGrid.dispose();
+ }
+ };
}
+ private static TabItem createTab(IDisposableComponent disposableComponent,
+ IMessageProvider messageProvider, String titleKey)
+ {
+ TabItem tabItem = new TabItem(messageProvider.getMessage(titleKey));
+ tabItem.setLayout(new FitLayout());
+ Component component = disposableComponent.getComponent();
+ component.setHeight("100%");
+ tabItem.add(component);
+ return tabItem;
+ }
+
private ProteinByExperimentBrowserGrid(
final IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
{
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinSummaryGrid.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinSummaryGrid.java
new file mode 100644
index 00000000000..80e6fe30c69
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinSummaryGrid.java
@@ -0,0 +1,111 @@
+/*
+ * Copyright 2009 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.List;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.GenericConstants;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.IViewContext;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.framework.IColumnDefinitionKind;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.AbstractSimpleBrowserGrid;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.grid.IDisposableComponent;
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
+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.IColumnDefinition;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseModificationKind;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientServiceAsync;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.columns.ProteinSummaryColDefKind;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinSummaryByExperimentCriteria;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSummary;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+class ProteinSummaryGrid extends AbstractSimpleBrowserGrid<ProteinSummary>
+{
+ private static final String PREFIX =
+ GenericConstants.ID_PREFIX + "protein-summary";
+
+ // browser consists of the grid and additional toolbars (paging, filtering)
+ public static final String BROWSER_ID = PREFIX + "_main";
+
+ public static final String GRID_ID = PREFIX + "_grid";
+
+ static IDisposableComponent create(IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
+ {
+ return new ProteinSummaryGrid(viewContext).asDisposableWithoutToolbar();
+ }
+
+ private final IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext;
+
+ private ListProteinSummaryByExperimentCriteria criteria;
+
+ ProteinSummaryGrid(IViewContext<IPhosphoNetXClientServiceAsync> viewContext)
+ {
+ super(viewContext.getCommonViewContext(), BROWSER_ID, GRID_ID, false,
+ PhosphoNetXDisplayTypeIDGenerator.PROTEIN_SUMMARY_BROWSER_GRID);
+ specificViewContext = viewContext;
+ }
+
+ void update(TechId experimentID)
+ {
+ criteria = new ListProteinSummaryByExperimentCriteria();
+ criteria.setExperimentID(experimentID);
+ refresh(true);
+ }
+
+ @Override
+ protected IColumnDefinitionKind<ProteinSummary>[] getStaticColumnsDefinition()
+ {
+ return ProteinSummaryColDefKind.values();
+ }
+
+ @Override
+ protected List<IColumnDefinition<ProteinSummary>> getInitialFilters()
+ {
+ return asColumnFilters(new ProteinSummaryColDefKind[0]);
+ }
+
+ @Override
+ protected void listEntities(DefaultResultSetConfig<String, ProteinSummary> resultSetConfig,
+ AbstractAsyncCallback<ResultSet<ProteinSummary>> callback)
+ {
+ if (criteria != null)
+ {
+ criteria.copyPagingConfig(resultSetConfig);
+ specificViewContext.getService().listProteinSummariesByExperiment(criteria, callback);
+ }
+ }
+
+ @Override
+ protected void prepareExportEntities(TableExportCriteria<ProteinSummary> exportCriteria,
+ AbstractAsyncCallback<String> callback)
+ {
+ specificViewContext.getService().prepareExportProteinSummary(exportCriteria, callback);
+ }
+
+ public DatabaseModificationKind[] getRelevantModifications()
+ {
+ return new DatabaseModificationKind[0];
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/ProteinSummaryColDefKind.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/ProteinSummaryColDefKind.java
new file mode 100644
index 00000000000..cdbb6283ee7
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/ProteinSummaryColDefKind.java
@@ -0,0 +1,91 @@
+/*
+ * Copyright 2009 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.columns;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.framework.AbstractColumnDefinitionKind;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.framework.IColumnDefinitionKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.GridRowModel;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.application.Dict;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSummary;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public enum ProteinSummaryColDefKind implements IColumnDefinitionKind<ProteinSummary>
+{
+ FDR(new AbstractColumnDefinitionKind<ProteinSummary>(Dict.FDR)
+ {
+ @Override
+ public String tryGetValue(ProteinSummary entity)
+ {
+ return Double.toString(entity.getFDR());
+ }
+
+ @Override
+ public Comparable<?> getComparableValue(GridRowModel<ProteinSummary> entity)
+ {
+ return entity.getOriginalObject().getFDR();
+ }
+ }), PROTEIN_COUNT(new AbstractColumnDefinitionKind<ProteinSummary>(Dict.PROTEIN_COUNT)
+ {
+ @Override
+ public String tryGetValue(ProteinSummary entity)
+ {
+ return Integer.toString(entity.getProteinCount());
+ }
+
+ @Override
+ public Comparable<?> getComparableValue(GridRowModel<ProteinSummary> entity)
+ {
+ return entity.getOriginalObject().getProteinCount();
+ }
+ }), PEPTIDE_COUNT(new AbstractColumnDefinitionKind<ProteinSummary>(Dict.PEPTIDE_COUNT)
+ {
+ @Override
+ public String tryGetValue(ProteinSummary entity)
+ {
+ return Integer.toString(entity.getPeptideCount());
+ }
+
+ @Override
+ public Comparable<?> getComparableValue(GridRowModel<ProteinSummary> entity)
+ {
+ return entity.getOriginalObject().getPeptideCount();
+ }
+ }), ;
+
+ private final AbstractColumnDefinitionKind<ProteinSummary> columnDefinitionKind;
+
+ private ProteinSummaryColDefKind(AbstractColumnDefinitionKind<ProteinSummary> columnDefinitionKind)
+ {
+ this.columnDefinitionKind = columnDefinitionKind;
+ }
+
+ public String id()
+ {
+ return name();
+ }
+
+ public AbstractColumnDefinitionKind<ProteinSummary> getDescriptor()
+ {
+ return columnDefinitionKind;
+ }
+
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ListProteinSummaryByExperimentCriteria.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ListProteinSummaryByExperimentCriteria.java
new file mode 100644
index 00000000000..935a217acf3
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ListProteinSummaryByExperimentCriteria.java
@@ -0,0 +1,45 @@
+/*
+ * Copyright 2009 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;
+
+import com.google.gwt.user.client.rpc.IsSerializable;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.dto.DefaultResultSetConfig;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSummary;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ListProteinSummaryByExperimentCriteria extends DefaultResultSetConfig<String, ProteinSummary>
+ implements IsSerializable
+{
+ private TechId experimentID;
+
+ public final TechId getExperimentID()
+ {
+ return experimentID;
+ }
+
+ public final void setExperimentID(TechId experimentID)
+ {
+ this.experimentID = experimentID;
+ }
+
+}
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 6e6db44b7f2..6a2876facb3 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
@@ -12,18 +12,21 @@ var phosphonetx = {
// Protein grid
accession_number: "Accession Number",
protein_description: "Protein",
- coverage: "Coverage",
+ coverage: "Protein Coverage (in %)",
false_discovery_rate: "FDR",
// Protein in experiment viewer
protein_in_experiment_tab_label: "{0} in {1}",
experiment_label: "Experiment",
sequence_short_name: "",
+ protein_browser: "Proteins",
+ protein_summary: "Protein/Peptide Counts",
database_name_and_version: "Database",
sequence: "Amino Acid Sequence",
sequences: "Amino Acid Sequences",
data_set_proteins: "Data Sets",
data_set_perm_id: "Data Set",
+ protein_count: "Proteins",
peptide_count: "Peptides",
peptides: "Peptides ({0})",
sequence_name: "Sequence",
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/ListProteinSummaryProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/ListProteinSummaryProvider.java
new file mode 100644
index 00000000000..35a3f45637b
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/ListProteinSummaryProvider.java
@@ -0,0 +1,51 @@
+/*
+ * Copyright 2009 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;
+
+import java.util.List;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.client.web.server.resultset.IOriginalDataProvider;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IPhosphoNetXServer;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSummary;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+class ListProteinSummaryProvider implements IOriginalDataProvider<ProteinSummary>
+{
+ private final IPhosphoNetXServer server;
+ private final String sessionToken;
+ private final TechId experimentID;
+
+ ListProteinSummaryProvider(IPhosphoNetXServer server, String sessionToken,
+ TechId experimentID)
+ {
+ this.server = server;
+ this.sessionToken = sessionToken;
+ this.experimentID = experimentID;
+ }
+
+ public List<ProteinSummary> getOriginalData() throws UserFailureException
+ {
+ return server.listProteinSummariesByExperiment(sessionToken, experimentID);
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java
index 96a748d55f2..c09d7148368 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/PhosphoNetXClientService.java
@@ -35,6 +35,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNet
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentAndReferenceCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinByExperimentCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinSequenceCriteria;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinSummaryByExperimentCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListSampleAbundanceByProteinCriteria;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IPhosphoNetXServer;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.ResourceNames;
@@ -44,6 +45,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.DataSetProte
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinInfo;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSequence;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSummary;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.SampleWithPropertiesAndAbundance;
/**
@@ -105,6 +107,19 @@ public class PhosphoNetXClientService extends AbstractClientService implements
return prepareExportEntities(exportCriteria);
}
+ public ResultSet<ProteinSummary> listProteinSummariesByExperiment(ListProteinSummaryByExperimentCriteria criteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ final String sessionToken = getSessionToken();
+ return listEntities(criteria, new ListProteinSummaryProvider(server, sessionToken, criteria.getExperimentID()));
+ }
+
+ public String prepareExportProteinSummary(TableExportCriteria<ProteinSummary> exportCriteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ return prepareExportEntities(exportCriteria);
+ }
+
public ProteinByExperiment getProteinByExperiment(TechId experimentID, TechId proteinReferenceID)
throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
{
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java
index cedf3d99cc6..fca57b6d970 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServer.java
@@ -45,6 +45,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IDataSetProte
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IProteinDetailsBO;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IProteinSequenceTable;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IProteinInfoTable;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.IProteinSummaryTable;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.ISampleTable;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IPhosphoNetXDAOFactory;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IProteinQueryDAO;
@@ -56,6 +57,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.DataSetProte
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinInfo;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSequence;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSummary;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.SampleWithPropertiesAndAbundance;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReference;
@@ -138,6 +140,15 @@ public class PhosphoNetXServer extends AbstractServer<IPhosphoNetXServer> implem
return table.getProteinInfos();
}
+ public List<ProteinSummary> listProteinSummariesByExperiment(String sessionToken,
+ TechId experimentId) throws UserFailureException
+ {
+ final Session session = getSession(sessionToken);
+ IProteinSummaryTable summaryTable = specificBOFactory.createProteinSummaryTable(session);
+ summaryTable.load(experimentId);
+ return summaryTable.getProteinSummaries();
+ }
+
public ProteinByExperiment getProteinByExperiment(String sessionToken, TechId experimentID,
TechId proteinReferenceID) throws UserFailureException
{
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServerLogger.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServerLogger.java
index 4222fd2b29f..2f3197c65ea 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServerLogger.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/PhosphoNetXServerLogger.java
@@ -31,6 +31,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.DataSetProte
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinInfo;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSequence;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSummary;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.SampleWithPropertiesAndAbundance;
/**
@@ -70,6 +71,14 @@ public class PhosphoNetXServerLogger extends AbstractServerLogger implements IPh
.getLabel(), treatmentTypeCode, aggregateOnOriginal);
return null;
}
+
+ public List<ProteinSummary> listProteinSummariesByExperiment(String sessionToken,
+ TechId experimentId) throws UserFailureException
+ {
+ logAccess(sessionToken, "list_protein_summaries_by_experiment", "EXPERIMENT_ID(%s)",
+ experimentId);
+ return null;
+ }
public ProteinByExperiment getProteinByExperiment(String sessionToken, TechId experimentId,
TechId proteinReferenceID) throws UserFailureException
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java
index 602794065a4..00460f7cc89 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java
@@ -47,6 +47,11 @@ public class BusinessObjectFactory implements IBusinessObjectFactory
return new ProteinInfoTable(daoFactory, specificDAOFactory, session);
}
+ public IProteinSummaryTable createProteinSummaryTable(Session session)
+ {
+ return new ProteinSummaryTable(daoFactory, specificDAOFactory, session);
+ }
+
public IProteinSequenceTable createProteinSequenceTable(Session session)
{
return new ProteinSequenceTable(daoFactory, specificDAOFactory, session);
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ErrorModel.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ErrorModel.java
index 7b8fcb78faa..91a88da70a9 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ErrorModel.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ErrorModel.java
@@ -107,11 +107,19 @@ class ErrorModel
ProbabilityToFDRCalculator calculator = getCalculator(protein.getDataSetID());
return calculator.calculateFDR(protein.getProbability()) <= falseDiscoveryRate;
}
-
+
void setFalseDiscoveryRateFor(IdentifiedProtein protein)
{
- ProbabilityToFDRCalculator calculator = getCalculator(protein.getDataSetID());
- protein.setFalseDiscoveryRate(calculator.calculateFDR(protein.getProbability()));
+ long dataSetID = protein.getDataSetID();
+ double probability = protein.getProbability();
+ protein.setFalseDiscoveryRate(calculateFalsDiscoveryRate(dataSetID, probability));
+ }
+
+ double calculateFalsDiscoveryRate(long dataSetID, double probability)
+ {
+ ProbabilityToFDRCalculator calculator = getCalculator(dataSetID);
+ double fdr = calculator.calculateFDR(probability);
+ return fdr;
}
private ProbabilityToFDRCalculator getCalculator(long dataSetID)
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IBusinessObjectFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IBusinessObjectFactory.java
index f36a260a889..2ab6190df08 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IBusinessObjectFactory.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IBusinessObjectFactory.java
@@ -29,6 +29,8 @@ public interface IBusinessObjectFactory
public IProteinInfoTable createProteinInfoTable(Session session);
+ public IProteinSummaryTable createProteinSummaryTable(Session session);
+
public IProteinSequenceTable createProteinSequenceTable(Session session);
public IDataSetProteinTable createDataSetProteinTable(Session session);
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IProteinSummaryTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IProteinSummaryTable.java
new file mode 100644
index 00000000000..a964c7fa627
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/IProteinSummaryTable.java
@@ -0,0 +1,36 @@
+/*
+ * Copyright 2009 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.server.business;
+
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSummary;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IProteinSummaryTable
+{
+
+ public void load(TechId experimentID);
+
+ public List<ProteinSummary> getProteinSummaries();
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinSummaryTable.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinSummaryTable.java
new file mode 100644
index 00000000000..c891781b433
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinSummaryTable.java
@@ -0,0 +1,124 @@
+/*
+ * Copyright 2009 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.server.business;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import net.lemnik.eodsql.DataSet;
+
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExperimentDAO;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+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.ProteinSummary;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProbabilityAndPeptide;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+class ProteinSummaryTable extends AbstractBusinessObject implements IProteinSummaryTable
+{
+ private static final double[] FDR_LEVELS = new double[] {0, 0.01, 0.025, 0.05, 0.1};
+
+ private static final class Counter
+ {
+ private final double fdrLevel;
+ private final Set<Long> proteins;
+ private final Set<String> peptides;
+
+ Counter(double fdrLevel)
+ {
+ this.fdrLevel = fdrLevel;
+ proteins = new HashSet<Long>();
+ peptides = new HashSet<String>();
+ }
+
+ public ProteinSummary getProteinSummary()
+ {
+ ProteinSummary proteinSummary = new ProteinSummary();
+ proteinSummary.setFDR(fdrLevel);
+ proteinSummary.setProteinCount(proteins.size());
+ proteinSummary.setPeptideCount(peptides.size());
+ return proteinSummary;
+ }
+
+ public void handle(double fdr, ProteinReferenceWithProbabilityAndPeptide protein)
+ {
+ if (fdr <= fdrLevel)
+ {
+ proteins.add(protein.getId());
+ peptides.add(protein.getPeptideSequence());
+ }
+ }
+ }
+
+ private List<ProteinSummary> summaries;
+
+ ProteinSummaryTable(IDAOFactory daoFactory, IPhosphoNetXDAOFactory specificDAOFactory,
+ Session session)
+ {
+ super(daoFactory, specificDAOFactory, session);
+ }
+
+ public List<ProteinSummary> getProteinSummaries()
+ {
+ return summaries;
+ }
+
+ public void load(TechId experimentID)
+ {
+ IExperimentDAO experimentDAO = getDaoFactory().getExperimentDAO();
+ String permID = experimentDAO.getByTechId(experimentID).getPermId();
+ IProteinQueryDAO dao = getSpecificDAOFactory().getProteinQueryDAO();
+ ErrorModel errorModel = new ErrorModel(getSpecificDAOFactory());
+ DataSet<ProteinReferenceWithProbabilityAndPeptide> resultSet = dao.listProteinsWithProbabilityAndPeptidesByExperiment(permID);
+ List<Counter> counters = new ArrayList<Counter>(FDR_LEVELS.length);
+ for (double fdrLevel : FDR_LEVELS)
+ {
+ counters.add(new Counter(fdrLevel));
+ }
+ try
+ {
+ for (ProteinReferenceWithProbabilityAndPeptide protein : resultSet)
+ {
+ long dataSetID = protein.getDataSetID();
+ double probability = protein.getProbability();
+ double fdr = errorModel.calculateFalsDiscoveryRate(dataSetID, probability);
+ for (Counter counter : counters)
+ {
+ counter.handle(fdr, protein);
+ }
+ }
+ summaries = new ArrayList<ProteinSummary>(counters.size());
+ for (Counter counter : counters)
+ {
+ summaries.add(counter.getProteinSummary());
+ }
+ } finally
+ {
+ resultSet.close();
+ }
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java
index 9ea1d906da7..1d9f8daeeeb 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/IProteinQueryDAO.java
@@ -26,6 +26,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProbabilityFDRMapp
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReference;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithPeptideSequence;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProbability;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProbabilityAndPeptide;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.SampleAbundance;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.Sequence;
@@ -50,6 +51,16 @@ public interface IProteinQueryDAO extends BaseQuery
+ "left join samples on a.samp_id = samples.id "
+ "where e.perm_id = ?{1} order by pr.accession_number, samples.perm_id")
public DataSet<ProteinReferenceWithProbability> listProteinsByExperiment(String experimentPermID);
+
+ @Select(sql = "select p.dase_id as data_set_id, p.probability, s.prre_id as id, pe.sequence "
+ + "from identified_proteins as ip left join sequences as s on ip.sequ_id = s.id "
+ + "left join proteins as p on ip.prot_id = p.id "
+ + "left join peptides as pe on pe.prot_id = p.id "
+ + "left join data_sets as d on p.dase_id = d.id "
+ + "left join experiments as e on d.expe_id = e.id "
+ + "where e.perm_id = ?{1} ")
+ public DataSet<ProteinReferenceWithProbabilityAndPeptide> listProteinsWithProbabilityAndPeptidesByExperiment(
+ String experimentPermID);
@Select("select distinct s.prre_id, s.amino_acid_sequence, pe.sequence "
+ "from identified_proteins as ip "
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IPhosphoNetXServer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IPhosphoNetXServer.java
index ce73f84b4ce..8935dcee6f7 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IPhosphoNetXServer.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/IPhosphoNetXServer.java
@@ -34,6 +34,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.DataSetProte
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinInfo;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSequence;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSummary;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.SampleWithPropertiesAndAbundance;
/**
@@ -61,6 +62,13 @@ public interface IPhosphoNetXServer extends IServer
TechId experimentId, double falseDiscoveryRate, AggregateFunction function,
String treatmentTypeCode, boolean aggregateOnOriginal) throws UserFailureException;
+
+ @Transactional
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<ProteinSummary> listProteinSummariesByExperiment(String sessionToken,
+ @AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class) TechId experimentId)
+ throws UserFailureException;
+
@Transactional
@RolesAllowed(RoleSet.OBSERVER)
public ProteinByExperiment getProteinByExperiment(String sessionToken,
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinInfo.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinInfo.java
index acfe23f355e..f53b613680e 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinInfo.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinInfo.java
@@ -43,22 +43,6 @@ public class ProteinInfo implements Serializable, IsSerializable
private String description;
- /*
-* New column: Protein Coverage. It contains the ratio (in %)
-
-sum of the lengths of all peptide sequences / length of the protein sequence
-
-where overlapping peptide sequences count only once.
-* New table:
-
-|FDR|0|1|2.5|5|10|
-|Number of Proteins|..|..|..|..|..|
-|Number of Peptides|..|..|..|..|..|
-
-These values are the number of proteins/peptides per experiment for FDR value less than or equal the specified one.
-
-This table could appear in the same tab as 'Protein of an Experiment' table.
- */
private double coverage;
private Map<Long, Double> abundances;
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinSummary.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinSummary.java
new file mode 100644
index 00000000000..a6bba8abacc
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinSummary.java
@@ -0,0 +1,69 @@
+/*
+ * Copyright 2009 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 ProteinSummary implements Serializable, IsSerializable
+{
+ private static final long serialVersionUID = ServiceVersionHolder.VERSION;
+ private double fdr;
+
+ private int proteinCount;
+
+ private int peptideCount;
+
+ public double getFDR()
+ {
+ return fdr;
+ }
+
+ public void setFDR(double fdr)
+ {
+ this.fdr = fdr;
+ }
+
+ public int getProteinCount()
+ {
+ return proteinCount;
+ }
+
+ public void setProteinCount(int proteinCount)
+ {
+ this.proteinCount = proteinCount;
+ }
+
+ public int getPeptideCount()
+ {
+ return peptideCount;
+ }
+
+ public void setPeptideCount(int peptideCount)
+ {
+ this.peptideCount = peptideCount;
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithPeptideSequence.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithPeptideSequence.java
index c1a29f78629..e61ffa75e27 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithPeptideSequence.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithPeptideSequence.java
@@ -28,6 +28,9 @@ public class ProteinReferenceWithPeptideSequence
@ResultColumn("prre_id")
private long id;
+ @ResultColumn("dase_id")
+ private long dataSetID;
+
@ResultColumn("amino_acid_sequence")
private String proteinSequence;
@@ -44,6 +47,16 @@ public class ProteinReferenceWithPeptideSequence
this.id = id;
}
+ public long getDataSetID()
+ {
+ return dataSetID;
+ }
+
+ public void setDataSetID(long dataSetID)
+ {
+ this.dataSetID = dataSetID;
+ }
+
public String getProteinSequence()
{
return proteinSequence;
@@ -63,5 +76,6 @@ public class ProteinReferenceWithPeptideSequence
{
this.peptideSequence = peptideSequence;
}
+
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithProbabilityAndPeptide.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithProbabilityAndPeptide.java
new file mode 100644
index 00000000000..b0ec609f8d7
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithProbabilityAndPeptide.java
@@ -0,0 +1,41 @@
+/*
+ * Copyright 2009 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 ProteinReferenceWithProbabilityAndPeptide extends ProteinReferenceWithProbability
+{
+ @ResultColumn("sequence")
+ private String peptideSequence;
+
+ public String getPeptideSequence()
+ {
+ return peptideSequence;
+ }
+
+ public void setPeptideSequence(String peptideSequence)
+ {
+ this.peptideSequence = peptideSequence;
+ }
+
+}
--
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