flat protein/molecule list for a Skyline document

resources/queries/protein/Sequences.query.xml

@@ -0,0 +1,13 @@
+<query xmlns="http://labkey.org/data/xml/query">
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="Sequences" tableDbType="TABLE">
+                <columns>
+                    <column columnName="ProtSequence">
+                        <displayWidth>200</displayWidth>
+                    </column>
+                </columns>
+            </table>
+        </tables>
+    </metadata>
+</query>

resources/queries/targetedms/Protein/.qview.xml

@@ -0,0 +1,16 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+            label="Proteins" canOverride="true">
+    <columns>
+        <column name="Label" />
+        <column name="Description" />
+        <column name="Accession" />
+        <column name="PreferredName" />
+        <column name="Gene" />
+        <column name="Species" />
+
+        <column name="SequenceId/ProtSequence" />
+        <column name="Note" />
+
+    </columns>
+
+</customView>

resources/schemas/targetedms.xml

@@ -179,15 +179,15 @@
             <column columnName="DocumentGUID"/>
             <column columnName="PeptideGroupCount">
                 <formatString>#,###</formatString>
-                <url>/targetedms-showPrecursorList.view?id=${Id}</url>
+                <url>/targetedms-showProteinList.view?id=${Id}</url>
             </column>
             <column columnName="PeptideCount">
                 <formatString>#,###</formatString>
-                <url>/targetedms-showPrecursorList.view?id=${Id}</url>
+                <url>/targetedms-showPeptideList.view?id=${Id}</url>
             </column>
             <column columnName="SmallMoleculeCount">
                 <formatString>#,###</formatString>
-                <url>/targetedms-showPrecursorList.view?id=${Id}</url>
+                <url>/targetedms-showMoleculeList.view?id=${Id}</url>
             </column>
             <column columnName="PrecursorCount">
                 <formatString>#,###</formatString>

src/org/labkey/targetedms/TargetedMSController.java

@@ -258,9 +258,10 @@
 import org.labkey.targetedms.view.CalibrationCurvesView;
 import org.labkey.targetedms.view.ChromatogramGridView;
 import org.labkey.targetedms.view.ChromatogramsDataRegion;
+import org.labkey.targetedms.view.DocumentGeneralMoleculesView;
+import org.labkey.targetedms.view.DocumentPeptideGroupView;
 import org.labkey.targetedms.view.DocumentPrecursorsView;
 import org.labkey.targetedms.view.DocumentTransitionsView;
-import org.labkey.targetedms.view.DocumentView;
 import org.labkey.targetedms.view.FiguresOfMeritView;
 import org.labkey.targetedms.view.GroupComparisonView;
 import org.labkey.targetedms.view.InstrumentSummaryWebPart;
@@ -4377,7 +4378,7 @@ public void addNavTrail(NavTree root, TargetedMSRun run)
     // Action to display a document's transition or precursor list, with both proteomics and small molecule views
     // ------------------------------------------------------------------------
     @RequiresPermission(ReadPermission.class)
-    public abstract class ShowRunSplitDetailsAction<VIEWTYPE extends DocumentView> extends AbstractShowRunDetailsAction<RunDetailsForm, VIEWTYPE>
+    public abstract class ShowRunSplitDetailsAction<VIEWTYPE extends QueryView> extends AbstractShowRunDetailsAction<RunDetailsForm, VIEWTYPE>
     {
         public ShowRunSplitDetailsAction()
         {
@@ -4496,16 +4497,16 @@ public ShowPrecursorListAction(ViewContext ctx)
         @Override
         protected DocumentPrecursorsView createQueryView(RunDetailsForm form, BindException errors, boolean forExport, String dataRegion)
         {
-            DocumentPrecursorsView view;
-            if(PeptidePrecursorsView.DATAREGION_NAME.equals(dataRegion))
+            DocumentPrecursorsView view = null;
+            if (PeptidePrecursorsView.DATAREGION_NAME.equals(dataRegion))
             {
                 view = new PeptidePrecursorsView(getViewContext(),
                         new TargetedMSSchema(getUser(), getContainer()),
                         TargetedMSSchema.TABLE_EXPERIMENT_PRECURSOR,
                         form.getId(),
                         forExport);
             }
-            else
+            else if (SmallMoleculePrecursorsView.DATAREGION_NAME.equals(dataRegion))
             {
                 view = new SmallMoleculePrecursorsView(getViewContext(),
                         new TargetedMSSchema(getUser(), getContainer()),
@@ -4514,9 +4515,12 @@ protected DocumentPrecursorsView createQueryView(RunDetailsForm form, BindExcept
                         forExport);
             }
 
-            view.setShowExportButtons(true);
-            view.setShowDetailsColumn(false);
-            view.setButtonBarPosition(DataRegion.ButtonBarPosition.BOTH);
+            if (view != null)
+            {
+                view.setShowExportButtons(true);
+                view.setShowDetailsColumn(false);
+                view.setButtonBarPosition(DataRegion.ButtonBarPosition.BOTH);
+            }
 
             return view;
         }
@@ -4534,6 +4538,82 @@ public String getDataRegionNameSmallMolecule()
         }
     }
 
+    @RequiresPermission(ReadPermission.class)
+    public class ShowProteinListAction extends ShowRunSplitDetailsAction<QueryView>
+    {
+        @Override
+        protected QueryView createQueryView(RunDetailsForm form, BindException errors, boolean forExport, String dataRegion)
+        {
+            TargetedMSSchema schema = new TargetedMSSchema(getUser(), getContainer());
+            QueryView view;
+
+            if (TargetedMSSchema.TABLE_PEPTIDE_GROUP.equalsIgnoreCase(dataRegion))
+            {
+                view = new DocumentPeptideGroupView(getViewContext(), schema, form.getId(),
+                        TargetedMSSchema.TABLE_PEPTIDE_GROUP, "Proteins");
+            }
+            else
+            {
+                view = new DocumentPeptideGroupView(getViewContext(), schema, form.getId(),
+                        TargetedMSSchema.TABLE_MOLECULE_GROUP, "Molecule Lists");
+            }
+
+            view.setShowDetailsColumn(false);
+            view.setShowFilterDescription(false);
+            return view;
+        }
+
+        @Override
+        public String getDataRegionNamePeptide()
+        {
+            return TargetedMSSchema.TABLE_PEPTIDE_GROUP;
+        }
+
+        @Override
+        public String getDataRegionNameSmallMolecule()
+        {
+            return TargetedMSSchema.TABLE_MOLECULE_GROUP;
+        }
+    }
+
+    @RequiresPermission(ReadPermission.class)
+    public class ShowPeptideListAction extends ShowRunSingleDetailsAction<RunDetailsForm>
+    {
+        public ShowPeptideListAction()
+        {
+            super(RunDetailsForm.class, "Peptides", TargetedMSSchema.TABLE_PEPTIDE);
+        }
+
+        @Override
+        protected QueryView createQueryView(RunDetailsForm form, BindException errors, boolean forExport, String dataRegion)
+        {
+            TargetedMSSchema schema = new TargetedMSSchema(getUser(), getContainer());
+            DocumentGeneralMoleculesView view = new DocumentGeneralMoleculesView(getViewContext(), schema, form.getId(),
+                    TargetedMSSchema.TABLE_PEPTIDE, "Peptides");
+            view.setShowDetailsColumn(false);
+            return view;
+        }
+    }
+
+    @RequiresPermission(ReadPermission.class)
+    public class ShowMoleculeListAction extends ShowRunSingleDetailsAction<RunDetailsForm>
+    {
+        public ShowMoleculeListAction()
+        {
+            super(RunDetailsForm.class, "Small Molecules", TargetedMSSchema.TABLE_MOLECULE);
+        }
+
+        @Override
+        protected QueryView createQueryView(RunDetailsForm form, BindException errors, boolean forExport, String dataRegion)
+        {
+            TargetedMSSchema schema = new TargetedMSSchema(getUser(), getContainer());
+            DocumentGeneralMoleculesView view = new DocumentGeneralMoleculesView(getViewContext(), schema, form.getId(),
+                    TargetedMSSchema.TABLE_MOLECULE, "Small Molecules");
+            view.setShowDetailsColumn(false);
+            return view;
+        }
+    }
+
     @RequiresPermission(ReadPermission.class)
     public class ShowGroupComparisonAction extends ShowRunSplitDetailsAction<GroupComparisonView>
     {