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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
// 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;
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 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;
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 ( 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 )
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 )