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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
io
/
parsers
/
GeneralMsaParser.java
diff --git
a/forester/java/src/org/forester/io/parsers/GeneralMsaParser.java
b/forester/java/src/org/forester/io/parsers/GeneralMsaParser.java
index
6e79477
..
507ae1f
100644
(file)
--- a/
forester/java/src/org/forester/io/parsers/GeneralMsaParser.java
+++ b/
forester/java/src/org/forester/io/parsers/GeneralMsaParser.java
@@
-22,7
+22,7
@@
// 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;
@@
-48,7
+48,7
@@
public final class GeneralMsaParser {
private static final Pattern NAME_SEQ_PATTERN = Pattern.compile( "(\\S+)\\s+(\\S+)\\s*" );
private static final Pattern INDENTED_SEQ_PATTERN = Pattern.compile( "\\s+(\\S+)\\s*" );
private static final Pattern NON_INDENTED_SEQ_PATTERN = Pattern.compile( "(\\S+).*" );
private static final Pattern NAME_SEQ_PATTERN = Pattern.compile( "(\\S+)\\s+(\\S+)\\s*" );
private static final Pattern INDENTED_SEQ_PATTERN = Pattern.compile( "\\s+(\\S+)\\s*" );
private static final Pattern NON_INDENTED_SEQ_PATTERN = Pattern.compile( "(\\S+).*" );
- private static final Pattern PROBCONS_REGEX = Pattern.compile( "^CLUSTAL\\s" );
+ private static final Pattern PROBCONS_REGEX = Pattern.compile( "^CLUSTAL" );
private static final Pattern MUSCLE_REGEX = Pattern.compile( "^MUSCLE\\s\\(" );
private static final Pattern CLUSTAL_REGEX = Pattern.compile( "^PROBCONS\\s" );
private static final Pattern ANYTHING_REGEX = Pattern.compile( "[\\d\\s]+" );
private static final Pattern MUSCLE_REGEX = Pattern.compile( "^MUSCLE\\s\\(" );
private static final Pattern CLUSTAL_REGEX = Pattern.compile( "^PROBCONS\\s" );
private static final Pattern ANYTHING_REGEX = Pattern.compile( "[\\d\\s]+" );