From 17166c65d5897ae62d8f468a14789533943c4843 Mon Sep 17 00:00:00 2001 From: Qinhu Wang Date: Wed, 7 May 2014 02:09:30 +0800 Subject: [PATCH 1/2] Added support for clustal --- ftdetect/bio-vim.vim | 13 +++++++------ syntax/clustal.vim | 33 +++++++++++++++++++++++++++++++++ 2 files changed, 40 insertions(+), 6 deletions(-) create mode 100644 syntax/clustal.vim diff --git a/ftdetect/bio-vim.vim b/ftdetect/bio-vim.vim index 5b78b2b..2aa842c 100644 --- a/ftdetect/bio-vim.vim +++ b/ftdetect/bio-vim.vim @@ -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 diff --git a/syntax/clustal.vim b/syntax/clustal.vim new file mode 100644 index 0000000..5dc964a --- /dev/null +++ b/syntax/clustal.vim @@ -0,0 +1,33 @@ +" Vim syntax file +" Language: Clustal alignment +" Maintainer: Qinhu Wang +" Last Change: 2014 May 07 + +" 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" From 629c0c73669347d42d548a00ba9855d1cf4a0120 Mon Sep 17 00:00:00 2001 From: Qinhu Wang Date: Mon, 2 Feb 2015 11:32:42 +0800 Subject: [PATCH 2/2] update email --- syntax/clustal.vim | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/syntax/clustal.vim b/syntax/clustal.vim index 5dc964a..c5a5064 100644 --- a/syntax/clustal.vim +++ b/syntax/clustal.vim @@ -1,7 +1,7 @@ " Vim syntax file " Language: Clustal alignment -" Maintainer: Qinhu Wang -" Last Change: 2014 May 07 +" Maintainer: Qinhu Wang +" 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