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 c317830aec8dd40741f0663c54df0480b3879897..027f27bf771c0704da4639010a604108402ba703 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
@@ -22,8 +22,10 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.dto.TableExportCriteri
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.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.ProteinInfo;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSequence;
/**
*
@@ -40,5 +42,11 @@ public interface IPhosphoNetXClientService extends IClientService
public ProteinByExperiment getProteinByExperiment(TechId experimentID, TechId proteinReferenceID)
throws UserFailureException;
+
+ public ResultSet<ProteinSequence> listSequencesByProteinReference(ListProteinSequenceCriteria criteria)
+ throws UserFailureException;
+ public String prepareExportProteinSequences(TableExportCriteria<ProteinSequence> exportCriteria)
+ 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 18a23454fcb996f565821eaed92e89e2ef678961..a876608648fa593f9d5bc313e6c72ce44f0143fa 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
@@ -23,8 +23,10 @@ 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.TechId;
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.ProteinInfo;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSequence;
/**
*
@@ -36,7 +38,6 @@ public interface IPhosphoNetXClientServiceAsync extends IClientServiceAsync
/** @see IPhosphoNetXClientService#listProteinsByExperiment(ListProteinByExperimentCriteria) */
public void listProteinsByExperiment(ListProteinByExperimentCriteria criteria,
AsyncCallback<ResultSet<ProteinInfo>> callback);
-
/** @see IPhosphoNetXClientService#prepareExportProteins(TableExportCriteria) */
public void prepareExportProteins(TableExportCriteria<ProteinInfo> exportCriteria,
@@ -45,4 +46,13 @@ public interface IPhosphoNetXClientServiceAsync extends IClientServiceAsync
/** @see IPhosphoNetXClientService#getProteinByExperiment(TechId, TechId) */
public void getProteinByExperiment(TechId experimentID, TechId proteinReferenceID,
AsyncCallback<ProteinByExperiment> callback);
+
+ /** @see IPhosphoNetXClientService#listSequencesByProteinReference(ListProteinSequenceCriteria) */
+ public void listSequencesByProteinReference(ListProteinSequenceCriteria criteria,
+ AsyncCallback<ResultSet<ProteinSequence>> callback);
+
+ /** @see IPhosphoNetXClientService#prepareExportProteinSequences(TableExportCriteria) */
+ public void prepareExportProteinSequences(TableExportCriteria<ProteinSequence> exportCriteria,
+ AsyncCallback<String> callback);
+
}
\ No newline at end of file
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 f152a85458538b401b64d91e3f03394d9d0d18d9..d6cfad93f964f7c2567dbb880445993b28109611 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
@@ -35,6 +35,11 @@ public class Dict
// Protein Viewer
public static final String PROTEIN_IN_EXPERIMENT_TAB_LABEL = "protein_in_experiment_tab_label";
public static final String EXPERIMENT_LABEL = "experiment_label";
+ public static final String SEQUENCE_SHORT_NAME = "sequence_short_name";
+ public static final String DATABASE_NAME_AND_VERSION = "database_name_and_version";
+ public static final String SEQUENCE = "sequence";
+ public static final String SEQUENCES = "sequences";
+
}
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 435fa39e2a9c0e0f9f79b523a249af85dfbf3432..3c94d22a0769f4f94ea1ef3bf78cfdf50f88d08c 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
@@ -28,6 +28,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityType;
public enum PhosphoNetXDisplayTypeIDGenerator implements IDisplayTypeIDGenerator
{
PROTEIN_BY_EXPERIMENT_BROWSER_GRID("protein-by-experiment-browser-grid"),
+ PROTEIN_SEQUENCE_BROWSER_GRID("protein-sequence-browser-grid"),
;
private final String genericNameOrPrefix;
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinSequenceGrid.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinSequenceGrid.java
new file mode 100644
index 0000000000000000000000000000000000000000..58ccccf6b1afc40215f441b95d0e64c2d90cc61d
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinSequenceGrid.java
@@ -0,0 +1,103 @@
+/*
+ * 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.IColumnDefinition;
+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.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.ProteinSequenceColDefKind;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.dto.ListProteinSequenceCriteria;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSequence;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ProteinSequenceGrid extends AbstractSimpleBrowserGrid<ProteinSequence>
+{
+ private static final String PREFIX = GenericConstants.ID_PREFIX + "protein-sequence-browser";
+
+ public static final String BROWSER_ID = PREFIX + "_main";
+
+ public static final String GRID_ID = PREFIX + "_grid";
+
+ static IDisposableComponent create(IViewContext<IPhosphoNetXClientServiceAsync> viewContext, TechId proteinReferenceID)
+ {
+ return new ProteinSequenceGrid(viewContext, proteinReferenceID).asDisposableWithoutToolbar();
+ }
+
+ private final IViewContext<IPhosphoNetXClientServiceAsync> specificViewContext;
+
+ private ListProteinSequenceCriteria criteria;
+
+ private ProteinSequenceGrid(IViewContext<IPhosphoNetXClientServiceAsync> viewContext,
+ TechId proteinReferenceID)
+ {
+ super(viewContext.getCommonViewContext(), BROWSER_ID + proteinReferenceID,
+ GRID_ID + proteinReferenceID, true);
+ specificViewContext = viewContext;
+ criteria = new ListProteinSequenceCriteria();
+ criteria.setProteinReferenceID(proteinReferenceID);
+ setDisplayTypeIDGenerator(PhosphoNetXDisplayTypeIDGenerator.PROTEIN_SEQUENCE_BROWSER_GRID);
+ }
+
+ @Override
+ protected IColumnDefinitionKind<ProteinSequence>[] getStaticColumnsDefinition()
+ {
+ return ProteinSequenceColDefKind.values();
+ }
+
+ @Override
+ protected List<IColumnDefinition<ProteinSequence>> getInitialFilters()
+ {
+ return asColumnFilters(new ProteinSequenceColDefKind[] {});
+ }
+
+ @Override
+ protected void listEntities(DefaultResultSetConfig<String, ProteinSequence> resultSetConfig,
+ AbstractAsyncCallback<ResultSet<ProteinSequence>> callback)
+ {
+ criteria.copyPagingConfig(resultSetConfig);
+ specificViewContext.getService().listSequencesByProteinReference(criteria, callback);
+ }
+
+ @Override
+ protected void prepareExportEntities(TableExportCriteria<ProteinSequence> exportCriteria,
+ AbstractAsyncCallback<String> callback)
+ {
+ specificViewContext.getService().prepareExportProteinSequences(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/ProteinViewer.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/ProteinViewer.java
index 3db1af446b420c02221e947211563e2cbe89e8f9..1d5b16eb29751a33bfbb51154c3c97500c99b643 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
@@ -27,6 +27,7 @@ import com.extjs.gxt.ui.client.widget.layout.BorderLayout;
import com.extjs.gxt.ui.client.widget.layout.BorderLayoutData;
import ch.systemsx.cisd.openbis.generic.client.web.client.application.AbstractAsyncCallback;
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.BrowserSectionPanel;
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.framework.DatabaseModificationAwareComponent;
@@ -132,6 +133,8 @@ public class ProteinViewer extends
BorderLayoutData layoutData = createBorderLayoutData(LayoutRegion.WEST);
layoutData.setSize(400);
add(contentPanel, layoutData);
+ add(new BrowserSectionPanel(viewContext.getMessage(Dict.SEQUENCES), ProteinSequenceGrid
+ .create(viewContext, proteinreferenceID)), createRightBorderLayoutData());
layout();
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/ProteinSequenceColDefKind.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/ProteinSequenceColDefKind.java
new file mode 100644
index 0000000000000000000000000000000000000000..c5f814a3220459f0f265df817bac4180ebd80a0d
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/application/columns/ProteinSequenceColDefKind.java
@@ -0,0 +1,74 @@
+/*
+ * 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.plugin.phosphonetx.client.web.client.application.Dict;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSequence;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public enum ProteinSequenceColDefKind implements IColumnDefinitionKind<ProteinSequence>
+{
+ SHORT_NAME(new AbstractColumnDefinitionKind<ProteinSequence>(Dict.SEQUENCE_SHORT_NAME, 20)
+ {
+ @Override
+ public String tryGetValue(ProteinSequence entity)
+ {
+ return entity.getShortName();
+ }
+ }),
+ DATABASE(new AbstractColumnDefinitionKind<ProteinSequence>(Dict.DATABASE_NAME_AND_VERSION)
+ {
+ @Override
+ public String tryGetValue(ProteinSequence entity)
+ {
+ return entity.getDatabaseNameAndVersion();
+ }
+ }),
+ SEQUENCE(new AbstractColumnDefinitionKind<ProteinSequence>(Dict.SEQUENCE, 400)
+ {
+ @Override
+ public String tryGetValue(ProteinSequence entity)
+ {
+ return entity.getSequence();
+ }
+ }),
+ ;
+
+ private final AbstractColumnDefinitionKind<ProteinSequence> columnDefinitionKind;
+
+ private ProteinSequenceColDefKind(AbstractColumnDefinitionKind<ProteinSequence> columnDefinitionKind)
+ {
+ this.columnDefinitionKind = columnDefinitionKind;
+ }
+
+ public String id()
+ {
+ return name();
+ }
+
+ public AbstractColumnDefinitionKind<ProteinSequence> getDescriptor()
+ {
+ return columnDefinitionKind;
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ListProteinSequenceCriteria.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ListProteinSequenceCriteria.java
new file mode 100644
index 0000000000000000000000000000000000000000..7795c66738b0055e74ed1ed53bf0cfeb297c8540
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/client/dto/ListProteinSequenceCriteria.java
@@ -0,0 +1,44 @@
+/*
+ * 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.ProteinSequence;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ListProteinSequenceCriteria extends
+ DefaultResultSetConfig<String, ProteinSequence> implements IsSerializable
+{
+ private TechId proteinReferenceID;
+
+ public final TechId getProteinReferenceID()
+ {
+ return proteinReferenceID;
+ }
+
+ public final void setProteinReferenceID(TechId proteinReferenceID)
+ {
+ this.proteinReferenceID = proteinReferenceID;
+ }
+}
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 5ecb9cb5fdf4e1fd385fa62f622cad4b2bf35404..94845f627aa543a7a822971cc5305f10b1590d39 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
@@ -14,6 +14,10 @@ var phosphonetx = {
// Protein in experiment viewer
protein_in_experiment_tab_label: "{0} in {1}",
experiment_label: "Experiment",
+ sequence_short_name: "",
+ database_name_and_version: "Database",
+ sequence: "Amino Acid Sequence",
+ sequences: "Amino Acid Sequences",
// LAST LINE: KEEP IT AT THE END
lastline: "" // we need a line without a comma
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/ListProteinSequenceDataProvider.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/ListProteinSequenceDataProvider.java
new file mode 100644
index 0000000000000000000000000000000000000000..a0ce8cc96ea030fc23e0554f6b180ef89ddd901c
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/client/web/server/ListProteinSequenceDataProvider.java
@@ -0,0 +1,50 @@
+/*
+ * 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.ProteinSequence;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+class ListProteinSequenceDataProvider implements IOriginalDataProvider<ProteinSequence>
+{
+ private final IPhosphoNetXServer server;
+ private final String sessionToken;
+ private final TechId proteinReferenceID;
+
+ ListProteinSequenceDataProvider(IPhosphoNetXServer server, String sessionToken,
+ TechId proteinReferenceID)
+ {
+ this.server = server;
+ this.sessionToken = sessionToken;
+ this.proteinReferenceID = proteinReferenceID;
+ }
+
+ public List<ProteinSequence> getOriginalData() throws UserFailureException
+ {
+ return server.listProteinSequencesByProteinReference(sessionToken, proteinReferenceID);
+ }
+}
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 d4f3c7eed54fdc0e8089d91143d08cad340ac49d..a471a9c70ba98a170f4c969ed1f5041c3b061e0f 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
@@ -30,10 +30,12 @@ import ch.systemsx.cisd.openbis.generic.shared.IServer;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.client.web.client.IPhosphoNetXClientService;
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.ProteinInfo;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IPhosphoNetXServer;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.ResourceNames;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSequence;
/**
* @author Franz-Josef Elmer
@@ -86,7 +88,21 @@ public class PhosphoNetXClientService extends AbstractClientService implements
{
throw UserFailureExceptionTranslator.translate(e);
}
+ }
+ public ResultSet<ProteinSequence> listSequencesByProteinReference(
+ ListProteinSequenceCriteria criteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ final String sessionToken = getSessionToken();
+ return listEntities(criteria, new ListProteinSequenceDataProvider(server, sessionToken,
+ criteria.getProteinReferenceID()));
+ }
+
+ public String prepareExportProteinSequences(TableExportCriteria<ProteinSequence> exportCriteria)
+ throws ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException
+ {
+ return prepareExportEntities(exportCriteria);
}
}
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 68b5f87703b51ef7c54ab01699e7fc6b6cfabff0..2c9241cdb80f30b724b772c67494b488ed5c57e3 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
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.server;
+import java.util.ArrayList;
import java.util.List;
import javax.annotation.Resource;
@@ -96,7 +97,7 @@ public class PhosphoNetXServer extends AbstractServer<IPhosphoNetXServer> implem
return table.getProteinReferences();
}
- public ProteinByExperiment getProteinByExperiment(String sessionToken, TechId experimentId,
+ public ProteinByExperiment getProteinByExperiment(String sessionToken, TechId experimentID,
TechId proteinReferenceID) throws UserFailureException
{
getSessionManager().getSession(sessionToken);
@@ -110,18 +111,41 @@ public class PhosphoNetXServer extends AbstractServer<IPhosphoNetXServer> implem
}
proteinByExperiment.setUniprotID(proteinReference.getUniprotID());
proteinByExperiment.setDescription(proteinReference.getDescription());
+ return proteinByExperiment;
+ }
+
+ public List<ProteinSequence> listProteinSequencesByProteinReference(String sessionToken,
+ TechId proteinReferenceID) throws UserFailureException
+ {
+ IProteinQueryDAO proteinQueryDAO = specificDAOFactory.getProteinQueryDAO();
DataSet<Sequence> sequences =
proteinQueryDAO.listProteinSequencesByProteinReference(proteinReferenceID.getId());
+ ArrayList<ProteinSequence> proteinSequences =
+ new ArrayList<ProteinSequence>(sequences.size());
+ int number = 0;
for (Sequence sequence : sequences)
{
ProteinSequence proteinSequence = new ProteinSequence();
proteinSequence.setId(new TechId(sequence.getId()));
+ proteinSequence.setShortName(createShortName(number++));
proteinSequence.setSequence(sequence.getSequence());
proteinSequence.setDatabaseNameAndVersion(sequence.getDatabaseNameAndVersion());
- proteinByExperiment.addSequence(proteinSequence);
+ proteinSequences.add(proteinSequence);
}
sequences.close();
- return proteinByExperiment;
+ return proteinSequences;
+ }
+
+ private String createShortName(int number)
+ {
+ StringBuilder builder = new StringBuilder();
+ int n = number;
+ while (n > 0)
+ {
+ builder.insert(0, "ABCEDEFGHIJKLMNOPQRSTUVWXYZ".charAt(n % 26));
+ n /= 26;
+ }
+ return builder.toString();
}
}
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 0998bbd83ccac5411f8b0e8da2eb52779643c688..8f97366476e81937c32ae1e7f404335dede26efa 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
@@ -22,13 +22,10 @@ import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.server.AbstractServerLogger;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
-import ch.systemsx.cisd.openbis.generic.shared.dto.AttachmentPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.SampleGenerationDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.IPhosphoNetXServer;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSequence;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReference;
/**
@@ -42,27 +39,6 @@ public class PhosphoNetXServerLogger extends AbstractServerLogger implements IPh
super(sessionManager, invocationSuccessful, elapsedTime);
}
- public SampleGenerationDTO getSampleInfo(String sessionToken, SampleIdentifier sampleIdentifier)
- throws UserFailureException
- {
- logAccess(sessionToken, "get_sample_info", "CODE(%s)", sampleIdentifier);
- return null;
- }
-
- public SampleGenerationDTO getSampleInfo(String sessionToken, TechId sampleId)
- throws UserFailureException
- {
- logAccess(sessionToken, "get_sample_info", "ID(%s)", sampleId);
- return null;
- }
-
- public void registerSample(String sessionToken, NewSample newSample,
- List<AttachmentPE> attachments)
- {
- logTracking(sessionToken, "register_sample", "SAMPLE_TYPE(%s) SAMPLE(%s) ATTACHMENTS(%s)",
- newSample.getSampleType(), newSample.getIdentifier(), attachments.size());
- }
-
public List<ProteinReference> listProteinsByExperiment(String sessionToken,
TechId experimentId, double falseDiscoveryRate) throws UserFailureException
{
@@ -79,4 +55,12 @@ public class PhosphoNetXServerLogger extends AbstractServerLogger implements IPh
return null;
}
+ public List<ProteinSequence> listProteinSequencesByProteinReference(String sessionToken,
+ TechId proteinReferenceID) throws UserFailureException
+ {
+ logAccess(sessionToken, "list_protein_sequences_by_reference",
+ "PROTEIN_REFERENCE_ID(%s)", proteinReferenceID);
+ return null;
+ }
+
}
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 4a1a89415827cb7a03a4eb54a5258b8e9b7c82be..a0df8f0b13f44cc240e0e62eb96f0218357805ac 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
@@ -20,6 +20,7 @@ import net.lemnik.eodsql.BaseQuery;
import net.lemnik.eodsql.DataSet;
import net.lemnik.eodsql.Select;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.IdentifiedProtein;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProbabilityFDRMapping;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReference;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProbability;
@@ -46,7 +47,21 @@ public interface IProteinQueryDAO extends BaseQuery
@Select("select * from protein_references where id = ?{1}")
public ProteinReference tryToGetProteinReference(long proteinReferenceID);
- @Select("select s.id, s.amino_acid_sequence, d.name_and_version "
- + "from sequences as s left join databases as d on s.db_id = d.id where s.prre_id = ?{1}")
+ @Select("select s.id, amino_acid_sequence, name_and_version "
+ + "from sequences as s join databases as d on s.db_id = d.id "
+ + "where s.prre_id = ?{1} order by name_and_version")
public DataSet<Sequence> listProteinSequencesByProteinReference(long proteinReferenceID);
+
+ @Select("select ds.id as data_set_id, ds.perm_id as data_set_perm_id, p.id as protein_id, "
+ + "probability, count(pe.id) as peptide_count, amino_acid_sequence, name_and_version "
+ + "from data_sets as ds join proteins as p on p.dase_id = ds.id "
+ + " join identified_proteins as i on i.prot_id = p.id "
+ + " join sequences as s on i.sequ_id = s.id "
+ + " join databases as db on s.db_id = db.id "
+ + " left join peptides as pe on pe.prot_id = p.id "
+ + "where s.prre_id = ?{2} and ds.expe_id = ?{1} "
+ + "group by data_set_id, data_set_perm_id, protein_id, probability, "
+ + " amino_acid_sequence, name_and_version order by data_set_perm_id")
+ public DataSet<IdentifiedProtein> listProteinsByProteinReferenceAndExperiment(
+ long experimentID, long proteinReferenceID);
}
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 618ecb74fa40e12deb2ed131e4fe15bd87ed89c5..61b936b02f1d3ee79294016deb345e56062a104b 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
@@ -28,6 +28,7 @@ import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RolesAll
import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.AbstractTechIdPredicate.ExperimentTechIdPredicate;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinByExperiment;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.basic.dto.ProteinSequence;
import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReference;
/**
@@ -49,5 +50,8 @@ public interface IPhosphoNetXServer extends IServer
@AuthorizationGuard(guardClass = ExperimentTechIdPredicate.class)
TechId experimentId, TechId proteinReferenceID) throws UserFailureException;
-
+ @Transactional
+ @RolesAllowed(RoleSet.OBSERVER)
+ public List<ProteinSequence> listProteinSequencesByProteinReference(String sessionToken,
+ TechId proteinReferenceID) throws UserFailureException;
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinSequence.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinSequence.java
index d90d82a9fa526bb50601b5ca6049468bb920273f..e8a00621c49687c8d01e70bbfab0b8f4434a36bd 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinSequence.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/basic/dto/ProteinSequence.java
@@ -32,12 +32,24 @@ public class ProteinSequence implements IsSerializable, Serializable
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
+ private String shortName;
+
private TechId id;
private String sequence;
private String databaseNameAndVersion;
+ public final String getShortName()
+ {
+ return shortName;
+ }
+
+ public final void setShortName(String version)
+ {
+ this.shortName = version;
+ }
+
public final TechId getId()
{
return id;
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IdentifiedProtein.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IdentifiedProtein.java
index b1c3e58082a23128b41fd100ddab4b9797534dfe..7f78dcd9148a9777b64627932329b6ba86681cbf 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IdentifiedProtein.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/IdentifiedProtein.java
@@ -34,11 +34,14 @@ public class IdentifiedProtein extends AbstractDTOWithID
@ResultColumn("protein_id")
private long proteinID;
- @ResultColumn("uniprot_id")
- private String uniprotID;
+ @ResultColumn("peptide_count")
+ private int peptideCount;
- @ResultColumn("description")
- private String description;
+ @ResultColumn("amino_acid_sequence")
+ private String sequence;
+
+ @ResultColumn("name_and_version")
+ private String database;
@ResultColumn("probability")
private double probability;
@@ -55,24 +58,24 @@ public class IdentifiedProtein extends AbstractDTOWithID
this.dataSetPermID = dataSetPermID;
}
- public final String getUniprotID()
+ public final int getPeptideCount()
{
- return uniprotID;
+ return peptideCount;
}
- public final void setUniprotID(String uniprotID)
+ public final void setPeptideCount(int uniprotID)
{
- this.uniprotID = uniprotID;
+ this.peptideCount = uniprotID;
}
- public final String getDescription()
+ public final String getSequence()
{
- return description;
+ return sequence;
}
- public final void setDescription(String description)
+ public final void setSequence(String description)
{
- this.description = description;
+ this.sequence = description;
}
public final long getDataSetID()
@@ -115,5 +118,15 @@ public class IdentifiedProtein extends AbstractDTOWithID
this.falseDiscoveryRate = falseDiscoveryRate;
}
+ public final String getDatabase()
+ {
+ return database;
+ }
+
+ public final void setDatabase(String database)
+ {
+ this.database = database;
+ }
+
}