LMS-1028 ProteinViewer: ProteinSequenceGrid added

SVN: 11736

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;
+    
 }

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

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";
+    
     
 
 }

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;

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

+/*
+ * 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];
+    }
+
+}

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();
     }
 

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

+/*
+ * 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;
+    }
+
+}

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

+/*
+ * 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;
+    }
+}

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

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

+/*
+ * 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);
+    }
+}

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);
     }
 
 }

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();
     }
 
 }

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;
+    }
+
 }

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);
 }

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;
 }

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;

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;
+    }
+
 
 }