- mc = MsaCompactor.reduceLength( msa, length, step, realign );
- }
- System.out.println( MsaMethods.calcGapRatio( mc.getMsa() ) );
- for( final String id : mc.getRemovedSeqIds() ) {
- System.out.println( id );
- }
- mc.writeMsa( out, MSA_FORMAT.PHYLIP, ".aln" );
+ if ( length >= msa.getLength() ) {
+ ForesterUtil.fatalError( PRG_NAME, "target MSA length (" + length
+ + ") is greater than or equal to MSA original length (" + msa.getLength() + ")" );
+ }
+ // TODO if < shortest seq -> error
+ mc = MsaCompactor.reduceLength( msa, length, step, realign, norm, path_to_mafft, out );
+ }
+ //System.out.println( MsaMethods.calcGapRatio( mc.getMsa() ) );
+ // for( final String id : mc.getRemovedSeqIds() ) {
+ // System.out.println( id );
+ //}
+ //mc.writeMsa( out, MSA_FORMAT.PHYLIP, ".aln" );