From 2224d6880deda78eb4b20f322ad4e0e7ab4b5d78 Mon Sep 17 00:00:00 2001
From: Fengchao <fcyucn@gmail.com>
Date: Sun, 28 Jan 2024 17:04:26 -0500
Subject: [PATCH] Add "best score delta mass only" score.

---
 lib/id/pep.go     | 2 ++
 lib/rep/psm.go    | 7 ++++---
 lib/spc/pepxml.go | 1 +
 3 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/lib/id/pep.go b/lib/id/pep.go
index c373a8fb..73d522b7 100644
--- a/lib/id/pep.go
+++ b/lib/id/pep.go
@@ -112,6 +112,7 @@ type MSFraggerLoc struct {
 	MSFraggerLocalizationScores                 string
 	MSFraggerScoreAll                           string
 	MSFraggerScoreOnlyShifted                   string
+	MSFraggerBestScoreOnlyShifted               string
 	MSFraggerLocalizationScoreWithPTMIons       string
 	MSFraggerLocalizationSecondScoreWithPTMIons string
 	MSFraggerLocalizationScoreWithoutPTMIons    string
@@ -505,6 +506,7 @@ func processSpectrumQuery(sq spc.SpectrumQuery, mods mod.Modifications, decoyTag
 				MSFraggerLocalizationScores:                 i.PTMResult.LocalizationScores,
 				MSFraggerScoreAll:                           i.PTMResult.ScoreAll,
 				MSFraggerScoreOnlyShifted:                   i.PTMResult.ScoreOnlyShifted,
+				MSFraggerBestScoreOnlyShifted:               i.PTMResult.BestScoreOnlyShifted,
 				MSFraggerLocalizationScoreWithPTMIons:       i.PTMResult.BestScoreWithPTMIons,
 				MSFraggerLocalizationSecondScoreWithPTMIons: i.PTMResult.SecondBestScoreWithPTMIons,
 				MSFraggerLocalizationScoreWithoutPTMIons:    i.PTMResult.ScoreWithoutPTMIons,
diff --git a/lib/rep/psm.go b/lib/rep/psm.go
index f9a9cfd3..e24efb14 100644
--- a/lib/rep/psm.go
+++ b/lib/rep/psm.go
@@ -236,7 +236,7 @@ func (evi PSMEvidenceList) PSMReport(workspace, brand, decoyTag string, channels
 	}
 
 	if hasLoc {
-		header += "\tMSFragger Localization\tBest Score with Delta Mass\tBest Matched Ions with Delta Mass\tSecond Best Score with Delta Mass\tSecond Best Matched Ions with Delta Mass\tBest Score without Delta Mass\tMatched Ions without Delta mass\tLocalization Scores\tScore All\tMatched Ions All\tScore Delta Mass Only\tMatched Ions Delta Mass Only"
+		header += "\tMSFragger Localization\tBest Score with Delta Mass\tBest Matched Ions with Delta Mass\tSecond Best Score with Delta Mass\tSecond Best Matched Ions with Delta Mass\tBest Score without Delta Mass\tMatched Ions without Delta mass\tLocalization Scores\tScore All\tMatched Ions All\tScore Delta Mass Only\tMatched Ions Delta Mass Only\tBest Score Delta Mass Only"
 	}
 
 	if hasIonMob {
@@ -618,7 +618,7 @@ func (evi PSMEvidenceList) PSMReport(workspace, brand, decoyTag string, channels
 			if MSFraggerLoc == nil {
 				MSFraggerLoc = &id.MSFraggerLoc{}
 			}
-			line = fmt.Sprintf("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s",
+			line = fmt.Sprintf("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s",
 				line,
 				MSFraggerLoc.MSFragerLocalization,
 				MSFraggerLoc.MSFraggerLocalizationScoreWithPTM,
@@ -631,7 +631,8 @@ func (evi PSMEvidenceList) PSMReport(workspace, brand, decoyTag string, channels
 				MSFraggerLoc.MSFraggerScoreAll,
 				MSFraggerLoc.MSFraggerScoreAllIons,
 				MSFraggerLoc.MSFraggerScoreOnlyShifted,
-				MSFraggerLoc.MSFraggerScoreOnlyShiftedIons)
+				MSFraggerLoc.MSFraggerScoreOnlyShiftedIons,
+				MSFraggerLoc.MSFraggerBestScoreOnlyShifted)
 		}
 
 		if hasIonMob {
diff --git a/lib/spc/pepxml.go b/lib/spc/pepxml.go
index f770103f..98d32147 100644
--- a/lib/spc/pepxml.go
+++ b/lib/spc/pepxml.go
@@ -228,4 +228,5 @@ type PTMResult struct {
 	ScoreAllIons               string `xml:"score_all_matched_ions,attr"`
 	ScoreOnlyShifted           string `xml:"score_only_shifted,attr"`
 	ScoreOnlyShiftedIons       string `xml:"score_only_shifted_matched_ions,attr"`
+	BestScoreOnlyShifted       string `xml:"best_score_only_shifted,attr"`
 }