From 40d33b2501fe838180595d301af03851b35b8108 Mon Sep 17 00:00:00 2001
From: Fengchao <fyuab@connect.ust.hk>
Date: Wed, 25 Apr 2018 14:30:05 +0800
Subject: [PATCH] Delete q-value column in the decoy output to avoid a
 confusion.

---
 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 1dbdbc7..07b3f3e 100644
--- a/src/main/java/proteomics/ECL2.java
+++ b/src/main/java/proteomics/ECL2.java
@@ -293,14 +293,14 @@ private static void saveTargetResult(Map<String, CalFDR.Entry> result, Map<Strin
 
         if (dev) {
             intraTargetWriter.write("scan_num,spectrum_id,spectrum_mz,spectrum_mass,peptide_mass,rt,C13_correction,charge,score,delta_C,ppm,peptide,protein,protein_annotation_1,protein_annotation_2,e_value,q_value,mgf_title,,MS1_pearson_correlation_coefficient,candidate_num,point_num,r_square,slope,intercept,start_idx,end_idx,chain_score_1,chain_rank_1,chain_score_2,chain_rank_2\n");
-            intraDecoyWriter.write("scan_num,spectrum_id,spectrum_mz,spectrum_mass,peptide_mass,rt,C13_correction,charge,score,delta_C,ppm,peptide,protein,protein_annotation_1,protein_annotation_2,e_value,q_value,mgf_title,,MS1_pearson_correlation_coefficient,candidate_num,point_num,r_square,slope,intercept,start_idx,end_idx,chain_score_1,chain_rank_1,chain_score_2,chain_rank_2\n");
+            intraDecoyWriter.write("scan_num,spectrum_id,spectrum_mz,spectrum_mass,peptide_mass,rt,C13_correction,charge,score,delta_C,ppm,peptide,protein,protein_annotation_1,protein_annotation_2,e_value,mgf_title,,MS1_pearson_correlation_coefficient,candidate_num,point_num,r_square,slope,intercept,start_idx,end_idx,chain_score_1,chain_rank_1,chain_score_2,chain_rank_2\n");
             interTargetWriter.write("scan_num,spectrum_id,spectrum_mz,spectrum_mass,peptide_mass,rt,C13_correction,charge,score,delta_C,ppm,peptide,protein,protein_annotation_1,protein_annotation_2,e_value,q_value,mgf_title,,MS1_pearson_correlation_coefficient,candidate_num,point_num,r_square,slope,intercept,start_idx,end_idx,chain_score_1,chain_rank_1,chain_score_2,chain_rank_2\n");
-            interDecoyWriter.write("scan_num,spectrum_id,spectrum_mz,spectrum_mass,peptide_mass,rt,C13_correction,charge,score,delta_C,ppm,peptide,protein,protein_annotation_1,protein_annotation_2,e_value,q_value,mgf_title,,MS1_pearson_correlation_coefficient,candidate_num,point_num,r_square,slope,intercept,start_idx,end_idx,chain_score_1,chain_rank_1,chain_score_2,chain_rank_2\n");
+            interDecoyWriter.write("scan_num,spectrum_id,spectrum_mz,spectrum_mass,peptide_mass,rt,C13_correction,charge,score,delta_C,ppm,peptide,protein,protein_annotation_1,protein_annotation_2,e_value,mgf_title,,MS1_pearson_correlation_coefficient,candidate_num,point_num,r_square,slope,intercept,start_idx,end_idx,chain_score_1,chain_rank_1,chain_score_2,chain_rank_2\n");
         } else {
             intraTargetWriter.write("scan_num,spectrum_id,spectrum_mz,spectrum_mass,peptide_mass,rt,C13_correction,charge,score,delta_C,ppm,peptide,protein,protein_annotation_1,protein_annotation_2,e_value,q_value,mgf_title,\n");
-            intraDecoyWriter.write("scan_num,spectrum_id,spectrum_mz,spectrum_mass,peptide_mass,rt,C13_correction,charge,score,delta_C,ppm,peptide,protein,protein_annotation_1,protein_annotation_2,e_value,q_value,mgf_title,\n");
+            intraDecoyWriter.write("scan_num,spectrum_id,spectrum_mz,spectrum_mass,peptide_mass,rt,C13_correction,charge,score,delta_C,ppm,peptide,protein,protein_annotation_1,protein_annotation_2,e_value,mgf_title,\n");
             interTargetWriter.write("scan_num,spectrum_id,spectrum_mz,spectrum_mass,peptide_mass,rt,C13_correction,charge,score,delta_C,ppm,peptide,protein,protein_annotation_1,protein_annotation_2,e_value,q_value,mgf_title,\n");
-            interDecoyWriter.write("scan_num,spectrum_id,spectrum_mz,spectrum_mass,peptide_mass,rt,C13_correction,charge,score,delta_C,ppm,peptide,protein,protein_annotation_1,protein_annotation_2,e_value,q_value,mgf_title,\n");
+            interDecoyWriter.write("scan_num,spectrum_id,spectrum_mz,spectrum_mass,peptide_mass,rt,C13_correction,charge,score,delta_C,ppm,peptide,protein,protein_annotation_1,protein_annotation_2,e_value,mgf_title,\n");
         }
         List<CalFDR.Entry> entryList = new ArrayList<>(result.values());
         entryList.sort(Comparator.reverseOrder());
@@ -329,13 +329,13 @@ private static void saveTargetResult(Map<String, CalFDR.Entry> result, Map<Strin
                         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");
                         } 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")) : "-") + "," + 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");
+                            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");
                         }
                     } 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");
                         } 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")) : "-") + "," + 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");
+                            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");
                         }
                     }
                 } else {
@@ -343,13 +343,13 @@ private static void saveTargetResult(Map<String, CalFDR.Entry> result, Map<Strin
                         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");
                         } 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")) : "-") + "," + entry.qValue + ",\"" + 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) + "\",\"" + String.join(";", proAnnotationList2) + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + ",\"" + sqlResultSet.getString("mgfTitle") + "\",\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");
                         } 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")) : "-") + "," + entry.qValue + ",\"" + 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) + "\",\"" + String.join(";", proAnnotationList2) + "\"," + (cal_evalue ? String.format(Locale.US, "%E", sqlResultSet.getDouble("eValue")) : "-") + ",\"" + sqlResultSet.getString("mgfTitle") + "\",\n");
                         }
                     }
                 }