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more test for isDuplication() and isSpecation() added (phyloXML encoded
[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
msa
/
Mafft.java
diff --git
a/forester/java/src/org/forester/msa/Mafft.java
b/forester/java/src/org/forester/msa/Mafft.java
index
ec72c0d
..
5a96bc3
100644
(file)
--- a/
forester/java/src/org/forester/msa/Mafft.java
+++ b/
forester/java/src/org/forester/msa/Mafft.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;
@@
-35,7
+35,7
@@
import java.util.List;
import org.forester.io.parsers.FastaParser;
import org.forester.io.writers.SequenceWriter;
import org.forester.io.writers.SequenceWriter.SEQ_FORMAT;
import org.forester.io.parsers.FastaParser;
import org.forester.io.writers.SequenceWriter;
import org.forester.io.writers.SequenceWriter.SEQ_FORMAT;
-import org.forester.sequence.Sequence;
+import org.forester.sequence.MolecularSequence;
import org.forester.util.SystemCommandExecutor;
public final class Mafft extends MsaInferrer {
import org.forester.util.SystemCommandExecutor;
public final class Mafft extends MsaInferrer {
@@
-72,7
+72,8
@@
public final class Mafft extends MsaInferrer {
}
@Override
}
@Override
- public Msa infer( final List<Sequence> seqs, final List<String> opts ) throws IOException, InterruptedException {
+ public Msa infer( final List<MolecularSequence> seqs, final List<String> opts ) throws IOException,
+ InterruptedException {
final File file = File.createTempFile( "__mafft_input_", ".fasta" );
file.deleteOnExit();
final BufferedWriter writer = new BufferedWriter( new FileWriter( file ) );
final File file = File.createTempFile( "__mafft_input_", ".fasta" );
file.deleteOnExit();
final BufferedWriter writer = new BufferedWriter( new FileWriter( file ) );
@@
-98,7
+99,7
@@
public final class Mafft extends MsaInferrer {
_error = stderr.toString();
if ( _exit_code != 0 ) {
throw new IOException( "MAFFT program failed, exit code: " + _exit_code + "\nCommand:\n" + my_opts
_error = stderr.toString();
if ( _exit_code != 0 ) {
throw new IOException( "MAFFT program failed, exit code: " + _exit_code + "\nCommand:\n" + my_opts
- + "\nError:\n" + stderr );
+ + "\nError:\n" + stderr );
}
final StringBuilder stdout = command_executor.getStandardOutputFromCommand();
if ( ( stdout == null ) || ( stdout.length() < 2 ) ) {
}
final StringBuilder stdout = command_executor.getStandardOutputFromCommand();
if ( ( stdout == null ) || ( stdout.length() < 2 ) ) {