iterating nh parser

[jalview.git] / forester / java / src / org / forester / io / parsers / HmmscanPerDomainTableParser.java

diff --git a/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java b/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java
index 0bb224c..ada802a 100644 (file)
--- a/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java
+++ b/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java
@@ -23,7 +23,7 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.io.parsers;
 
@@ -64,6 +64,7 @@ public final class HmmscanPerDomainTableParser {
     private static final ReturnType       RETURN_TYPE_DEFAULT         = ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN;
     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 final Set<DomainId>           _filter;
     private final FilterType              _filter_type;
     private final File                    _input_file;
@@ -447,6 +448,10 @@ public final class HmmscanPerDomainTableParser {
             else if ( isIgnoreDufs() && uc_id.startsWith( "DUF" ) ) {
                 ++_domains_ignored_due_to_duf;
             }
+            else if ( IGNORE_REPLACED_RRMS
+                    && ( uc_id.contains( "RRM_1" ) || uc_id.contains( "RRM_3" ) || uc_id.contains( "RRM_5" ) || uc_id
+                            .contains( "RRM_6" ) ) ) {
+            }
             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 )