From c3c6c205a0b514229025a5218b88eab1adee80fc Mon Sep 17 00:00:00 2001 From: Fengchao Date: Wed, 14 Mar 2018 17:49:25 +0800 Subject: [PATCH] Using ProteomicsLibrary methods instead. --- src/main/java/proteomics/Index/BuildIndex.java | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/src/main/java/proteomics/Index/BuildIndex.java b/src/main/java/proteomics/Index/BuildIndex.java index 97d374a..022e94c 100644 --- a/src/main/java/proteomics/Index/BuildIndex.java +++ b/src/main/java/proteomics/Index/BuildIndex.java @@ -226,11 +226,8 @@ private Map> buildSeqProMap(Map pro_seq_map, for (String pro_id : pro_seq_map.keySet()) { String pro_seq = pro_seq_map.get(pro_id); Set seq_set = mass_tool_obj.buildChainSet(pro_seq, linker_type); - if (cutNTermM && pro_seq.startsWith("M")) { - seq_set.addAll(mass_tool_obj.buildChainSet(pro_seq.substring(1), linker_type)); - } for (String target_seq : seq_set) { - if ((target_seq.length() >= min_chain_length) && (target_seq.length() <= max_chain_length) && !target_seq.contains("B") && !target_seq.contains("J") && !target_seq.contains("X") && !target_seq.contains("Z")) { + if ((target_seq.length() >= min_chain_length) && (target_seq.length() <= max_chain_length) && !MassTool.containsNonAAAndNC(target_seq)) { if (!for_check_duplicate.contains(target_seq.replace('L', 'I'))) { // Add the sequence to the check set for duplicate check for_check_duplicate.add(target_seq.replace('L', 'I')); // "L" and "I" have the same mass @@ -268,7 +265,7 @@ private Map> buildSeqProMap(Map pro_seq_map, decoy_seq_set.addAll(mass_tool_obj.buildChainSet((new StringBuilder(pro_seq.substring(1))).reverse().toString(), linker_type)); } for (String decoy_seq : decoy_seq_set) { - if ((decoy_seq.length() >= min_chain_length) && (decoy_seq.length() <= max_chain_length) && !decoy_seq.contains("B") && !decoy_seq.contains("J") && !decoy_seq.contains("X") && !decoy_seq.contains("Z")) { + if ((decoy_seq.length() >= min_chain_length) && (decoy_seq.length() <= max_chain_length) && !MassTool.containsNonAAAndNC(decoy_seq)) { if (!for_check_duplicate.contains(decoy_seq.replace('L', 'I'))) { for_check_duplicate.add(decoy_seq.replace('L', 'I'));