+ final private void write( final File outfile, final double gr ) throws IOException {
+ writeMsa( outfile + "_" + _msa.getNumberOfSequences() + "_" + _msa.getLength() + "_"
+ + ForesterUtil.roundToInt( gr * 100 ) + ".fasta" );
+ }
+
+ final private void writeMsa( final String outfile ) throws IOException {
+ final Writer w = ForesterUtil.createBufferedWriter( outfile );
+ _msa.write( w, MSA_FORMAT.FASTA );
+ w.close();
+ }
+
+ final private StringBuilder msaStatsAsSB() {
+ final StringBuilder sb = new StringBuilder();
+ sb.append( _msa.getLength() );
+ sb.append( "\t" );
+ sb.append( _msa.getNumberOfSequences() );
+ sb.append( "\t" );
+ sb.append( ForesterUtil.round( MsaMethods.calcGapRatio( _msa ), 4 ) );
+ sb.append( "\t" );
+ return sb;
+ }
+