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more test for isDuplication() and isSpecation() added (phyloXML encoded
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
msa
/
MsaInferrer.java
diff --git
a/forester/java/src/org/forester/msa/MsaInferrer.java
b/forester/java/src/org/forester/msa/MsaInferrer.java
index
8266648
..
45fec85
100644
(file)
--- a/
forester/java/src/org/forester/msa/MsaInferrer.java
+++ b/
forester/java/src/org/forester/msa/MsaInferrer.java
@@
-21,7
+21,7
@@
// 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.msa;
package org.forester.msa;
@@
-29,6
+29,7
@@
import java.io.File;
import java.io.IOException;
import java.util.List;
import java.io.IOException;
import java.util.List;
+import org.forester.sequence.MolecularSequence;
import org.forester.util.SystemCommandExecutor;
public abstract class MsaInferrer {
import org.forester.util.SystemCommandExecutor;
public abstract class MsaInferrer {
@@
-47,4
+48,7
@@
public abstract class MsaInferrer {
}
public abstract Msa infer( File path_to_input_seqs, List<String> opts ) throws IOException, InterruptedException;
}
public abstract Msa infer( File path_to_input_seqs, List<String> opts ) throws IOException, InterruptedException;
+
+ public abstract Msa infer( final List<MolecularSequence> seqs, final List<String> opts ) throws IOException,
+ InterruptedException;
}
}