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 47340357f3a1f3c350bb5a90e869687565eda2e0..c83f36f775a42a4f16b91341b31d4cb1f8d9174c 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
@@ -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";
+
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ExperimentViewer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ExperimentViewer.java
index 4887d4eac8da65205242412cb3f1a5ade7512b8a..f109ad81097b84692b8fc508f7e4bc4199e02dee 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ExperimentViewer.java
+++ b/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);
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 5f23d58d878368ccd59e012148e0479df81b7262..ce797587fc45d81c521ddce2c6d8ded3ed7815a4 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
@@ -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()
{
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 493f87cd26dc7f4e12f157667ad8d5d97d585387..476656598a243b089d820b8bf5779d71ed4927c2 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
@@ -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());
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java
index 991b92750f6c9a0ea4ad0a90dda1d7b17b3243d1..a3ad1d695744cd9786cb857fee5811d03a1b4fd7 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java
@@ -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));
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/RowLayoutManager.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/RowLayoutManager.java
new file mode 100644
index 0000000000000000000000000000000000000000..13f9ecc831068887ab94d357ec0b9e83eb4a5d7e
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/RowLayoutManager.java
@@ -0,0 +1,164 @@
+/*
+ * 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
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 6c538ee56e1a005b2fc889cc99b754d629e93da0..53eceb32476282ecc6e284a6f717f99070e78b2f 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
@@ -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",
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinDetailsBO.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinDetailsBO.java
index 53f16b3c145087bd2fe4fd61ae98e34e897c4f19..de7baf49b7269e728bbfebe10ec832764b9dbb53 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinDetailsBO.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/ProteinDetailsBO.java
@@ -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)
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 4b87704e51cea73a5d1a43b12c335531cc8de11c..2888433b7adb6ca0addab2fc34fe4c5db3bc2b63 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
@@ -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 "
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/IndistinguishableProteinInfo.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/IndistinguishableProteinInfo.java
new file mode 100644
index 0000000000000000000000000000000000000000..7098559d0b258ed06065e47ce8b219f388234e66
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/IndistinguishableProteinInfo.java
@@ -0,0 +1,69 @@
+/*
+ * 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;
+ }
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinDetails.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinDetails.java
index 8495c70c047b9b7195a8be099e7d7db0da8337b2..aa306a7c62763caf53595b4084ca2b6a9f2a5f16 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinDetails.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinDetails.java
@@ -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;
+ }
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IndistinguishableProtein.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IndistinguishableProtein.java
new file mode 100644
index 0000000000000000000000000000000000000000..05aaac1a08afc8f2978303e9bddd7aeb66ecb381
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IndistinguishableProtein.java
@@ -0,0 +1,43 @@
+/*
+ * 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;
+ }
+
+}