From 859cbf10040482d4632f9ad47b92c4da4a9fe94b Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Wed, 23 Oct 2013 01:00:24 +0000 Subject: [PATCH] hDGE_amylase missspelled issue --- .../src/org/forester/io/parsers/HmmscanPerDomainTableParser.java | 3 +++ 1 file changed, 3 insertions(+) diff --git a/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java b/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java index 4495009..d62d69e 100644 --- a/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java +++ b/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java @@ -64,6 +64,7 @@ public final class HmmscanPerDomainTableParser { private static final boolean IGNORE_DUFS_DEFAULT = false; private static final int MAX_ALLOWED_OVERLAP_DEFAULT = -1; private static final boolean IGNORE_REPLACED_RRMS = false; + private static final boolean IGNORE_hDGE_amylase = true; //TODO eventually remove me, added 10/22/13 private final Set _filter; private final FilterType _filter_type; private final File _input_file; @@ -451,6 +452,8 @@ public final class HmmscanPerDomainTableParser { && ( uc_id.contains( "RRM_1" ) || uc_id.contains( "RRM_3" ) || uc_id.contains( "RRM_5" ) || uc_id .contains( "RRM_6" ) ) ) { } + else if ( IGNORE_hDGE_amylase && ( uc_id.equals( "hDGE_amylase" ) ) ) { + } else if ( isIgnoreVirusLikeIds() && ( uc_id.contains( VIR ) || uc_id.contains( PHAGE ) || uc_id.contains( RETRO ) || uc_id.contains( TRANSPOS ) || uc_id.startsWith( RV ) || uc_id.startsWith( GAG ) -- 1.7.10.2