plugins/sam_seq.lua

@@ -3,35 +3,32 @@ Description="Generate coloured bio sequences in Sequence Alignment Maps" -- optional parameter: syntax description function syntaxUpdate(desc) -    t = {}-    t["A"] = "144;238;144" --144, 238, 144-    t["T"] = "240;128;128" --240, 128, 128-    t["C"] = "173;216;230" --173, 216, 230-    t["G"] = "255;160;122" --255, 160, 122--    function Decorate(token, state, kwclass)--        if ( (HL_OUTPUT == HL_FORMAT_HTML or HL_OUTPUT == HL_FORMAT_XHTML or HL_OUTPUT == HL_FORMAT_TRUECOLOR)-            and #token > 63 and state == HL_KEYWORD and not string.match(token,"[^ATCG]") ) then--        retVal = ""-        for c in token:gmatch"." do-            if (HL_OUTPUT == HL_FORMAT_HTML or HL_OUTPUT == HL_FORMAT_XHTML) then-                retVal = retVal .. "<span class='elem_".. c .. "'>".. c .. "</span>"-            elseif (HL_OUTPUT == HL_FORMAT_TRUECOLOR) then-                retVal = retVal .. "\27[48;2;".. t[c] .. "m".. c .. "\27m"-            end--        --"\033[48;5;"<< ( int ) rgb2xterm ( bg_rgb ) << "m"-+  t = {}+  t["A"] = "144;238;144" --144, 238, 144+  t["T"] = "240;128;128" --240, 128, 128+  t["C"] = "173;216;230" --173, 216, 230+  t["G"] = "255;160;122" --255, 160, 122++  function Decorate(token, state, kwclass)++    if ( (HL_OUTPUT == HL_FORMAT_HTML or HL_OUTPUT == HL_FORMAT_XHTML or HL_OUTPUT == HL_FORMAT_TRUECOLOR)+        and #token > 63 and state == HL_KEYWORD and not string.match(token,"[^ATCG]") ) then++      retVal = ""+      for c in token:gmatch"." do+        if (HL_OUTPUT == HL_FORMAT_HTML or HL_OUTPUT == HL_FORMAT_XHTML) then+          retVal = retVal .. "<span class='elem_".. c .. "'>".. c .. "</span>"+        elseif (HL_OUTPUT == HL_FORMAT_TRUECOLOR) then+          retVal = retVal .. "\27[48;2;".. t[c] .. "m".. c .. "\27m"         end-        return retVal-    end+      end+      return retVal     end+  end end  function themeUpdate(desc)-    if (HL_OUTPUT == HL_FORMAT_HTML or HL_OUTPUT == HL_FORMAT_XHTML) then+  if (HL_OUTPUT == HL_FORMAT_HTML or HL_OUTPUT == HL_FORMAT_XHTML) then      Injections[#Injections+1]=[[ span.elem_A {@@ -46,12 +43,11 @@ span.elem_C { span.elem_G {   background-color: lightsalmon; }- ]]-    end+]]+  end end  Plugins={--    { Type="lang", Chunk=syntaxUpdate },-    { Type="theme", Chunk=themeUpdate }+  { Type="lang", Chunk=syntaxUpdate },+  { Type="theme", Chunk=themeUpdate } }