From 1abf1826fb7b31c479ce8531863f88680f1848a9 Mon Sep 17 00:00:00 2001
From: Fengchao <fcyucn@gmail.com>
Date: Sun, 21 Jan 2024 16:41:40 -0500
Subject: [PATCH] Propagate new localization scores to psm.tsv

---
 lib/id/pep.go     | 4 ++++
 lib/rep/psm.go    | 8 +++++---
 lib/spc/pepxml.go | 2 ++
 3 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/lib/id/pep.go b/lib/id/pep.go
index eef2f4e5..c373a8fb 100644
--- a/lib/id/pep.go
+++ b/lib/id/pep.go
@@ -111,10 +111,12 @@ type MSFraggerLoc struct {
 	MSFraggerLocalizationScoreWithoutPTM        string
 	MSFraggerLocalizationScores                 string
 	MSFraggerScoreAll                           string
+	MSFraggerScoreOnlyShifted                   string
 	MSFraggerLocalizationScoreWithPTMIons       string
 	MSFraggerLocalizationSecondScoreWithPTMIons string
 	MSFraggerLocalizationScoreWithoutPTMIons    string
 	MSFraggerScoreAllIons                       string
+	MSFraggerScoreOnlyShiftedIons               string
 }
 
 // PepIDList is a list of PeptideSpectrumMatch
@@ -502,10 +504,12 @@ func processSpectrumQuery(sq spc.SpectrumQuery, mods mod.Modifications, decoyTag
 				MSFraggerLocalizationScoreWithoutPTM:        i.PTMResult.ScoreWithoutPTM,
 				MSFraggerLocalizationScores:                 i.PTMResult.LocalizationScores,
 				MSFraggerScoreAll:                           i.PTMResult.ScoreAll,
+				MSFraggerScoreOnlyShifted:                   i.PTMResult.ScoreOnlyShifted,
 				MSFraggerLocalizationScoreWithPTMIons:       i.PTMResult.BestScoreWithPTMIons,
 				MSFraggerLocalizationSecondScoreWithPTMIons: i.PTMResult.SecondBestScoreWithPTMIons,
 				MSFraggerLocalizationScoreWithoutPTMIons:    i.PTMResult.ScoreWithoutPTMIons,
 				MSFraggerScoreAllIons:                       i.PTMResult.ScoreAllIons,
+				MSFraggerScoreOnlyShiftedIons:               i.PTMResult.ScoreOnlyShiftedIons,
 			}
 		}
 
diff --git a/lib/rep/psm.go b/lib/rep/psm.go
index 48f2a7c8..f9a9cfd3 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"
+		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"
 	}
 
 	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",
+			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,
 				MSFraggerLoc.MSFragerLocalization,
 				MSFraggerLoc.MSFraggerLocalizationScoreWithPTM,
@@ -629,7 +629,9 @@ func (evi PSMEvidenceList) PSMReport(workspace, brand, decoyTag string, channels
 				MSFraggerLoc.MSFraggerLocalizationScoreWithoutPTMIons,
 				MSFraggerLoc.MSFraggerLocalizationScores,
 				MSFraggerLoc.MSFraggerScoreAll,
-				MSFraggerLoc.MSFraggerScoreAllIons)
+				MSFraggerLoc.MSFraggerScoreAllIons,
+				MSFraggerLoc.MSFraggerScoreOnlyShifted,
+				MSFraggerLoc.MSFraggerScoreOnlyShiftedIons)
 		}
 
 		if hasIonMob {
diff --git a/lib/spc/pepxml.go b/lib/spc/pepxml.go
index 350881e1..f770103f 100644
--- a/lib/spc/pepxml.go
+++ b/lib/spc/pepxml.go
@@ -226,4 +226,6 @@ type PTMResult struct {
 	LocalizationScores         string `xml:"localization_scores,attr"`
 	ScoreAll                   string `xml:"score_all,attr"`
 	ScoreAllIons               string `xml:"score_all_matched_ions,attr"`
+	ScoreOnlyShifted           string `xml:"score_only_shifted,attr"`
+	ScoreOnlyShiftedIons       string `xml:"score_only_shifted_matched_ions,attr"`
 }