From 267408ac177cca30787b84e96e92a986d5c6850f Mon Sep 17 00:00:00 2001 From: Fengchao Date: Tue, 30 Jan 2018 16:40:57 +0800 Subject: [PATCH] Don't half the total score if two sequences are the same. --- src/main/java/proteomics/Search/Search.java | 22 ++++----------------- 1 file changed, 4 insertions(+), 18 deletions(-) diff --git a/src/main/java/proteomics/Search/Search.java b/src/main/java/proteomics/Search/Search.java index 5089fad..7956c4a 100644 --- a/src/main/java/proteomics/Search/Search.java +++ b/src/main/java/proteomics/Search/Search.java @@ -122,32 +122,18 @@ ResultEntry doSearch(SpectrumEntry spectrumEntry, SparseVector xcorrPL) throws I // only two sequences with the same binary mod type can be linked. if (chain_entry_map.get(chain_score_entry_1.getSeq()).binaryModType == chain_entry_map.get(chain_score_entry_2.getSeq()).binaryModType) { - double score; - if (chain_score_entry_1.getPtmFreeSeq().contentEquals(chain_score_entry_2.getPtmFreeSeq())) { - score = (chain_score_entry_1.getScore() + chain_score_entry_2.getScore()) * 0.5; - ++candidate_num; - } else { - score = chain_score_entry_1.getScore() + chain_score_entry_2.getScore(); - ++candidate_num; - } + double score = chain_score_entry_1.getScore() + chain_score_entry_2.getScore(); + ++candidate_num; // calculate second score double second_score = 0; double temp_1 = -1; if (chain_score_entry_1.getSecondSeq() != null) { - if (chain_score_entry_1.getSecondPtmFreeSeq().contentEquals(chain_score_entry_2.getPtmFreeSeq())) { - temp_1 = (chain_score_entry_1.getSecondScore() + chain_score_entry_2.getScore()) * 0.5; - } else { - temp_1 = chain_score_entry_1.getSecondScore() + chain_score_entry_2.getScore(); - } + temp_1 = chain_score_entry_1.getSecondScore() + chain_score_entry_2.getScore(); } double temp_2 = -1; if (chain_score_entry_2.getSecondSeq() != null) { - if (chain_score_entry_1.getPtmFreeSeq().contentEquals(chain_score_entry_2.getSecondPtmFreeSeq())) { - temp_2 = (chain_score_entry_1.getScore() + chain_score_entry_2.getSecondScore()) * 0.5; - } else { - temp_2 = chain_score_entry_1.getScore() + chain_score_entry_2.getSecondScore(); - } + temp_2 = chain_score_entry_1.getScore() + chain_score_entry_2.getSecondScore(); } if (temp_1 > 0) {