chore: only use precursor for peak difference creations

michaelwenk · michaelwenk · commit f69af0fe7328 · 2025-05-24T00:20:49.000+02:00
diff --git a/pkg/database/postgres.go b/pkg/database/postgres.go
@@ -5,7 +5,6 @@ import (
 	"errors"
 	"fmt"
 	"log"
-	"math"
 	"regexp"
 	"slices"
 	"strconv"
@@ -112,10 +111,10 @@ func (db *PostgresSQLDB) GetIndexes() []Index {
 	indexes = append(indexes, Index{IndexName: "browse_options_atomcount_index", TableName: "browse_options", Columns: []string{"atomcount"}})
 
 	indexes = append(indexes, Index{IndexName: "peak_differences_spectrum_id_index", TableName: "peak_differences", Columns: []string{"spectrum_id"}})
+	indexes = append(indexes, Index{IndexName: "peak_differences_peak_id_index", TableName: "peak_differences", Columns: []string{"peak_id"}})
+	indexes = append(indexes, Index{IndexName: "peak_differences_precursor_mass_id_index", TableName: "peak_differences", Columns: []string{"precursor_mass"}})
 	indexes = append(indexes, Index{IndexName: "peak_differences_difference_index", TableName: "peak_differences", Columns: []string{"difference"}})
-	indexes = append(indexes, Index{IndexName: "peak_differences_peak1_id_index", TableName: "peak_differences", Columns: []string{"peak1_id"}})
-	indexes = append(indexes, Index{IndexName: "peak_differences_peak2_id_index", TableName: "peak_differences", Columns: []string{"peak2_id"}})
-	indexes = append(indexes, Index{IndexName: "peak_differences_min_rel_intensity_index", TableName: "peak_differences", Columns: []string{"min_rel_intensity"}})
+	indexes = append(indexes, Index{IndexName: "peak_differences_rel_intensity_index", TableName: "peak_differences", Columns: []string{"rel_intensity"}})
 
 	indexes = append(indexes, Index{IndexName: "records_massbank_id_index", TableName: "records", Columns: []string{"massbank_id"}})
 	indexes = append(indexes, Index{IndexName: "records_accession_index", TableName: "records", Columns: []string{"accession"}})
@@ -1147,10 +1146,10 @@ func (p *PostgresSQLDB) NeutralLossSearch(neutralLoss *[]float64, tolerance *flo
 		for i := 0; i < neutralLossesCount; i++ {
 			parameters = append(parameters, strconv.FormatFloat((*neutralLoss)[i]-*tolerance, 'f', -1, 64))
 			parameters = append(parameters, strconv.FormatFloat((*neutralLoss)[i]+*tolerance, 'f', -1, 64))
-			with = with + "t" + strconv.Itoa(i+1) + " AS (SELECT spectrum_id, array_agg(ARRAY[peak1_id, peak2_id]) AS agg FROM peak_differences WHERE difference BETWEEN $" + strconv.Itoa(len(parameters)-1) + " AND $" + strconv.Itoa(len(parameters))
+			with = with + "t" + strconv.Itoa(i+1) + " AS (SELECT spectrum_id, array_agg(ARRAY[peak_id, precursor_mass]) AS agg FROM peak_differences WHERE difference BETWEEN $" + strconv.Itoa(len(parameters)-1) + " AND $" + strconv.Itoa(len(parameters))
 			if minRelIntensity != nil {
 				parameters = append(parameters, strconv.FormatInt(*minRelIntensity, 10))
-				with = with + " AND min_rel_intensity >= $" + strconv.Itoa(len(parameters))
+				with = with + " AND rel_intensity >= $" + strconv.Itoa(len(parameters))
 			}
 			with = with + " GROUP BY spectrum_id)"
 			if i > 0 {
@@ -1167,6 +1166,7 @@ func (p *PostgresSQLDB) NeutralLossSearch(neutralLoss *[]float64, tolerance *flo
 		selectAggregations = selectAggregations + ")::json"
 
 		query = with + " SELECT " + selectAggregations + ", browse_options.accession, browse_options.atomcount " + from + " JOIN spectrum ON spectrum.id = t1.spectrum_id JOIN browse_options ON browse_options.massbank_id = spectrum.massbank_id;"
+
 		stmt, err := p.database.Prepare(query)
 		if err != nil {
 			return nil, nil, nil, err
@@ -1880,40 +1880,43 @@ func (p *PostgresSQLDB) AddRecord(record *massbank.MassBank2, metaDataId string,
 		return err
 	}
 
-	if (msType == "MS2" || msType == "MS3" || msType == "MS4") && *record.Peak.NumPeak > 1 {
-		var sb strings.Builder
-		sb.WriteString("INSERT INTO peak_differences (spectrum_id, difference, peak1_id, peak2_id, min_rel_intensity) VALUES")
-		var diff float64
-		var toInsert = false
-		for i := 0; i < len(insertedPeaks.Id); i++ {
-			for j := i + 1; j < len(insertedPeaks.Id); j++ {
-				if insertedPeaks.Mz[i] >= insertedPeaks.Mz[j] {
-					diff = insertedPeaks.Mz[i] - insertedPeaks.Mz[j]
-				} else {
-					diff = insertedPeaks.Mz[j] - insertedPeaks.Mz[i]
-				}
-				if diff > 11.5 {
-					sb.WriteString(fmt.Sprintf(" (%d, %f, %d, %d, %f)", spectrumId, diff, insertedPeaks.Id[i], insertedPeaks.Id[j], math.Min(float64(insertedPeaks.Rel[i]), float64(insertedPeaks.Rel[j]))))
-					if j < len(insertedPeaks.Id)-1 {
+	if (msType == "MS2" || msType == "MS3" || msType == "MS4") && *record.Peak.NumPeak > 1 && record.MassSpectrometry.FocusedIon != nil {
+		var precursorStr = ""
+		for _, subProp := range *record.MassSpectrometry.FocusedIon {
+			if subProp.Subtag == "PRECURSOR_M/Z" {
+				precursorStr = subProp.Value
+				break
+			}
+		}
+		if precursorStr != "" {
+			precursorMass, err := strconv.ParseFloat(precursorStr, 64)
+			if err == nil {
+				var sb strings.Builder
+				sb.WriteString("INSERT INTO peak_differences (spectrum_id, peak_id, precursor_mass, difference, rel_intensity) VALUES")
+				var diff float64
+				var toInsert = false
+				for i := 0; i < len(insertedPeaks.Id); i++ {
+					if insertedPeaks.Mz[i] >= precursorMass {
+						diff = insertedPeaks.Mz[i] - precursorMass
+					} else {
+						diff = precursorMass - insertedPeaks.Mz[i]
+					}
+					sb.WriteString(fmt.Sprintf(" (%d, %d, %f, %f, %f)", spectrumId, insertedPeaks.Id[i], precursorMass, diff, float64(insertedPeaks.Rel[i])))
+					if i < len(insertedPeaks.Id)-1 {
 						sb.WriteString(",")
 					}
 					toInsert = true
-				} else {
-					toInsert = false
 				}
-			}
-			if toInsert && i < len(insertedPeaks.Id)-2 {
-				sb.WriteString(",")
-			}
-		}
-		if toInsert {
-			sb.WriteString(";")
-			_, err = tx.Exec(sb.String())
-			if err != nil {
-				if err2 := tx.Rollback(); err2 != nil {
-					return errors.New("Could not rollback after error: " + err2.Error() + "\n:" + err.Error())
+				if toInsert {
+					sb.WriteString(";")
+					_, err = tx.Exec(sb.String())
+					if err != nil {
+						if err2 := tx.Rollback(); err2 != nil {
+							return errors.New("Could not rollback after error: " + err2.Error() + "\n:" + err.Error())
+						}
+						return err
+					}
 				}
-				return err
 			}
 		}
 	}
@@ -1936,6 +1939,7 @@ func (p *PostgresSQLDB) AddRecord(record *massbank.MassBank2, metaDataId string,
 		if err2 := tx.Rollback(); err2 != nil {
 			return errors.New("Could not rollback after error: " + err2.Error() + "\n:" + err.Error())
 		}
+		return err
 	}
 
 	err = tx.Commit()
@@ -1955,13 +1959,19 @@ func (p *PostgresSQLDB) AddRecords(records []*massbank.MassBank2, metaDataId str
 		return errors.New("records and mb3RecordJsons must have the same length")
 	}
 
+	start := time.Now()
+
 	for i, record := range records {
 		err := p.AddRecord(record, metaDataId, mb3RecordJsons[i])
 		if err != nil {
 			return err
 		}
 	}
 
+	elapsed := time.Since(start)
+	fmt.Printf("\n -> AddRecord function took %s", elapsed)
+	fmt.Println()
+
 	return nil
 }
 
@@ -2163,11 +2173,11 @@ func (p *PostgresSQLDB) Init() error {
 		);
 
 		CREATE TABLE peak_differences (
-			spectrum_id INT NOT NULL REFERENCES spectrum(id) ON UPDATE CASCADE ON DELETE CASCADE,
-			difference FLOAT NOT NULL,	
-			peak1_id INT NOT NULL REFERENCES peak(id) ON UPDATE CASCADE ON DELETE CASCADE,
-			peak2_id INT NOT NULL REFERENCES peak(id) ON UPDATE CASCADE ON DELETE CASCADE,
-			min_rel_intensity FLOAT NOT NULL
+			spectrum_id INT NOT NULL REFERENCES spectrum(id) ON UPDATE CASCADE ON DELETE CASCADE,			
+			peak_id INT NOT NULL REFERENCES peak(id) ON UPDATE CASCADE ON DELETE CASCADE,
+			precursor_mass FLOAT NOT NULL,
+			difference FLOAT NOT NULL,			
+			rel_intensity FLOAT NOT NULL
 		);
 
 		CREATE TABLE IF NOT EXISTS records (
diff --git a/pkg/mb3dbtool/main.go b/pkg/mb3dbtool/main.go
@@ -90,6 +90,7 @@ func main() {
 
 		err = db.AddRecords(mbfiles, metaId, mb3RecordStrings)
 		if err != nil {
+			println("Could not add records: " + err.Error())
 			panic(err)
 		}
 
diff --git a/web-frontend/src/elements/basic/Chart.tsx b/web-frontend/src/elements/basic/Chart.tsx
@@ -125,10 +125,8 @@ function Chart({
 
   const filteredNeutralLossData = useMemo(
     () =>
-      neutralLossData.filter(
-        (nl) =>
-          filteredPeakData.some((p) => p.id === nl.peak1_id) &&
-          filteredPeakData.some((p) => p.id === nl.peak2_id),
+      neutralLossData.filter((nl) =>
+        filteredPeakData.some((p) => p.id === nl.peak_id),
       ),
     [filteredPeakData, neutralLossData],
   );
@@ -401,7 +399,6 @@ function Chart({
             xScale={xScale}
             yScale={yScale}
             showLabel={isShowLabel}
-            strokeColour="red"
             disableOnHover={disableOnHover}
           />
         ))
diff --git a/web-frontend/src/elements/basic/ChartElement.tsx b/web-frontend/src/elements/basic/ChartElement.tsx
@@ -20,7 +20,7 @@ function ChartElement({
   xScale,
   yScale,
   showLabel = false,
-  strokeColour = 'red',
+  strokeColour,
   disableOnHover = false,
 }: InputProps) {
   const highlight = useHighlight([pd.id]);
@@ -74,27 +74,44 @@ function ChartElement({
         style={
           highlight.isActive
             ? { opacity: 1, stroke: 'black', strokeWidth: 2 }
-            : { stroke: strokeColour }
+            : {
+                stroke: strokeColour
+                  ? strokeColour
+                  : pd.id === 'precursor'
+                    ? 'blue'
+                    : 'red',
+              }
         }
       >
         <line
           x1={xScaled}
           x2={xScaled}
           y1={yScale.range()[0]}
-          y2={yScale(pd.rel || 0)}
+          y2={yScale(pd.rel ?? 0)}
         />
         {highlight.isActive && (
-          <circle cx={xScaled} cy={yScale(pd.rel || 0)} r={3} />
+          <circle cx={xScaled} cy={yScale(pd.rel ?? 0)} r={3} />
         )}
-        {((!disableShowLabel && showLabel) || highlight.isActive) && (
+        {pd.id === 'precursor' ? (
           <text
             className="hover-label"
-            transform={`translate(${xScale(pd.mz)} ${
-              pd.rel < 0 ? yScale(pd.rel || 0) + 20 : yScale(pd.rel || 0) - 10
-            }) rotate(-30)`}
+            transform={`translate(${xScale(pd.mz) - 50} ${
+              pd.rel < 0 ? yScale(pd.rel ?? 0) + 20 : yScale(pd.rel ?? 0) - 10
+            })`}
           >
-            {pd.mz.toFixed(4)}
+            {'precursor: ' + pd.mz.toFixed(4)}
           </text>
+        ) : (
+          ((!disableShowLabel && showLabel) || highlight.isActive) && (
+            <text
+              className="hover-label"
+              transform={`translate(${xScale(pd.mz)} ${
+                pd.rel < 0 ? yScale(pd.rel ?? 0) + 20 : yScale(pd.rel ?? 0) - 10
+              }) rotate(-30)`}
+            >
+              {pd.mz.toFixed(4)}
+            </text>
+          )
         )}
       </g>
     ),
@@ -104,6 +121,7 @@ function ChartElement({
       handleOnMouseEnter,
       handleOnMouseLeave,
       highlight.isActive,
+      pd.id,
       pd.mz,
       pd.rel,
       showLabel,
diff --git a/web-frontend/src/elements/common/Resizable.tsx b/web-frontend/src/elements/common/Resizable.tsx
@@ -8,6 +8,7 @@ import { Content } from 'antd/es/layout/layout';
 import { Splitter, Tabs, TabsProps } from 'antd';
 import NeutralLossTable from '../record/NeutralLossTable';
 import NeutralLoss from '../../types/peak/NeutralLoss';
+import getRecordPeakListWithPrecursor from '../../utils/getRecordPeakListWithPrecursor';
 
 const sidebarWidth = 7;
 const tabsHeight = 55;
@@ -44,7 +45,7 @@ function Resizable({
   }, [minPeakTableWith, width]);
 
   const [filteredPeakData, setFilteredPeakData] = useState<Peak[]>(
-    record.peak.peak.values,
+    getRecordPeakListWithPrecursor(record),
   );
 
   const [filteredPeakData2, setFilteredPeakData2] = useState<
@@ -82,7 +83,7 @@ function Resizable({
   const chart = useMemo(
     () => (
       <Chart
-        peakData={record.peak.peak.values}
+        peakData={getRecordPeakListWithPrecursor(record)}
         peakData2={record2 ? record2.peak.peak.values : undefined}
         neutralLossData={record.peak.neutral_loss}
         onZoom={handleOnZoom}
@@ -91,15 +92,7 @@ function Resizable({
         disableExport={disableExport}
       />
     ),
-    [
-      chartWidth,
-      disableExport,
-      handleOnZoom,
-      height,
-      record.peak.neutral_loss,
-      record.peak.peak.values,
-      record2,
-    ],
+    [chartWidth, disableExport, handleOnZoom, height, record, record2],
   );
 
   const peakTable = useMemo(() => {
diff --git a/web-frontend/src/elements/record/NeutralLossTable.tsx b/web-frontend/src/elements/record/NeutralLossTable.tsx
@@ -25,10 +25,10 @@ function NeutralLossTable({ neutralLosses, peaks, width, height }: InputProps) {
         .sort((nl1, nl2) => nl1.difference - nl2.difference)
         .map((nl) => {
           return {
-            key: nl.peak1_id + '_' + nl.peak2_id,
+            key: nl.peak_id + '_' + nl.precursor_mass,
             difference: nl.difference.toFixed(4),
-            peak1: peaks.find((p) => p.id === nl.peak1_id)?.mz.toFixed(4) ?? '',
-            peak2: peaks.find((p) => p.id === nl.peak2_id)?.mz.toFixed(4) ?? '',
+            peak1: peaks.find((p) => p.id === nl.peak_id)?.mz.toFixed(4) ?? '',
+            peak2: nl.precursor_mass.toFixed(4) ?? '',
           } as NeutralLossTableDataType;
         }),
     [neutralLosses, peaks],
@@ -39,7 +39,12 @@ function NeutralLossTable({ neutralLosses, peaks, width, height }: InputProps) {
       setActiveKey(key);
       highlightData.dispatch({
         type: 'SHOW',
-        payload: { convertedHighlights: new Set<string>(key.split('_')) },
+        payload: {
+          convertedHighlights: new Set<string>([
+            key.split('_')[0],
+            'precursor',
+          ]),
+        },
       });
     },
     [highlightData],
@@ -50,7 +55,12 @@ function NeutralLossTable({ neutralLosses, peaks, width, height }: InputProps) {
       setActiveKey(undefined);
       highlightData.dispatch({
         type: 'HIDE',
-        payload: { convertedHighlights: new Set<string>(key.split('_')) },
+        payload: {
+          convertedHighlights: new Set<string>([
+            key.split('_')[0],
+            'precursor',
+          ]),
+        },
       });
     },
     [highlightData],
diff --git a/web-frontend/src/elements/record/PeakTable.tsx b/web-frontend/src/elements/record/PeakTable.tsx
@@ -52,9 +52,9 @@ function PeakTable({ peaks, width, height }: InputProps) {
         (p) =>
           ({
             key: p.id,
-            mz: p.mz ? p.mz.toFixed(4) : 0,
-            intensity: p.intensity ? p.intensity.toFixed(1) : 0,
-            rel: p.rel ? p.rel : 0,
+            mz: p.mz ? p.mz.toFixed(4) : '',
+            intensity: p.intensity ? p.intensity.toFixed(1) : '',
+            rel: p.rel ? p.rel : '',
           }) as PeakTableDataType,
       ),
     [peaks],
diff --git a/web-frontend/src/elements/routes/pages/search/SpectralHitsViewComponent.tsx b/web-frontend/src/elements/routes/pages/search/SpectralHitsViewComponent.tsx
@@ -27,22 +27,19 @@ function SpectralHitsViewComponent({
     const record = { peak: { peak: { values: reference } } } as Record;
     if (hit.peakPairs && hit.peakPairs.length > 0) {
       const _neutralLossPeakPairs = hit.peakPairs?.map((nlp) => {
-        const [peak1_id, peak2_id] = nlp.split('_').map((p) => 'peak-' + p);
-        return { peak1_id, peak2_id };
+        const split = nlp.split('_');
+        return { peakId: 'peak-' + split[0], precursor_mass: Number(split[1]) };
       });
       const neutralLossData: NeutralLoss[] = [];
       for (const nlp of _neutralLossPeakPairs) {
-        const peak1 = hit.record.peak.peak.values.find(
-          (p) => p.id === nlp.peak1_id,
+        const peak = hit.record.peak.peak.values.find(
+          (p: Peak) => p.id === nlp.peakId,
         );
-        const peak2 = hit.record.peak.peak.values.find(
-          (p) => p.id === nlp.peak2_id,
-        );
-        if (peak1 && peak2) {
-          const difference = Math.abs(peak1.mz - peak2.mz);
+        if (peak) {
+          const difference = Math.abs(peak.mz - nlp.precursor_mass);
           neutralLossData.push({
-            peak1_id: peak1.id,
-            peak2_id: peak2.id,
+            peak_id: peak.id,
+            precursor_mass: nlp.precursor_mass,
             difference,
           });
         }
diff --git a/web-frontend/src/types/peak/NeutralLoss.d.ts b/web-frontend/src/types/peak/NeutralLoss.d.ts
@@ -1,7 +1,7 @@
 interface NeutralLoss {
   difference: number;
-  peak1_id: string | number;
-  peak2_id: string | number;
+  peak_id: string | number;
+  precursor_mass: number;
 }
 
 export default NeutralLoss;
diff --git a/web-frontend/src/utils/getRecordPeakListWithPrecursor.ts b/web-frontend/src/utils/getRecordPeakListWithPrecursor.ts

Original file line number	Diff line number	Diff line change
`@@ -90,6 +90,7 @@ func main() {`
`90`	`90`
`91`	`91`	`err = db.AddRecords(mbfiles, metaId, mb3RecordStrings)`
`92`	`92`	`if err != nil {`
	`93`	`+ println("Could not add records: " + err.Error())`
`93`	`94`	`panic(err)`
`94`	`95`	`}`
`95`	`96`
Original file line number	Diff line number	Diff line change
`@@ -1,7 +1,7 @@`
`1`	`1`	`interface NeutralLoss {`
`2`	`2`	`difference: number;`
`3`		`- peak1_id: string \| number;`
`4`		`- peak2_id: string \| number;`
	`3`	`+ peak_id: string \| number;`
	`4`	`+ precursor_mass: number;`
`5`	`5`	`}`
`6`	`6`
`7`	`7`	`export default NeutralLoss;`