Issue 550 - Show modified peptide forms in sequence view

src/org/labkey/targetedms/TargetedMSController.java

@@ -249,6 +249,7 @@
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
+import java.util.Objects;
 import java.util.Set;
 import java.util.function.Function;
 import java.util.function.Predicate;
@@ -2384,6 +2385,8 @@ public static class ChromatogramForm extends AbstractChartForm
         private boolean _update;
         private Long _chromInfoId;
         private Long _highlightChromInfoId;
+        private long _replicateId;
+        private String _peptideForm;
 
         public ChromatogramForm()
         {
@@ -2400,6 +2403,15 @@ public void setId(long id)
             _id = id;
         }
 
+        public long getReplicateId()
+        {
+            return _replicateId;
+        }
+
+        public void setReplicateId(long replicateId)
+        {
+            _replicateId = replicateId;
+        }
 
         public String getReplicatesFilter()
         {
@@ -2586,6 +2598,16 @@ public void setChromInfoId(Long chromInfoId)
         {
             _chromInfoId = chromInfoId;
         }
+
+        public String getPeptideForm()
+        {
+            return _peptideForm;
+        }
+
+        public void setPeptideForm(String peptideForm)
+        {
+            _peptideForm = Objects.requireNonNullElse(peptideForm, PeptideCharacteristic.COMBINED_PEPTIDE);
+        }
     }
 
 
@@ -4746,7 +4768,8 @@ public ModelAndView getView(final ChromatogramForm form, BindException errors)
             // Peptide group details
             VBox result = new VBox();
 
-            Integer peptideCount = addProteinSummaryViews(result, group, _run, getUser(), getContainer());
+            var showStackedPeptides = form._peptideForm != null && form._peptideForm.equalsIgnoreCase("stacked");
+            Integer peptideCount = addProteinSummaryViews(result, group, _run, form.getReplicateId(), showStackedPeptides);
 
             GroupChromatogramsTableInfo tableInfo = new GroupChromatogramsTableInfo(new TargetedMSSchema(getUser(), getContainer()), form);
             ChromatogramsDataRegion chromatogramRegion = new ChromatogramsDataRegion(getViewContext(), tableInfo,
@@ -4879,7 +4902,7 @@ private QueryView createViewWithNoContainerFilterOptions(QuerySettings settings,
         return result;
     }
 
-    public static Integer addProteinSummaryViews(VBox box, PeptideGroup group, TargetedMSRun run, User user, Container container)
+    public static Integer addProteinSummaryViews(VBox box, PeptideGroup group, TargetedMSRun run, @Nullable Long replicateId, boolean showStackedPeptides)
     {
         Integer peptideCount = TargetedMSManager.getPeptideGroupPeptideCount(run, group.getId());
         boolean proteomics = peptideCount != null && peptideCount.intValue() > 0;
@@ -4893,10 +4916,20 @@ public static Integer addProteinSummaryViews(VBox box, PeptideGroup group, Targe
         if (group.getSequenceId() != null)
         {
             int seqId = group.getSequenceId().intValue();
-            List<PeptideCharacteristic> peptideCharacteristics = new ArrayList<>(PeptideManager.getPeptideCharacteristic(group.getId()));
+            List<PeptideCharacteristic> combinedPeptideCharacteristics = new ArrayList<>(PeptideManager.getCombinedPeptideCharacteristics(group.getId(), replicateId));
+            List<PeptideCharacteristic> modifiedPeptideCharacteristics = new ArrayList<>(PeptideManager.getModifiedPeptideCharacteristics(group.getId(), replicateId));;
+
+            List<Replicate> replicates = ReplicateManager.getReplicatesForRun(run.getRunId());
+            List<org.labkey.api.ms.Replicate> msReplicates = new ArrayList<>();
+            replicates.forEach(replicate -> {
+                var rep = new org.labkey.api.ms.Replicate();
+                rep.setName(replicate.getName());
+                rep.setId(replicate.getId());
+                msReplicates.add(rep);
+            });
 
             ProteinService proteinService = ProteinService.get();
-            WebPartView<?> sequenceView = proteinService.getProteinCoverageView(seqId, peptideCharacteristics, 100, true, group.getAccession());
+            WebPartView<?> sequenceView = proteinService.getProteinCoverageViewWithSettings(seqId, combinedPeptideCharacteristics, 100, true, group.getAccession(), msReplicates, modifiedPeptideCharacteristics, showStackedPeptides);
 
             sequenceView.setTitle("Sequence Coverage");
             sequenceView.enableExpandCollapse("SequenceCoverage", false);

src/org/labkey/targetedms/parser/Replicate.java

@@ -23,6 +23,7 @@
  */
 public class Replicate extends AnnotatedEntity<ReplicateAnnotation>
 {
+    private long _id;
     private long _runId;
     private String _name;
 
@@ -36,6 +37,17 @@ public class Replicate extends AnnotatedEntity<ReplicateAnnotation>
 
     private List<SampleFile> _sampleFileList;
 
+    @Override
+    public long getId()
+    {
+        return _id;
+    }
+
+    @Override
+    public void setId(long id)
+    {
+        _id = id;
+    }
 
     public long getRunId()
     {

src/org/labkey/targetedms/passport/PassportController.java

@@ -149,7 +149,7 @@ public ModelAndView getView(ProteinForm form, BindException errors) throws IOExc
             VBox result = new VBox();
             PeptideGroup group = PeptideGroupManager.getPeptideGroup(getContainer(), _protein.getPepGroupId());
             _run = TargetedMSManager.getRun(group.getRunId());
-            TargetedMSController.addProteinSummaryViews(result, group, _run, getUser(), getContainer());
+            TargetedMSController.addProteinSummaryViews(result, group, _run, null, false);
 
             if (beforeAfter)
             {

src/org/labkey/targetedms/query/PeptideManager.java

@@ -15,19 +15,22 @@
 
 package org.labkey.targetedms.query;
 
+import org.jetbrains.annotations.Nullable;
 import org.labkey.api.cache.CacheLoader;
 import org.labkey.api.cache.CacheManager;
 import org.labkey.api.data.Container;
 import org.labkey.api.data.DatabaseCache;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.SqlSelector;
+import org.labkey.api.data.dialect.SqlDialect;
 import org.labkey.api.protein.PeptideCharacteristic;
 import org.labkey.targetedms.TargetedMSManager;
 import org.labkey.targetedms.parser.GeneralMoleculeChromInfo;
 import org.labkey.targetedms.parser.Peptide;
 
 import java.util.Collection;
 import java.util.List;
+import java.util.Objects;
 import java.util.Set;
 
 /**
@@ -94,18 +97,31 @@ public static Collection<Peptide> getPeptidesForGroup(long peptideGroupId)
         return new SqlSelector(TargetedMSManager.getSchema(), sql).getArrayList(Peptide.class);
     }
 
-    public static List<PeptideCharacteristic> getPeptideCharacteristic(long peptideGroupId)
+    private static String appendLog10IntensitySql(SqlDialect sqlDialect)
     {
-        var sqlDialect = TargetedMSManager.getSqlDialect();
-        var pgLog10Intensity = "LOG(" + sqlDialect.getNumericCast(new SQLFragment("MAX(X.Intensity)")).getSQL() + ")";
-        var sqlServerLog10Intensity = "LOG10(MAX(X.Intensity))";
-        var pgConfidenceValueToRound = "-LOG(" + sqlDialect.getNumericCast(new SQLFragment("MAX(X.Confidence)")).getSQL() + ")";
+        var pgLog10Intensity = " CASE WHEN MAX(X.Intensity) IS NOT NULL AND MAX(X.Intensity) != 0 THEN LOG(" + sqlDialect.getNumericCast(new SQLFragment("MAX(X.Intensity)")).getSQL() + ") ELSE 0 END ";
+        var sqlServerLog10Intensity = " CASE WHEN MAX(X.Intensity) IS NOT NULL AND MAX(X.Intensity) != 0 THEN LOG10(MAX(X.Intensity)) ELSE 0 END ";
+        return sqlDialect.isPostgreSQL() ? pgLog10Intensity : sqlServerLog10Intensity;
+    }
+
+    private static String appendLog10ConfidenceSql(SqlDialect sqlDialect)
+    {
+        var pgConfidenceValueToRound = " CASE WHEN MAX(X.Confidence) IS NOT NULL AND MAX(X.Confidence) != 0 THEN -LOG(" + sqlDialect.getNumericCast(new SQLFragment("MAX(X.Confidence)")).getSQL() + ")  ELSE 0 END ";
         var pgLog10Confidence = "ROUND(" + sqlDialect.getNumericCast(new SQLFragment(pgConfidenceValueToRound)).getSQL() + ",4)";
-        var sqlServerLog10Confidence = "ROUND(-LOG10(MAX(X.Confidence)),4)";
-        var log10IntensitySql = sqlDialect.isPostgreSQL() ? pgLog10Intensity : sqlServerLog10Intensity;
-        var log10ConfidenceSql = sqlDialect.isPostgreSQL() ? pgLog10Confidence : sqlServerLog10Confidence;
-        SQLFragment sql = new SQLFragment("SELECT X.Sequence, " + log10IntensitySql + " AS Intensity, " + log10ConfidenceSql + " AS Confidence FROM ");
-        sql.append("(SELECT pep.Sequence, SUM(TotalArea) AS Intensity, MAX(qvalue) AS Confidence FROM ");
+        var sqlServerLog10Confidence = " CASE WHEN MAX(X.Confidence) IS NOT NULL AND MAX(X.Confidence) != 0 THEN ROUND(-LOG10(MAX(X.Confidence)),4)  ELSE 0 END ";
+        return sqlDialect.isPostgreSQL() ? pgLog10Confidence : sqlServerLog10Confidence;
+    }
+
+    public static List<PeptideCharacteristic> getCombinedPeptideCharacteristics(long peptideGroupId, @Nullable Long replicateId)
+    {
+        var shouldFilterAndGroupByReplicate = null != replicateId && !Objects.equals(replicateId, Long.valueOf(0));
+        var sqlDialect = TargetedMSManager.getSqlDialect();
+
+        SQLFragment sql = new SQLFragment("SELECT X.Sequence, " + appendLog10IntensitySql(sqlDialect) + " AS Intensity, " + appendLog10ConfidenceSql(sqlDialect) + " AS Confidence, ");
+        sql.append(" MAX(X.Intensity) AS RawIntensity, MAX(X.Confidence) AS RawConfidence, X.StartIndex, X.EndIndex FROM ");
+        sql.append("(SELECT pep.Sequence, pep.StartIndex, pep.EndIndex, ");
+        sql.append(" CASE WHEN SUM(TotalArea) IS NULL OR SUM(TotalArea) < 1 THEN 1 ELSE SUM(TotalArea) END AS Intensity, ");
+        sql.append(" MAX(qvalue) AS Confidence FROM ");
         sql.append(TargetedMSManager.getTableInfoPrecursorChromInfo(), "pci");
         sql.append(" INNER JOIN ").append(TargetedMSManager.getTableInfoGeneralPrecursor(), "p");
         sql.append(" ON p.Id = pci.PrecursorId");
@@ -115,10 +131,58 @@ public static List<PeptideCharacteristic> getPeptideCharacteristic(long peptideG
         sql.append(" ON gm.id = pep.Id");
         sql.append(" INNER JOIN ").append(TargetedMSManager.getTableInfoSampleFile(), "sf");
         sql.append(" ON sf.Id = pci.SampleFileId");
+        if (shouldFilterAndGroupByReplicate)
+        {
+            sql.append(" INNER JOIN ").append(TargetedMSManager.getTableInfoReplicate(), "rep");
+            sql.append(" ON rep.Id = sf.ReplicateId");
+        }
         sql.append(" WHERE gm.PeptideGroupId=? ");
-        sql.append(" GROUP BY pep.Sequence,pci.SampleFileId ) X ");
-        sql.append(" GROUP BY X.Sequence");
         sql.add(peptideGroupId);
+        if (shouldFilterAndGroupByReplicate)
+        {
+            sql.append(" AND rep.Id=? ");
+            sql.add(replicateId);
+        }
+        sql.append(" GROUP BY pep.Sequence,pci.SampleFileId, pep.StartIndex, pep.EndIndex ) X ");
+        sql.append(" GROUP BY X.Sequence, X.StartIndex, X.EndIndex ");
+        return new SqlSelector(TargetedMSManager.getSchema(), sql).getArrayList(PeptideCharacteristic.class);
+    }
+
+    public static List<PeptideCharacteristic> getModifiedPeptideCharacteristics(long peptideGroupId, @Nullable Long replicateId)
+    {
+        var shouldFilterAndGroupByReplicate = null != replicateId && !Objects.equals(replicateId, Long.valueOf(0));
+        var sqlDialect = TargetedMSManager.getSqlDialect();
+
+        SQLFragment sql = new SQLFragment("SELECT X.Sequence, X.PeptideModifiedSequence AS ModifiedSequence, X.StartIndex, X.EndIndex ,");
+        sql.append(appendLog10IntensitySql(sqlDialect) + " AS Intensity, " + appendLog10ConfidenceSql(sqlDialect) + " AS Confidence, ");
+        sql.append(" MAX(X.Intensity) AS RawIntensity, MAX(X.Confidence) AS RawConfidence FROM ");
+        sql.append("(SELECT pep.Sequence, pep.PeptideModifiedSequence, pep.StartIndex, pep.EndIndex, ");
+        sql.append(" CASE WHEN SUM(TotalArea) IS NULL OR SUM(TotalArea) < 1 THEN 1 ELSE SUM(TotalArea) END AS Intensity, ");
+        sql.append(" MAX(qvalue) AS Confidence FROM ");
+        sql.append(TargetedMSManager.getTableInfoPrecursorChromInfo(), "pci");
+        sql.append(" INNER JOIN ").append(TargetedMSManager.getTableInfoGeneralPrecursor(), "p");
+        sql.append(" ON p.Id = pci.PrecursorId");
+        sql.append(" INNER JOIN ").append(TargetedMSManager.getTableInfoPeptide(),"pep");
+        sql.append(" ON p.GeneralMoleculeId = pep.Id");
+        sql.append(" INNER JOIN ").append(TargetedMSManager.getTableInfoGeneralMolecule(),"gm");
+        sql.append(" ON gm.id = pep.Id");
+        sql.append(" INNER JOIN ").append(TargetedMSManager.getTableInfoSampleFile(), "sf");
+        sql.append(" ON sf.Id = pci.SampleFileId");
+        if (shouldFilterAndGroupByReplicate)
+        {
+            sql.append(" INNER JOIN ").append(TargetedMSManager.getTableInfoReplicate(), "rep");
+            sql.append(" ON rep.Id = sf.ReplicateId");
+        }
+        sql.append(" WHERE gm.PeptideGroupId=? ");
+        sql.add(peptideGroupId);
+        if (shouldFilterAndGroupByReplicate)
+        {
+            sql.append(" AND rep.Id=? ");
+            sql.add(replicateId);
+        }
+        sql.append(" GROUP BY pep.Sequence,pci.SampleFileId, pep.PeptideModifiedSequence, pep.StartIndex, pep.EndIndex ) X ");
+        sql.append(" GROUP BY X.Sequence, X.PeptideModifiedSequence, X.StartIndex, X.EndIndex ");
+
         return new SqlSelector(TargetedMSManager.getSchema(), sql).getArrayList(PeptideCharacteristic.class);
     }