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Added support for clustal #1

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Added support for clustal #1

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17166c6
Added support for clustal
May 6, 2014
629c0c7
update email
wangqinhu Feb 2, 2015
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13 changes: 7 additions & 6 deletions ftdetect/bio-vim.vim
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Original file line number Diff line number Diff line change
@@ -1,8 +1,9 @@
augroup filetypedetect
au BufNewFile,BufRead *.fasta setf fasta
au BufNewFile,BufRead *.faa setf fasta_aa
au BufNewFile,BufRead *.{ffn,fna} setf fasta_nt
au BufNewFile,BufRead *.gff setf gff
au BufNewFile,BufRead *.{gbk,genbank} setf genbank
au BufRead,BufNewFile *.{nex,nexus,nxs,nx} setf nexus
au BufNewFile,BufRead *.{fasta,fas,fsa,fa} setf fasta
au BufNewFile,BufRead *.faa setf fasta_aa
au BufNewFile,BufRead *.{ffn,fna,fnt} setf fasta_nt
au BufNewFile,BufRead *.gff setf gff
au BufNewFile,BufRead *.{gb,gp,gbk,genbank} setf genbank
au BufRead,BufNewFile *.{nex,nexus,nxs,nx} setf nexus
au BufRead,BufNewFile *.aln setf clustal
augroup END
33 changes: 33 additions & 0 deletions syntax/clustal.vim
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Original file line number Diff line number Diff line change
@@ -0,0 +1,33 @@
" Vim syntax file
" Language: Clustal alignment
" Maintainer: Qinhu Wang <[email protected]>
" Last Change: Feb 2, 2015

" For version 5.x: Clear all syntax items
" For version 6.x: Quit when a syntax file was already loaded
if version < 600
syntax clear
elseif exists("b:current_syntax")
finish
endif

" Clustal body
syn match seq_id "^\S\+\s\+"
syn match group1 "[GPST]"
syn match group2 "[HKR]"
syn match group3 "[FWY]"
syn match group4 "[ILMV]"
syn match gap "-"

" Clustal header
syn region clustalHeader start=/^CLUSTAL/ end=/\n$/ oneline

highlight clustalHeader ctermfg=blue guifg=blue
highlight seq_id ctermfg=magenta guifg=magenta
highlight group1 ctermfg=yellow guifg=yellow
highlight group2 ctermfg=red guifg=red
highlight group3 ctermfg=blue guifg=blue
highlight group4 ctermfg=green guifg=green
highlight gap ctermfg=grey guifg=grey

let b:current_syntax = "clustal"