From: cmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Date: Wed, 23 Oct 2013 01:00:24 +0000 (+0000)
Subject: hDGE_amylase missspelled issue
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=859cbf10040482d4632f9ad47b92c4da4a9fe94b;p=jalview.git

hDGE_amylase missspelled issue
---

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<String>             _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 )