From 7837bf00730cab406c76ee5b817a3a35ffc8e9f4 Mon Sep 17 00:00:00 2001
From: Fengchao <fyuab@connect.ust.hk>
Date: Tue, 2 Oct 2018 09:35:29 +0800
Subject: [PATCH] Eliminate additional "" from the text columns.

---
 src/main/java/proteomics/ECL2.java | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/main/java/proteomics/ECL2.java b/src/main/java/proteomics/ECL2.java
index d946064..9331c34 100644
--- a/src/main/java/proteomics/ECL2.java
+++ b/src/main/java/proteomics/ECL2.java
@@ -331,29 +331,29 @@ private static void saveTargetResult(Map<String, CalFDR.Entry> result, Map<Strin
                 if (dev) {
                     if (sqlResultSet.getString("clType").contentEquals("intra_protein")) {
                         if (sqlResultSet.getInt("hitType") == 0) {
-                            intraTargetWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1) + "\",\"" + String.join(";", proAnnotationList2) + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + "," + entry.qValue + ",\"" + sqlResultSet.getString("mgfTitle") + "\",," + sqlResultSet.getDouble("ms1PearsonCorrelationCoefficient") + "," + sqlResultSet.getInt("candidateNum") + "," + sqlResultSet.getInt("pointCount") + "," + sqlResultSet.getDouble("rSquare") + "," + sqlResultSet.getDouble("slope") + "," + sqlResultSet.getDouble("intercept") + "," + sqlResultSet.getInt("startIdx") + "," + sqlResultSet.getInt("endIdx") + "," + sqlResultSet.getDouble("chainScore1") + "," + sqlResultSet.getInt("chainRank1") + "," + sqlResultSet.getDouble("chainScore2") + "," + sqlResultSet.getInt("chainRank2") + "\n");
+                            intraTargetWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1).replaceAll("\"", "") + "\",\"" + String.join(";", proAnnotationList2).replaceAll("\"", "") + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + "," + entry.qValue + ",\"" + sqlResultSet.getString("mgfTitle").replaceAll("\"", "") + "\",," + sqlResultSet.getDouble("ms1PearsonCorrelationCoefficient") + "," + sqlResultSet.getInt("candidateNum") + "," + sqlResultSet.getInt("pointCount") + "," + sqlResultSet.getDouble("rSquare") + "," + sqlResultSet.getDouble("slope") + "," + sqlResultSet.getDouble("intercept") + "," + sqlResultSet.getInt("startIdx") + "," + sqlResultSet.getInt("endIdx") + "," + sqlResultSet.getDouble("chainScore1") + "," + sqlResultSet.getInt("chainRank1") + "," + sqlResultSet.getDouble("chainScore2") + "," + sqlResultSet.getInt("chainRank2") + "\n");
                         } else {
-                            intraDecoyWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1) + "\",\"" + String.join(";", proAnnotationList2) + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + ",\"" + sqlResultSet.getString("mgfTitle") + "\",," + sqlResultSet.getDouble("ms1PearsonCorrelationCoefficient") + "," + sqlResultSet.getInt("candidateNum") + "," + sqlResultSet.getInt("pointCount") + "," + sqlResultSet.getDouble("rSquare") + "," + sqlResultSet.getDouble("slope") + "," + sqlResultSet.getDouble("intercept") + "," + sqlResultSet.getInt("startIdx") + "," + sqlResultSet.getInt("endIdx") + "," + sqlResultSet.getDouble("chainScore1") + "," + sqlResultSet.getInt("chainRank1") + "," + sqlResultSet.getDouble("chainScore2") + "," + sqlResultSet.getInt("chainRank2") + "\n");
+                            intraDecoyWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1).replaceAll("\"", "") + "\",\"" + String.join(";", proAnnotationList2).replaceAll("\"", "") + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + ",\"" + sqlResultSet.getString("mgfTitle").replaceAll("\"", "") + "\",," + sqlResultSet.getDouble("ms1PearsonCorrelationCoefficient") + "," + sqlResultSet.getInt("candidateNum") + "," + sqlResultSet.getInt("pointCount") + "," + sqlResultSet.getDouble("rSquare") + "," + sqlResultSet.getDouble("slope") + "," + sqlResultSet.getDouble("intercept") + "," + sqlResultSet.getInt("startIdx") + "," + sqlResultSet.getInt("endIdx") + "," + sqlResultSet.getDouble("chainScore1") + "," + sqlResultSet.getInt("chainRank1") + "," + sqlResultSet.getDouble("chainScore2") + "," + sqlResultSet.getInt("chainRank2") + "\n");
                         }
                     } else {
                         if (sqlResultSet.getInt("hitType") == 0) {
-                            interTargetWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1) + "\",\"" + String.join(";", proAnnotationList2) + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + "," + entry.qValue + ",\"" + sqlResultSet.getString("mgfTitle") + "\",," + sqlResultSet.getDouble("ms1PearsonCorrelationCoefficient") + "," + sqlResultSet.getInt("candidateNum") + "," + sqlResultSet.getInt("pointCount") + "," + sqlResultSet.getDouble("rSquare") + "," + sqlResultSet.getDouble("slope") + "," + sqlResultSet.getDouble("intercept") + "," + sqlResultSet.getInt("startIdx") + "," + sqlResultSet.getInt("endIdx") + "," + sqlResultSet.getDouble("chainScore1") + "," + sqlResultSet.getInt("chainRank1") + "," + sqlResultSet.getDouble("chainScore2") + "," + sqlResultSet.getInt("chainRank2") + "\n");
+                            interTargetWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1).replaceAll("\"", "") + "\",\"" + String.join(";", proAnnotationList2).replaceAll("\"", "") + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + "," + entry.qValue + ",\"" + sqlResultSet.getString("mgfTitle").replaceAll("\"", "") + "\",," + sqlResultSet.getDouble("ms1PearsonCorrelationCoefficient") + "," + sqlResultSet.getInt("candidateNum") + "," + sqlResultSet.getInt("pointCount") + "," + sqlResultSet.getDouble("rSquare") + "," + sqlResultSet.getDouble("slope") + "," + sqlResultSet.getDouble("intercept") + "," + sqlResultSet.getInt("startIdx") + "," + sqlResultSet.getInt("endIdx") + "," + sqlResultSet.getDouble("chainScore1") + "," + sqlResultSet.getInt("chainRank1") + "," + sqlResultSet.getDouble("chainScore2") + "," + sqlResultSet.getInt("chainRank2") + "\n");
                         } else {
-                            interDecoyWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1) + "\",\"" + String.join(";", proAnnotationList2) + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + ",\"" + sqlResultSet.getString("mgfTitle") + "\",," + sqlResultSet.getDouble("ms1PearsonCorrelationCoefficient") + "," + sqlResultSet.getInt("candidateNum") + "," + sqlResultSet.getInt("pointCount") + "," + sqlResultSet.getDouble("rSquare") + "," + sqlResultSet.getDouble("slope") + "," + sqlResultSet.getDouble("intercept") + "," + sqlResultSet.getInt("startIdx") + "," + sqlResultSet.getInt("endIdx") + "," + sqlResultSet.getDouble("chainScore1") + "," + sqlResultSet.getInt("chainRank1") + "," + sqlResultSet.getDouble("chainScore2") + "," + sqlResultSet.getInt("chainRank2") + "\n");
+                            interDecoyWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1).replaceAll("\"", "") + "\",\"" + String.join(";", proAnnotationList2).replaceAll("\"", "") + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + ",\"" + sqlResultSet.getString("mgfTitle").replaceAll("\"", "") + "\",," + sqlResultSet.getDouble("ms1PearsonCorrelationCoefficient") + "," + sqlResultSet.getInt("candidateNum") + "," + sqlResultSet.getInt("pointCount") + "," + sqlResultSet.getDouble("rSquare") + "," + sqlResultSet.getDouble("slope") + "," + sqlResultSet.getDouble("intercept") + "," + sqlResultSet.getInt("startIdx") + "," + sqlResultSet.getInt("endIdx") + "," + sqlResultSet.getDouble("chainScore1") + "," + sqlResultSet.getInt("chainRank1") + "," + sqlResultSet.getDouble("chainScore2") + "," + sqlResultSet.getInt("chainRank2") + "\n");
                         }
                     }
                 } else {
                     if (sqlResultSet.getString("clType").contentEquals("intra_protein")) {
                         if (sqlResultSet.getInt("hitType") == 0) {
-                            intraTargetWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1) + "\",\"" + String.join(";", proAnnotationList2) + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + "," + entry.qValue + ",\"" + sqlResultSet.getString("mgfTitle") + "\"\n");
+                            intraTargetWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1).replaceAll("\"", "") + "\",\"" + String.join(";", proAnnotationList2).replaceAll("\"", "") + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + "," + entry.qValue + ",\"" + sqlResultSet.getString("mgfTitle").replaceAll("\"", "") + "\"\n");
                         } else {
-                            intraDecoyWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1) + "\",\"" + String.join(";", proAnnotationList2) + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + ",\"" + sqlResultSet.getString("mgfTitle") + "\",\n");
+                            intraDecoyWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1).replaceAll("\"", "") + "\",\"" + String.join(";", proAnnotationList2).replaceAll("\"", "") + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + ",\"" + sqlResultSet.getString("mgfTitle").replaceAll("\"", "") + "\",\n");
                         }
                     } else {
                         if (sqlResultSet.getInt("hitType") == 0) {
-                            interTargetWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1) + "\",\"" + String.join(";", proAnnotationList2) + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + "," + entry.qValue + ",\"" + sqlResultSet.getString("mgfTitle") + "\",\n");
+                            interTargetWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1).replaceAll("\"", "") + "\",\"" + String.join(";", proAnnotationList2).replaceAll("\"", "") + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + "," + entry.qValue + ",\"" + sqlResultSet.getString("mgfTitle").replaceAll("\"", "") + "\",\n");
                         } else {
-                            interDecoyWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1) + "\",\"" + String.join(";", proAnnotationList2) + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + ",\"" + sqlResultSet.getString("mgfTitle") + "\",\n");
+                            interDecoyWriter.write(sqlResultSet.getInt("scanNum") + "," + entry.scanId + "," + sqlResultSet.getDouble("precursorMz") + "," + sqlResultSet.getDouble("precursorMass") + "," + sqlResultSet.getDouble("theoMass") + "," + sqlResultSet.getInt("rt") + "," + sqlResultSet.getInt("isotopeCorrectionNum") + "," + sqlResultSet.getInt("precursorCharge") + "," + sqlResultSet.getDouble("score") + "," + sqlResultSet.getDouble("deltaC") + "," + sqlResultSet.getDouble("ppm") + "," + sqlResultSet.getString("seq1") + "-" + sqlResultSet.getInt("linkSite1") + "-" + sqlResultSet.getString("seq2") + "-" + sqlResultSet.getInt("linkSite2") + "," + sqlResultSet.getString("proId1") + "-" + sqlResultSet.getString("proId2") + ",\"" + String.join(";", proAnnotationList1).replaceAll("\"", "") + "\",\"" + String.join(";", proAnnotationList2).replaceAll("\"", "") + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + ",\"" + sqlResultSet.getString("mgfTitle").replaceAll("\"", "") + "\",\n");
                         }
                     }
                 }