[Sashimi-commit] SF.net SVN: sashimi:[9470] trunk/trans_proteomic_ pipeline/src/Visualization/Comet/plot-msms/plot-msms-js.cpp

[<en...@us...>]

Revision: 9470
          http://sourceforge.net/p/sashimi/code/9470
Author:   eng_jk
Date:     2025-12-08 19:41:23 +0000 (Mon, 08 Dec 2025)
Log Message:
-----------
Correct parsing of MS1 peaks for mzML files with ion mobility dimension.

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/plot-msms-js.cpp

Modified: trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/plot-msms-js.cpp
===================================================================
--- trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/plot-msms-js.cpp	2025-04-30 00:57:04 UTC (rev 9469)
+++ trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/plot-msms-js.cpp	2025-12-08 19:41:23 UTC (rev 9470)
@@ -1556,7 +1556,7 @@
    }
 
    if (scanHeaderMS.msLevel == (scanHeader.msLevel - 1))
-    {
+   {
       RAMPREAL *pPeaks;
       int n = 0;
       int bFirstDataPoint=1;
@@ -1565,19 +1565,23 @@
       double dLowMass = scanHeader.precursorMZ - 0.25;
       double dHighMass = scanHeader.precursorMZ + 0.25;
       
+      RAMPREAL fMass;
+      RAMPREAL fInten;
+      RAMPREAL fIonMob;
+
       // Open a scan
       pPeaks = readPeaks(fp_, index_[iScanNum]);
       printf("\nms1peaks = [");
       while (pPeaks != NULL && pPeaks[n] != -1)
-       {
-	 RAMPREAL fMass;
-	 RAMPREAL fInten;
-	 
-	 fMass = pPeaks[n];
+      {
+         fMass = pPeaks[n];
          n++;
          fInten = pPeaks[n];
          n++;
 
+         if ((fp_->fileType == 3 || fp_->fileType == 1) && fp_->mzML->getIonMobility())
+            fIonMob=pPeaks[n++];
+
          if (fInten > 0.0)
          {
             if (dLowMass<fMass && fMass<dHighMass)
@@ -1602,10 +1606,10 @@
 
       printf("\nms1scanLabel = \"%d, RT %0.2f\";\n", iScanNum, scanHeaderMS.retentionTime);
       pEnvironment.iMS1Scan = iScanNum;
-  }
+   }
    else
    {
-     printf("\nms1scanLabel = \" %d is not a valid precursor scan!\";\n",iScanNum);
+      printf("\nms1scanLabel = \" %d is not a valid precursor scan!\";\n",iScanNum);
       printf("ms1peaks= [[0.0,0.0]];\n");
    }
 }

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