From 2254fc9c76828f91e94918e6e89c6e55a14a1ed4 Mon Sep 17 00:00:00 2001
From: Yamei Deng <aimee.d.ym@gmail.com>
Date: Thu, 18 Jan 2024 23:54:32 -0500
Subject: [PATCH] export score_all attribute to a new column in psm.tsv

---
 Makefile          | 2 +-
 lib/id/pep.go     | 4 +++-
 lib/rep/psm.go    | 7 ++++---
 lib/spc/pepxml.go | 1 +
 4 files changed, 9 insertions(+), 5 deletions(-)

diff --git a/Makefile b/Makefile
index 233fffe4..069a29de 100644
--- a/Makefile
+++ b/Makefile
@@ -7,7 +7,7 @@ VERSION = $(shell date +%Y%m%d)
 BUILD = $(shell  date +%Y%m%d%H%M)
 
 TAG = v5.1.1
-RC = RC02
+RC = RC03
 
 LDFLAGS = -ldflags "-w -s -extldflags -static -X main.version=${TAG} -X main.build=${BUILD}"
 
diff --git a/lib/id/pep.go b/lib/id/pep.go
index fa6cae0a..4c570f77 100644
--- a/lib/id/pep.go
+++ b/lib/id/pep.go
@@ -109,6 +109,7 @@ type MSFraggerLoc struct {
 	MSFraggerLocalizationScoreWithPTM    string
 	MSFraggerLocalizationScoreWithoutPTM string
 	MSFraggerLocalizationScores          string
+	MSFraggerScoreAll                    string
 }
 
 // PepIDList is a list of PeptideSpectrumMatch
@@ -493,7 +494,8 @@ func processSpectrumQuery(sq spc.SpectrumQuery, mods mod.Modifications, decoyTag
 				MSFragerLocalization:                 i.PTMResult.LocalizationPeptide,
 				MSFraggerLocalizationScoreWithPTM:    i.PTMResult.BestScoreWithPTM,
 				MSFraggerLocalizationScoreWithoutPTM: i.PTMResult.ScoreWithoutPTM,
-				MSFraggerLocalizationScores:          i.PTMResult.LocalizationScores}
+				MSFraggerLocalizationScores:          i.PTMResult.LocalizationScores,
+				MSFraggerScoreAll:                    i.PTMResult.ScoreAll}
 		}
 
 		// to be able to accept multiple entries with the same spectrum name, we fuse the
diff --git a/lib/rep/psm.go b/lib/rep/psm.go
index d089b92e..1aa7836f 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 Score without Delta Mass\tLocalization Scores"
+		header += "\tMSFragger Localization\tBest Score with Delta Mass\tBest Score without Delta Mass\tLocalization Scores\tScore All"
 	}
 
 	if hasIonMob {
@@ -618,12 +618,13 @@ 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",
+			line = fmt.Sprintf("%s\t%s\t%s\t%s\t%s\t%s",
 				line,
 				MSFraggerLoc.MSFragerLocalization,
 				MSFraggerLoc.MSFraggerLocalizationScoreWithPTM,
 				MSFraggerLoc.MSFraggerLocalizationScoreWithoutPTM,
-				MSFraggerLoc.MSFraggerLocalizationScores)
+				MSFraggerLoc.MSFraggerLocalizationScores,
+				MSFraggerLoc.MSFraggerScoreAll)
 		}
 
 		if hasIonMob {
diff --git a/lib/spc/pepxml.go b/lib/spc/pepxml.go
index b9f77b74..0d43975d 100644
--- a/lib/spc/pepxml.go
+++ b/lib/spc/pepxml.go
@@ -220,4 +220,5 @@ type PTMResult struct {
 	ScoreWithoutPTM     string `xml:"score_without_ptm,attr"`
 	LocalizationPeptide string `xml:"localization_peptide,attr"`
 	LocalizationScores  string `xml:"localization_scores,attr"`
+	ScoreAll            string `xml:"scores_all,attr"`
 }