From 924f103b10bbe97a1d3fcf019759819662066d1f Mon Sep 17 00:00:00 2001 From: Fengchao Date: Mon, 29 Jan 2018 11:17:22 +0800 Subject: [PATCH] Add Others database type. --- src/main/java/proteomics/TheoSeq/DbTool.java | 11 +++++++++-- src/main/resources/parameter.def | 2 +- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/src/main/java/proteomics/TheoSeq/DbTool.java b/src/main/java/proteomics/TheoSeq/DbTool.java index 4ef9bf3..5da9a26 100644 --- a/src/main/java/proteomics/TheoSeq/DbTool.java +++ b/src/main/java/proteomics/TheoSeq/DbTool.java @@ -26,7 +26,10 @@ public DbTool(String db_name, String databaseType) { header_pattern = Pattern.compile("^>([^\\s]+)[\\s|]+(.+)$"); } else if (databaseType.contentEquals("UniProt") || databaseType.contentEquals("SwissProt")) { header_pattern = Pattern.compile("^>[^|]+\\|(.+)\\|(.+)$"); - } else { + } else if (databaseType.contentEquals("Others")) { + header_pattern = Pattern.compile("^>(.+)$"); + } + else { header_pattern = null; logger.error("Incorrect database type ({}) in the parameter file.", databaseType); System.exit(1); @@ -44,7 +47,11 @@ public DbTool(String db_name, String databaseType) { pro_seq_map.put(id, seq.toString()); } id = head_matcher.group(1).trim(); - annotate = head_matcher.group(2).trim(); + if (databaseType.contentEquals("Others")) { + annotate = id; + } else { + annotate = head_matcher.group(2).trim(); + } pro_annotate_map.put(id, annotate); new_pro = true; } else if (!line.isEmpty()) { diff --git a/src/main/resources/parameter.def b/src/main/resources/parameter.def index ba8e1bc..4567094 100644 --- a/src/main/resources/parameter.def +++ b/src/main/resources/parameter.def @@ -6,7 +6,7 @@ dev = 0 # Output development information. # Database db = small+random50.fasta # The protein database. -database_type = UniProt # Different types have different fasta header patterns. Available values: UniProt, SwissProt, TAIR +database_type = UniProt # Different types have different fasta header patterns. Available values: UniProt, SwissProt, TAIR, Others missed_cleavage = 2 # Maximum number of allowed missed cleavage. min_precursor_mass = 1000 max_precursor_mass = 12000