Ticket 53573: Formatting adjustments to the Peptide Map report (#1098)

labkey-jeckels · web-flow · commit 5d44a846a654 · 2025-08-04T15:29:29.000-07:00
diff --git a/resources/queries/targetedms/PeptideIds.query.xml b/resources/queries/targetedms/PeptideIds.query.xml
@@ -17,6 +17,7 @@
                                 <property name="showNextAndPrevious">true</property>
                                 <property name="useParens">true</property>
                                 <property name="exportFormatted">true</property>
+                                <property name="highlightFixed">false</property>
                             </properties>
                         </displayColumnFactory>
                     </column>
diff --git a/src/org/labkey/targetedms/parser/PeptideSettings.java b/src/org/labkey/targetedms/parser/PeptideSettings.java
@@ -493,7 +493,7 @@ public Boolean getExplicitMod()
 
         public boolean isModExplicit()
         {
-            return _explicitMod == null ? false : _explicitMod;
+            return _explicitMod != null && _explicitMod;
         }
 
         public void setExplicitMod(Boolean explicitMod)
diff --git a/src/org/labkey/targetedms/query/CrossLinkedPeptideDisplayColumn.java b/src/org/labkey/targetedms/query/CrossLinkedPeptideDisplayColumn.java
@@ -173,29 +173,29 @@ public DisplayColumn createRenderer(ColumnInfo colInfo)
             return new CrossLinkedPeptideDisplayColumn(colInfo, (match, sequence, modification) ->
             {
                 String label = match.protein().getLabel();
-                String suffix = getChainAbbreviation(label);
-                return (match.index() + 1) + "-" + (match.index() + getPeptideLength(sequence.getUnmodified(), modification)) + suffix;
+                String prefix = getChainPrefix(label);
+                return prefix + (match.index() + 1) + "-" + (match.index() + getPeptideLength(sequence.getUnmodified(), modification));
             });
         }
     }
 
-    public static @NotNull String getChainAbbreviation(String label)
+    public static @NotNull String getChainPrefix(String label)
     {
         String result = "";
         if (label != null)
         {
             label = label.toLowerCase();
             if (label.endsWith("_hc"))
             {
-                result = "HC";
+                result = "H";
             }
             if (label.endsWith("_hcstar"))
             {
-                result = "HC*";
+                result = "*";
             }
             if (label.endsWith("_lc"))
             {
-                result = "LC";
+                result = "L";
             }
         }
         return result;
@@ -221,7 +221,7 @@ public DisplayColumn createRenderer(ColumnInfo colInfo)
                         {
                             for (int linkIndex : sequence.getLinkIndices())
                             {
-                                bonds.add(Character.toString(sequence.getUnmodified().charAt(linkIndex)) + (match.index() + linkIndex + 1) + getChainAbbreviation(match.protein().getLabel()));
+                                bonds.add(Character.toString(sequence.getUnmodified().charAt(linkIndex)) + (match.index() + linkIndex + 1) + getChainPrefix(match.protein().getLabel()));
                             }
                         }
                         allBonds.add(bonds);
diff --git a/src/org/labkey/targetedms/query/ModificationManager.java b/src/org/labkey/targetedms/query/ModificationManager.java
@@ -265,13 +265,15 @@ public static PeptideSettings.ModificationSettings getSettings(long runId)
     /**
      * @return    PeptideId -> (Set of indexes where the peptide has structural modifications)
      */
-    private static Map<Long, Set<Pair<Integer, Integer>>> getPeptideStructuralModIndexMap(long runId)
+    private static Map<Long, Set<Pair<Integer, Integer>>> getPeptideStructuralModIndexMap(long runId, boolean includeFixedMods)
     {
         SQLFragment sql = new SQLFragment();
         sql.append(" SELECT mod.PeptideId AS peptideId, mod.IndexAA AS indexAA, mod.PeptideIndex AS peptideIndex");
         sql.append(" FROM ");
         sql.append(TargetedMSManager.getTableInfoPeptideStructuralModification(), "mod");
         sql.append(" , ");
+        sql.append(TargetedMSManager.getTableInfoRunStructuralModification(), "runmod");
+        sql.append(" , ");
         sql.append(TargetedMSManager.getTableInfoGeneralMolecule(), "gm");
         sql.append(" , ");
         sql.append(TargetedMSManager.getTableInfoPeptideGroup(), "pg");
@@ -285,6 +287,15 @@ private static Map<Long, Set<Pair<Integer, Integer>>> getPeptideStructuralModInd
         sql.append(" gm.peptideGroupId = pg.id ");
         sql.append(" AND ");
         sql.append(" mod.peptideId = gm.id ");
+        sql.append(" AND ");
+        sql.append(" runmod.StructuralModId = mod.StructuralModId");
+        sql.append(" AND ");
+        sql.append(" runmod.RunId = run.Id");
+        if (!includeFixedMods)
+        {
+            sql.append(" AND (runmod.variable = ? OR runmod.ExplicitMod IS NOT NULL)");
+            sql.add(true);
+        }
 
         final Map<Long, Set<Pair<Integer, Integer>>> peptideModIndexMap = new HashMap<>();
 
@@ -342,17 +353,25 @@ private static Map<Pair<Long,Long>, Set<Integer>> getPeptideIsotopeModIndexMap(l
         return Collections.unmodifiableMap(peptideModIndexMap);
     }
 
-    /** Pair is the index of the cross-linked peptide (or 0 for non-cross-linked peptides) and the amino acid index */
-    public static Set<Pair<Integer, Integer>> getStructuralModIndexes(long peptideId, Long runId)
+    /**
+     * Pair is the index of the cross-linked peptide (or 0 for non-cross-linked peptides) and the amino acid index
+     * @param includeFixedMods Whether to include fixed modifications
+     * @return Set of pairs of peptide index and amino acid index
+     */
+    public static Set<Pair<Integer, Integer>> getStructuralModIndexes(long peptideId, Long runId, boolean includeFixedMods)
     {
-        if(runId == null)
+        if (runId == null)
         {
+            if (!includeFixedMods)
+            {
+                throw new UnsupportedOperationException();
+            }
             Map<Pair<Integer, Integer>, Double> modMap = getPeptideStructuralModsMap(peptideId);
             return new HashSet<>(modMap.keySet());
         }
         else
         {
-            Map<Long, Set<Pair<Integer, Integer>>> modIndexesForRun = PEPTIDE_STR_MOD_INDEXES.get(String.valueOf(runId), null, (runId1, argument) -> getPeptideStructuralModIndexMap(Long.valueOf(runId1)));
+            Map<Long, Set<Pair<Integer, Integer>>> modIndexesForRun = PEPTIDE_STR_MOD_INDEXES.get(runId + "-" + includeFixedMods, null, (runId1, argument) -> getPeptideStructuralModIndexMap(runId, includeFixedMods));
             return modIndexesForRun.getOrDefault(peptideId, Collections.emptySet());
         }
     }
diff --git a/src/org/labkey/targetedms/query/ModifiedSequenceDisplayColumn.java b/src/org/labkey/targetedms/query/ModifiedSequenceDisplayColumn.java
@@ -64,10 +64,15 @@ public abstract class ModifiedSequenceDisplayColumn extends IconColumn
     public static final String PRECURSOR_COLUMN_NAME = "ModifiedPrecursorDisplayColumn";
 
     public ModifiedSequenceDisplayColumn(ColumnInfo colInfo)
+    {
+        this(colInfo, true);
+    }
+
+    public ModifiedSequenceDisplayColumn(ColumnInfo colInfo, boolean highlightFixed)
     {
         super(colInfo);
 
-        _htmlMaker = new ModifiedPeptideHtmlMaker();
+        _htmlMaker = new ModifiedPeptideHtmlMaker(highlightFixed);
     }
 
     ModifiedPeptideHtmlMaker getHtmlMaker()
@@ -147,6 +152,7 @@ public static class PeptideDisplayColumnFactory implements DisplayColumnFactory
         private boolean _exportStrippedHtml = false;
         private boolean _showNextAndPrevious = false;
         private boolean _useParens = false;
+        private boolean _highlightFixed = true;
         /** Optionally, the name of the column that identifies the animo acid and index within the protein to highlight as modified */
         private String _modificationSite;
 
@@ -161,6 +167,7 @@ public PeptideDisplayColumnFactory(MultiValuedMap<String, String> map)
             _useParens = getBooleanProperty(map, "useParens", _useParens);
             _exportStrippedHtml = getBooleanProperty(map, "exportFormatted", _exportStrippedHtml);
             _modificationSite = map == null || map.get("modificationSite").isEmpty() ? null : map.get("modificationSite").iterator().next();
+            _highlightFixed = getBooleanProperty(map, "highlightFixed", _highlightFixed);
         }
 
         private boolean getBooleanProperty(MultiValuedMap<String, String> map, String propertyName, boolean defaultValue)
@@ -176,7 +183,7 @@ private boolean getBooleanProperty(MultiValuedMap<String, String> map, String pr
         @Override
         public DisplayColumn createRenderer(ColumnInfo colInfo)
         {
-            return new ModifiedSequenceDisplayColumn.PeptideCol(colInfo, _showNextAndPrevious, _useParens, _exportStrippedHtml, _modificationSite);
+            return new ModifiedSequenceDisplayColumn.PeptideCol(colInfo, _showNextAndPrevious, _useParens, _exportStrippedHtml, _highlightFixed, _modificationSite);
         }
     }
 
@@ -190,12 +197,12 @@ public static class PeptideCol extends ModifiedSequenceDisplayColumn
 
         public PeptideCol(ColumnInfo colInfo)
         {
-            this(colInfo, false, false, false, null);
+            this(colInfo, false, false, false, true, null);
         }
 
-        public PeptideCol(ColumnInfo colInfo, boolean showNextAndPrevious, boolean useParens, boolean exportStrippedHtml, String modificationSite)
+        public PeptideCol(ColumnInfo colInfo, boolean showNextAndPrevious, boolean useParens, boolean exportStrippedHtml, boolean highlightFixed, String modificationSite)
         {
-            super(colInfo);
+            super(colInfo, highlightFixed);
             _showNextAndPrevious = showNextAndPrevious;
             _useParens = useParens;
             _modificationSite = modificationSite;
diff --git a/src/org/labkey/targetedms/query/SiteLocationDisplayColumnFactory.java b/src/org/labkey/targetedms/query/SiteLocationDisplayColumnFactory.java
@@ -76,7 +76,7 @@ public void writeCell(Sheet sheet, int column, int row, RenderContext ctx)
                 };
 
                 String chain = _col.getChainLabel(ctx);
-                String chainPrefix = CrossLinkedPeptideDisplayColumn.getChainAbbreviation(chain);
+                String chainPrefix = CrossLinkedPeptideDisplayColumn.getChainPrefix(chain);
                 if (!chainPrefix.isEmpty())
                 {
                     chainPrefix = chainPrefix + " ";
diff --git a/src/org/labkey/targetedms/view/ModifiedPeptideHtmlMaker.java b/src/org/labkey/targetedms/view/ModifiedPeptideHtmlMaker.java
@@ -54,6 +54,9 @@ public class ModifiedPeptideHtmlMaker
 
     /** RunId -> all proteins in that run */
     private final Map<Long, List<Protein>> _proteins = new HashMap<>();
+    
+    /** Whether to include fixed modifications in the formatting */
+    private final boolean _highlightFixedMods;
 
     private final static String[] HEX_PADDING = new String[] {
                                                         "",
@@ -66,8 +69,17 @@ public class ModifiedPeptideHtmlMaker
     };
 
     public ModifiedPeptideHtmlMaker()
+    {
+        this(true);
+    }
+    
+    /**
+     * @param highlightFixedMods Whether to include fixed modifications in the formatting
+     */
+    public ModifiedPeptideHtmlMaker(boolean highlightFixedMods)
     {
         _firstIsotopeLabelIdInDocMap = new HashMap<>();
+        _highlightFixedMods = highlightFixedMods;
     }
 
     public Pair<HtmlString, List<List<SequencePart>>> getPrecursorHtml(Precursor precursor, Long runId, TargetedMSSchema schema)
@@ -147,7 +159,7 @@ private Pair<HtmlString, List<List<SequencePart>>> getHtml(long peptideId, @Null
 
         if (strModIndices == null)
         {
-            strModIndices = ModificationManager.getStructuralModIndexes(peptideId, runId);
+            strModIndices = ModificationManager.getStructuralModIndexes(peptideId, runId, _highlightFixedMods);
         }
         Set<Integer> isotopeModIndices = null;
         if(isotopeLabelId != null)
diff --git a/test/src/org/labkey/test/tests/targetedms/TargetedMSMAMTest.java b/test/src/org/labkey/test/tests/targetedms/TargetedMSMAMTest.java
@@ -20,6 +20,8 @@
 import org.junit.experimental.categories.Category;
 import org.labkey.test.Locator;
 
+import static org.junit.Assert.assertTrue;
+
 @Category({})
 public class TargetedMSMAMTest extends TargetedMSTest
 {
@@ -60,6 +62,9 @@ public void testSteps()
         assertTextPresentInThisOrder("70-84", "325-333", "28-41", "190-196; 26-32");
         assertTextPresentInThisOrder("(K)ASTEGVAIQGQQGTR(L)", "(K)AQYEDIANR(S)", "(K)SVTEQGAELSNEER(N)");
         assertTextPresentInThisOrder("Carbamidomethyl Cysteine @ C157", "Carbamidomethyl Cysteine @ C245", "Carbamidomethyl Cysteine @ C94");
+
+        // Ensure that the Cystine isn't highlighted, as it's a fixed modification and that report doesn't want to call it out
+        assertTrue(getHtmlSource().contains("(K)YLECSALTQR(G)"));
     }
 
     @Test
@@ -77,5 +82,8 @@ public void testCrossLinkedPeptideMap()
         // Disulfide bonds
         assertTextPresentInThisOrder("Q364-T369-D364/\nN366-T369-D364", "V121-S345-Q142/\nQ124-S345-Q142");
         assertTextPresentInThisOrder("(A)LKPLALV(D)", "(G)AVVQDPA(Y)", "(F)YGEATSR(E)");
+
+        // Ensure that the highlighting is as expected for both crosslinking and modification
+        assertTrue(getHtmlSource().contains("(Y)<span style=\"font-weight:bold;color:green;text-decoration:underline;\">Q</span><span style=\"font-weight:bold;text-decoration:underline;\">M</span><span style=\"font-weight:bold;color:green;\">N</span>(D)"));
     }
 }

Original file line number	Diff line number	Diff line change
`@@ -493,7 +493,7 @@ public Boolean getExplicitMod()`
`493`	`493`
`494`	`494`	`public boolean isModExplicit()`
`495`	`495`	`{`
`496`		`- return _explicitMod == null ? false : _explicitMod;`
	`496`	`+ return _explicitMod != null && _explicitMod;`
`497`	`497`	`}`
`498`	`498`
`499`	`499`	`public void setExplicitMod(Boolean explicitMod)`
Original file line number	Diff line number	Diff line change
`@@ -173,29 +173,29 @@ public DisplayColumn createRenderer(ColumnInfo colInfo)`
`173`	`173`	`return new CrossLinkedPeptideDisplayColumn(colInfo, (match, sequence, modification) ->`
`174`	`174`	`{`
`175`	`175`	`String label = match.protein().getLabel();`
`176`		`- String suffix = getChainAbbreviation(label);`
`177`		`- return (match.index() + 1) + "-" + (match.index() + getPeptideLength(sequence.getUnmodified(), modification)) + suffix;`
	`176`	`+ String prefix = getChainPrefix(label);`
	`177`	`+ return prefix + (match.index() + 1) + "-" + (match.index() + getPeptideLength(sequence.getUnmodified(), modification));`
`178`	`178`	`});`
`179`	`179`	`}`
`180`	`180`	`}`
`181`	`181`
`182`		`- public static @NotNull String getChainAbbreviation(String label)`
	`182`	`+ public static @NotNull String getChainPrefix(String label)`
`183`	`183`	`{`
`184`	`184`	`String result = "";`
`185`	`185`	`if (label != null)`
`186`	`186`	`{`
`187`	`187`	`label = label.toLowerCase();`
`188`	`188`	`if (label.endsWith("_hc"))`
`189`	`189`	`{`
`190`		`- result = "HC";`
	`190`	`+ result = "H";`
`191`	`191`	`}`
`192`	`192`	`if (label.endsWith("_hcstar"))`
`193`	`193`	`{`
`194`		`- result = "HC*";`
	`194`	`+ result = "*";`
`195`	`195`	`}`
`196`	`196`	`if (label.endsWith("_lc"))`
`197`	`197`	`{`
`198`		`- result = "LC";`
	`198`	`+ result = "L";`
`199`	`199`	`}`
`200`	`200`	`}`
`201`	`201`	`return result;`
`@@ -221,7 +221,7 @@ public DisplayColumn createRenderer(ColumnInfo colInfo)`
`221`	`221`	`{`
`222`	`222`	`for (int linkIndex : sequence.getLinkIndices())`
`223`	`223`	`{`
`224`		`- bonds.add(Character.toString(sequence.getUnmodified().charAt(linkIndex)) + (match.index() + linkIndex + 1) + getChainAbbreviation(match.protein().getLabel()));`
	`224`	`+ bonds.add(Character.toString(sequence.getUnmodified().charAt(linkIndex)) + (match.index() + linkIndex + 1) + getChainPrefix(match.protein().getLabel()));`
`225`	`225`	`}`
`226`	`226`	`}`
`227`	`227`	`allBonds.add(bonds);`
Original file line number	Diff line number	Diff line change
`@@ -64,10 +64,15 @@ public abstract class ModifiedSequenceDisplayColumn extends IconColumn`
`64`	`64`	`public static final String PRECURSOR_COLUMN_NAME = "ModifiedPrecursorDisplayColumn";`
`65`	`65`
`66`	`66`	`public ModifiedSequenceDisplayColumn(ColumnInfo colInfo)`
	`67`	`+ {`
	`68`	`+ this(colInfo, true);`
	`69`	`+ }`
	`70`	`+`
	`71`	`+ public ModifiedSequenceDisplayColumn(ColumnInfo colInfo, boolean highlightFixed)`
`67`	`72`	`{`
`68`	`73`	`super(colInfo);`
`69`	`74`
`70`		`- _htmlMaker = new ModifiedPeptideHtmlMaker();`
	`75`	`+ _htmlMaker = new ModifiedPeptideHtmlMaker(highlightFixed);`
`71`	`76`	`}`
`72`	`77`
`73`	`78`	`ModifiedPeptideHtmlMaker getHtmlMaker()`
`@@ -147,6 +152,7 @@ public static class PeptideDisplayColumnFactory implements DisplayColumnFactory`
`147`	`152`	`private boolean _exportStrippedHtml = false;`
`148`	`153`	`private boolean _showNextAndPrevious = false;`
`149`	`154`	`private boolean _useParens = false;`
	`155`	`+ private boolean _highlightFixed = true;`
`150`	`156`	`/** Optionally, the name of the column that identifies the animo acid and index within the protein to highlight as modified */`
`151`	`157`	`private String _modificationSite;`
`152`	`158`
`@@ -161,6 +167,7 @@ public PeptideDisplayColumnFactory(MultiValuedMap<String, String> map)`
`161`	`167`	`_useParens = getBooleanProperty(map, "useParens", _useParens);`
`162`	`168`	`_exportStrippedHtml = getBooleanProperty(map, "exportFormatted", _exportStrippedHtml);`
`163`	`169`	`_modificationSite = map == null \|\| map.get("modificationSite").isEmpty() ? null : map.get("modificationSite").iterator().next();`
	`170`	`+ _highlightFixed = getBooleanProperty(map, "highlightFixed", _highlightFixed);`
`164`	`171`	`}`
`165`	`172`
`166`	`173`	`private boolean getBooleanProperty(MultiValuedMap<String, String> map, String propertyName, boolean defaultValue)`
`@@ -176,7 +183,7 @@ private boolean getBooleanProperty(MultiValuedMap<String, String> map, String pr`
`176`	`183`	`@Override`
`177`	`184`	`public DisplayColumn createRenderer(ColumnInfo colInfo)`
`178`	`185`	`{`
`179`		`- return new ModifiedSequenceDisplayColumn.PeptideCol(colInfo, _showNextAndPrevious, _useParens, _exportStrippedHtml, _modificationSite);`
	`186`	`+ return new ModifiedSequenceDisplayColumn.PeptideCol(colInfo, _showNextAndPrevious, _useParens, _exportStrippedHtml, _highlightFixed, _modificationSite);`
`180`	`187`	`}`
`181`	`188`	`}`
`182`	`189`
`@@ -190,12 +197,12 @@ public static class PeptideCol extends ModifiedSequenceDisplayColumn`
`190`	`197`
`191`	`198`	`public PeptideCol(ColumnInfo colInfo)`
`192`	`199`	`{`
`193`		`- this(colInfo, false, false, false, null);`
	`200`	`+ this(colInfo, false, false, false, true, null);`
`194`	`201`	`}`
`195`	`202`
`196`		`- public PeptideCol(ColumnInfo colInfo, boolean showNextAndPrevious, boolean useParens, boolean exportStrippedHtml, String modificationSite)`
	`203`	`+ public PeptideCol(ColumnInfo colInfo, boolean showNextAndPrevious, boolean useParens, boolean exportStrippedHtml, boolean highlightFixed, String modificationSite)`
`197`	`204`	`{`
`198`		`- super(colInfo);`
	`205`	`+ super(colInfo, highlightFixed);`
`199`	`206`	`_showNextAndPrevious = showNextAndPrevious;`
`200`	`207`	`_useParens = useParens;`
`201`	`208`	`_modificationSite = modificationSite;`
Original file line number	Diff line number	Diff line change
`@@ -76,7 +76,7 @@ public void writeCell(Sheet sheet, int column, int row, RenderContext ctx)`
`76`	`76`	`};`
`77`	`77`
`78`	`78`	`String chain = _col.getChainLabel(ctx);`
`79`		`- String chainPrefix = CrossLinkedPeptideDisplayColumn.getChainAbbreviation(chain);`
	`79`	`+ String chainPrefix = CrossLinkedPeptideDisplayColumn.getChainPrefix(chain);`
`80`	`80`	`if (!chainPrefix.isEmpty())`
`81`	`81`	`{`
`82`	`82`	`chainPrefix = chainPrefix + " ";`
Original file line number	Diff line number	Diff line change
`@@ -20,6 +20,8 @@`
`20`	`20`	`import org.junit.experimental.categories.Category;`
`21`	`21`	`import org.labkey.test.Locator;`
`22`	`22`
	`23`	`+import static org.junit.Assert.assertTrue;`
	`24`	`+`
`23`	`25`	`@Category({})`
`24`	`26`	`public class TargetedMSMAMTest extends TargetedMSTest`
`25`	`27`	`{`
`@@ -60,6 +62,9 @@ public void testSteps()`
`60`	`62`	`assertTextPresentInThisOrder("70-84", "325-333", "28-41", "190-196; 26-32");`
`61`	`63`	`assertTextPresentInThisOrder("(K)ASTEGVAIQGQQGTR(L)", "(K)AQYEDIANR(S)", "(K)SVTEQGAELSNEER(N)");`
`62`	`64`	`assertTextPresentInThisOrder("Carbamidomethyl Cysteine @ C157", "Carbamidomethyl Cysteine @ C245", "Carbamidomethyl Cysteine @ C94");`
	`65`	`+`
	`66`	`+ // Ensure that the Cystine isn't highlighted, as it's a fixed modification and that report doesn't want to call it out`
	`67`	`+ assertTrue(getHtmlSource().contains("(K)YLECSALTQR(G)"));`
`63`	`68`	`}`
`64`	`69`
`65`	`70`	`@Test`
`@@ -77,5 +82,8 @@ public void testCrossLinkedPeptideMap()`
`77`	`82`	`// Disulfide bonds`
`78`	`83`	`assertTextPresentInThisOrder("Q364-T369-D364/\nN366-T369-D364", "V121-S345-Q142/\nQ124-S345-Q142");`
`79`	`84`	`assertTextPresentInThisOrder("(A)LKPLALV(D)", "(G)AVVQDPA(Y)", "(F)YGEATSR(E)");`
	`85`	`+`
	`86`	`+ // Ensure that the highlighting is as expected for both crosslinking and modification`
	`87`	`+ assertTrue(getHtmlSource().contains("(Y)<span style=\"font-weight:bold;color:green;text-decoration:underline;\">Q</span><span style=\"font-weight:bold;text-decoration:underline;\">M</span><span style=\"font-weight:bold;color:green;\">N</span>(D)"));`
`80`	`88`	`}`
`81`	`89`	`}`