From ba35e16676c78887972cee9cfd6299282ece15e5 Mon Sep 17 00:00:00 2001 From: VeroDup Date: Mon, 2 Aug 2021 11:59:49 +0200 Subject: [PATCH] Revert "PM-mascot-parser: parse SCANS field from MGF data" : Not in release version This reverts commit c965d939 --- .../module/parser/mascot/MascotResultFile.scala | 13 ++----------- 1 file changed, 2 insertions(+), 11 deletions(-) diff --git a/pm-mascot-parser/src/main/scala/fr/proline/module/parser/mascot/MascotResultFile.scala b/pm-mascot-parser/src/main/scala/fr/proline/module/parser/mascot/MascotResultFile.scala index 5b9cbd54..11fcb560 100644 --- a/pm-mascot-parser/src/main/scala/fr/proline/module/parser/mascot/MascotResultFile.scala +++ b/pm-mascot-parser/src/main/scala/fr/proline/module/parser/mascot/MascotResultFile.scala @@ -767,7 +767,6 @@ class MascotResultFile( object MascotQuerySection { val QUERY_NUM = "query_num" val TITLE = "title" - val SCANS = "scans" val RTINSECONDS = "rtinseconds" val INDEX = "index" val CHARGE = "charge" @@ -785,14 +784,6 @@ class MascotResultFile( import MascotQuerySection._ lazy val queryNumber = underlyingMap(QUERY_NUM).toInt - - lazy val scanRangeOpt: Option[(Int, Int)] = if (!underlyingMap.contains(SCANS)) None - else { - val scansAsStr = underlyingMap(SCANS) - val scans = scansAsStr.split(",").map( _.split("-") ) - Some((scans.head.head.trim.toInt, scans.last.last.trim.toInt)) - } - lazy val rtRangeInSeconds: Option[(Float, Float)] = if (!underlyingMap.contains(RTINSECONDS)) None else { val rtInSecondsAsStr = underlyingMap(RTINSECONDS) @@ -886,8 +877,8 @@ class MascotResultFile( precursorCharge = msq.charge, firstCycle = toIntOrZero(specTitleFieldMap.getOrElse(titleFields.FIRST_CYCLE, 0)), lastCycle = toIntOrZero(specTitleFieldMap.getOrElse(titleFields.LAST_CYCLE, 0)), - firstScan = toIntOrZero(specTitleFieldMap.getOrElse(titleFields.FIRST_SCAN, scanRangeOpt.map(_._1).getOrElse(0))), - lastScan = toIntOrZero(specTitleFieldMap.getOrElse(titleFields.LAST_SCAN, scanRangeOpt.map(_._2).getOrElse(0))), + firstScan = toIntOrZero(specTitleFieldMap.getOrElse(titleFields.FIRST_SCAN, 0)), + lastScan = toIntOrZero(specTitleFieldMap.getOrElse(titleFields.LAST_SCAN, 0)), firstTime = toFloatOrMinusOne(specTitleFieldMap.getOrElse(titleFields.FIRST_TIME, firstRT)), lastTime = toFloatOrMinusOne(specTitleFieldMap.getOrElse(titleFields.LAST_TIME, lastRT)), mozList = Some(sortedMozList),