_mafft

#compdef mafft

# TODO: Some of the arguments shoudl only be completed if another
# one is already on the commandline. See mafft help for details.

_mafft() {
	local ret=1
	local -a args
	args+=(
		'--6merpair[Distance is calculated based on the number of shared 6mers]'
		'--auto[Automatically selects an appropriate strategy]'
		'--genafpair[All pairwise alignments are computed with a local algorithm with the generalized affine gap cost]'
		'--globalpair[All pairwise alignments are computed]'
		'--localpair[All pairwise alignments are computed with the Smith-Waterman algorithm]'
        '--aamatrix[Use a user-defined AA scoring matrix]:file:_files'
        '--amino[Assume the sequences are amino acid]'
        '--bl[BLOSUM number matrix is used]:number:'
        '--clustalout[Output format: clustal format]'
        '--dpparttree[The PartTree algorithm is used with distances based on DP]'
        '--ep[Offset value]:number:'
        '--fastapair[All pairwise alignments are computed with FASTA]'
        '--fastaparttree[The PartTree algorithm is used with distances based on FASTA]'
        '--fft[Use FFT approximation in group-to-group alignment]'
        '--fmodel[Incorporate the AA/nuc composition information into the scoring matrix]'
        '--groupsize[Do not make alignment larger than number sequences]:number:'
        '--inputorder[Output order: same as input]'
        '--jtt[JTT PAM number matrix is used]:number:'
        '--lep[Offset value at local pairwise alignment]:number:'
        '--lexp[Gap extension penalty at local pairwise alignment]:number:'
        '--LEXP[Gap extension penalty to skip the alignment]:number:'
        '--lop[Gap opening penalty at local pairwise alignment]:number:'
        '--LOP[Gap opening penalty to skip the alignment]:number:'
        '--maxiterate[number cycles of iterative refinement are performed]:number:'
        '--memsave[Use the Myers-Miller (1988) algorithm]'
        '--nofft[Do not use FFT approximation in group-to-group alignment]'
        '--noscore[Alignment score is not checked in the iterative refinement stage]'
        '--nuc[Assume the sequences are nucleotide]'
        '--op[Gap opening penalty at group-to-group alignment]:number:'
        '--partsize[The number of partitions in the PartTree algorithm]:number:'
        '--parttree[Use a fast tree-building method with the 6mer distance]'
        '--quiet[Do not report progress]'
        '--reorder[Output order: aligned]'
        '--retree[Guide tree is built number times in the progressive stage]:number:'
        '--seed[Seed alignments given in alignment_n are aligned with sequences in input]:file:_files'
        '--tm[Transmembrane PAM number matrix is used]:number:'
        '--treeout[Guide tree is output to the input.tree file]'
        '--weighti[Weighting factor for the consistency term]:number:'
        '--adjustdirection[Generate reverse complement sequences, as necessary, and align (based on 6 mer counting and faster)]'
        '--adjustdirectionaccurately[Generate reverse complement sequences, as necessary, and align (based on DP and slower)]'
        '--thread[Number of threads]:int:'
        '*:file:_files'
	)
	_arguments $args[@] && ret=0
	return ret
}

_mafft