X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fio%2Fparsers%2FHmmscanPerDomainTableParser.java;h=b5d1bc13d36c74b8c2fb3b114771faf5963bf66a;hb=877d1e4a2f3e2a937197dc57253ba2cead14a4d6;hp=84fbfe45d0d77673868fbf0d6ba192ac00ae073f;hpb=73c5b11c1a00e539afb246e345ebf3f042dded78;p=jalview.git

diff --git a/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java b/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java
index 84fbfe4..b5d1bc1 100644
--- a/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java
+++ b/forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java
@@ -41,11 +41,11 @@ import java.util.SortedSet;
 import java.util.TreeMap;
 import java.util.TreeSet;
 
+import org.forester.protein.BasicDomain;
 import org.forester.protein.BasicProtein;
 import org.forester.protein.Domain;
 import org.forester.protein.DomainId;
 import org.forester.protein.Protein;
-import org.forester.surfacing.BasicDomain;
 import org.forester.surfacing.SurfacingUtil;
 import org.forester.util.ForesterUtil;
 
@@ -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 )