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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
2aa4497
..
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;
@@
-64,7
+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 = true;
+ 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;