import java.io.FileInputStream;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import org.forester.io.parsers.FastaParser;
import org.forester.msa.Msa;
+import org.forester.sequence.BasicSequence;
import org.forester.sequence.Sequence;
import org.forester.util.ForesterUtil;
if ( found > 0 ) {
for( final Sequence found_seq : found_seqs ) {
if ( found_seq.getLength() >= 85 ) {
- all_found_seqs.add( found_seq );
+
+ all_found_seqs.add( BasicSequence.createAaSequence( id, found_seq.getMolecularSequenceAsString() ) );
}
}
if ( found > 1 ) {
System.exit( -1 );
}
}
+ String fasta_ary[] = new String[ all_found_seqs.size() ];
int i = 0;
for( Sequence sequence : all_found_seqs ) {
- System.out.println( i++ + ": " + sequence );
+ fasta_ary[ i ] = ">" + sequence.getIdentifier() + "\n" + sequence.getMolecularSequenceAsString();
+ System.out.println( sequence );
+ i++;
}
+ Arrays.sort( fasta_ary );
+
+ for( int j = 0; j < fasta_ary.length; ++j ) {
+ System.out.println( fasta_ary[ j ] );
+ }
+
System.out.println( "DONE." );
}
catch ( final Exception e ) {