HTMLColor := proc(what, color) description 'Converts any text into html format with color information what: any text color: color keyword, at least 2 (3 for blue and black) letters e.g. "ye" (yellow), "light blue", "pink", "li gr" etc'; col := uppercase(color); if not type(what, string) then return(''); fi; if SearchString('GRE', col)> -1 and SearchString('LIG', col)> -1 then code := '#00FF00' elif SearchString('BLU', col)> -1 and SearchString('LIG', col)> -1 then code := '#00FFFF' elif SearchString('GRE', col)> -1 and SearchString('OLI', col)> -1 then code := '#6B8E23' elif SearchString('GRE', col)> -1 and SearchString('BLU', col)> -1 then code := '#48D1CC' elif SearchString('BLU', col)> -1 and SearchString('BLA', col)> -1 then code := '#000080' elif SearchString('RED', col)> -1 then code := '#FF0000' elif SearchString('GRE', col)> -1 then code := '#008000' elif SearchString('BLU', col)> -1 then code := '#0000FF' elif SearchString('ORA', col)> -1 then code := '#CD853F' elif SearchString('YEL', col)> -1 then code := '#FFD700' elif SearchString('PUR', col)> -1 then code := '#9400D3' elif SearchString('GRA', col)> -1 then code := '#404040' elif SearchString('BRO', col)> -1 then code := '#800000' elif SearchString('PIN', col)> -1 then code := '#FF00FF' elif SearchString('BLA', col)> -1 then code := '#000000' elif SearchString('WHI', col)> -1 then code := '#FFFFFF' else code := '#FFFFFF'; fi; res := ''.what.''; return(res); end: HTMLTitle := proc(what: string, how: string) description 'Converts any text into html headings, bold or italiic text what: any text how: keyword, at least 1 letter e.g. "H1" (Heading 1), "Heading 4", "bold", "it" etc.'; h := uppercase(how); if SearchString('H', h) > -1 and SearchString('1', h) > -1 then code := 'H1' elif SearchString('H', h) > -1 and SearchString('2', h) > -1 then code := 'H2' elif SearchString('H', h) > -1 and SearchString('3', h) > -1 then code := 'H3' elif SearchString('H', h) > -1 and SearchString('4', h) > -1 then code := 'H4' elif SearchString('B', h) > -1 then code := 'B' elif SearchString('I', h) > -1 then code := 'I' else code := '' fi; if code <>'' then res := '<'.code.'>'.what.'' else res := what fi; return(res); end: HTMLCols := proc(what: array(string), border: integer) description 'Puts each element of the array into different columns. border: thickness of border (0 => invisible)'; out := ''; for i to length(what) do out := out.''; od; out := out.'
'.what[i].'
'; return(out); end: HTMLRows := proc(what: array(string), border: integer) description 'Puts each element of the array into different rows. border: thickness of border (0 => invisible)'; out := ''; for i to length(what) do out := out.''; od; out := out.'
'.what[i].'
'; return(out); end: HTMLprint := proc(what: anything, Directory: string, Filename: string) description 'Prints what either into a file (if specified) or just returns the string in html format. what: MultiAlign similar as print(), but creates a postscript file for the tree in the same directory, same filename with .ps extension what: string adds to the text and prints it Filename: Use NO extension. ".html" is added automatically'; if nargs > 1 then dir := Directory; if dir[length(dir)] <> '/' then dir := dir.'/'; fi; fi; width := 80; if type(what, MultiAlign) then msa := what; Seq := msa['Seq']; Align := msa['MSA']; Title := msa['Title']; Ref := msa[Reference]; order := msa['order']; out := ''; if Title <> 0 then out := out.HTMLTitle(Title, 'H3'); fi; if Align <> 0 then out := out.HTMLTitle('Multiple sequence alignment:\n', 'H4'); if Align[1] = Align[length(Align)] and length(Align)>length(msa['AllAll']) then Align := Align[1..length(Align)-1]; fi; sc := msa['Score']; AllAll := msa['AllAll']: out := out.sprintf('Score of the alignment: %5.3f
\nMaximum possible score: %5.3f

', sc[2], msa['max']); times:=round(length(Align[1])/width+0.5); for i to times do r := ''; for j to length(Ref) do r := r.sprintf('%a
\n', Ref[order[j]]); od; r := r.'Score'; a := ''; for j to length(Align) do w := order[j]; a := a.sprintf('%s
\n', Align[w,width*(i-1)+1 .. min(width*i,length(Align[w]))] ); od; if msa[7] <> 0 then a := a.sprintf('%s
\n',sc[1, width*(i-1)+1 .. min(width*i,length(sc[1]))] ); fi; out := out.HTMLCols([r, a], 0).'

'; od: else out := out.'There is no alignment
\n'; fi; if msa['pos'] <> 0 then tmp := 'Positions in original sequences: \n'; pos := msa['pos']; for i to length(pos)-1 do tmp := tmp.sprintf('%d (=%d): %d..%d, ',i,pos[i,1], pos[i, 2], pos[i,3]); od; tmp := tmp.sprintf('%d (=%d): %d..%d',i, pos[i,1],pos[i, 2], pos[i,3]); out := out.tmp.'
'; fi; if msa[4] <> 0 and nargs > 1 then out := out.''.HTMLTitle('Phylogenetic tree:\n', 'H4').''; Set(plotoutput = Filename.'.ps'); DrawTree(msa[4], 'Phylogenetic tree (MinSquare)'); fi; if nargs > 1 then HTMLprint(out, dir, Filename); fi; return(out); elif type(what, string) then if nargs > 1 then OpenAppending(dir.Filename.'.html'); fi; print(''); times:=round(length(what)/80+0.5); for i to times do printf('%s', what[width*(i-1)+1 .. min(width*i,length(what))] ); od; print(''); if nargs > 1 then OpenWriting(terminal); fi; fi; end: # ********************************* HTMLColorprint := proc(what: anything, Directory: string, Filename: string, Positions: array, Colors: array(string), index: integer, DP0) description 'Prints what either into a file (if specified) or just returns the string in html format. what: MultiAlign similar as print(), but creates a postscript file for the tree in the same directory, same filename with .ps extension string adds to the text and prints it Filename: Use NO extension. ".html" is added automatically'; Colors1 := ['blue', 'orange', 'pink', 'red', 'green', 'magenta','cyan', 'brown', 'yellow', 'black']; dir := Directory; if dir[length(dir)] <> '/' then dir := dir.'/'; fi; width := 80; msa := what: Seq := msa['Seq']: sec := GetSecondary(msa); Align := msa['MA']: Title := msa['Title']: if Title = 0 then Title := ''; fi; Ref := msa[Reference]: order := msa['order']: out := ''; if Title <> 0 then out := out.HTMLTitle(Title, 'H3'); fi; if Align <> 0 then out := out.HTMLTitle('Multiple sequence alignment:\n', 'H4'); msa['all']; if Align[1] = Align[length(Align)] and length(Align)>length(msa['AllAll']) then Align := Align[1..length(Align)-1]; fi; out := out.sprintf('Score of the alignment: %5.3f
\nMaximum possible score: %5.3f

', msa['score',2], msa['max']); ot := OutTable(msa): if nargs > 5 then if index = 0 then nr := length(Colors) else nr := mod(index, length(Colors))+1; fi; for row from 1 to length(ot[2]) do for i to length(ot[2, row]) do part := HTMLColor(ot[2, row, i], Colors[nr]); ot[2, row, i] := part; od; od; else for pos from 1 to length(Positions) do nr := mod(pos, length(Colors))+1; if Positions[pos, 1] <> 0 then ot := ColorMSA(ot, msa, Positions[pos, 1], Colors[nr]); fi; od: fi; for i to length(ot[1]) do r := ''; for j to length(Ref) do r := r.sprintf('%s
\n', ot[1, i, order[j]]); od; for k from length(Ref)+1 to length(ot[2,i]) do if ot[1, i, k] <> 0 then r := r.sprintf('%s
\n', ot[1, i, k]); fi; od; a := ''; for j to length(Align) do a := a.sprintf('%s
\n', ot[2, i, order[j]]); od; for j from length(Align)+1 to length(ot[2,i]) do if ot[1, i, j] <> 0 then a := a.sprintf('%s
\n', ot[2, i, j]); fi; od; out := out.HTMLCols([r, a], 0).'

'; od: out := out.ShowRef(msa); else out := out.'There is no alignment
\n'; fi; if msa['pos'] <> 0 then tmp := 'Positions in original sequences: \n'; pos := msa['pos']; for i to length(pos)-1 do tmp := tmp.sprintf('%d (=%d): %d..%d, ',i,pos[i,1], pos[i, 2], pos[i,3]); od; tmp := tmp.sprintf('%d (=%d): %d..%d',i, pos[i,1],pos[i, 2], pos[i,3]); out := out.tmp.'
'; fi; if msa['Info'] <> 0 then tmp := sprintf('
'); inf := msa['Info']; if type(inf, array) then for i to length(inf) do tmp := tmp.sprintf('%s
',inf[i]); od; out := out.tmp.'
'; fi; fi; if msa[4] <> 0 and nargs > 1 then if nargs > 5 then out := out.''.HTMLTitle('Phylogenetic tree:\n', 'H4').''; Set(plotoutput = dir.Filename.index.'.ps'); else out := out.''.HTMLTitle('Phylogenetic tree:\n', 'H4').''; Set(plotoutput = dir.Filename.'.ps'); fi; t := msa['tree']; n := length(msa['align']); id := GetAnimals(msa['ref']); ancol := GetColor(Colors1, id); t1 := ChangeLeafLabels(t, msa['ref']); t1 := CT_Color(t1, ancol); t1 := AddSpecies(t1, id); DrawTree(t1, Title, Colors1, id, ancol); fi; out := out.'
**************************************************************
'; if nargs > 1 then HTMLprint(out, dir, Filename); fi; return(out); end: GetColor := proc(ColorNames, Species); spec := copy([]); n := length(ColorNames); colnr := 0; collist := CreateArray(1..length(Species)); for which to length(Species) do j := SearchArray(Species[which], spec); if j = 0 then spec := append(spec, Species[which]); colnr := colnr + 1; else colnr := j; fi; if colnr > n then colnr := mod(n, colnr); fi; collist[which] := colnr; od; return(collist); end: # ********************************** ColorMSA := proc(ot: array, msa: MultiAlign, Pos: array(array(integer)), color: string); Align := msa['ma']; Seq := msa['seq']; Aligncol := ot[2]; width := 80; for i to length(Pos) do seqnr := Pos[i,1]; gapseq := Align[seqnr]; left:= PosinMA(gapseq, Pos[i,2]); right:= PosinMA(gapseq, Pos[i,3]); if left >= right then return([ot[1], Aligncol]); fi; # if we are within the sequence if left < length(gapseq) then startrow := trunc(left/width) + 1; startx := PosinHTML(Aligncol[startrow, seqnr], mod(left, width)); if startx = 0 then startx := width; fi; endrow := trunc(right/width) + 1; endx := PosinHTML(Aligncol[endrow, seqnr], mod(right, width)); if endx = 0 then endx := min(width, length(Aligncol[endrow, seqnr])); fi; if startrow < endrow then part := HTMLColor(Aligncol[startrow, seqnr, startx..-1], color); Aligncol[startrow, seqnr] := Aligncol[startrow, seqnr, 1..startx-1].part ; for row from startrow+1 to endrow-1 do part := HTMLColor(Aligncol[row, seqnr], color); Aligncol[row, seqnr] := part; od; part := HTMLColor(Aligncol[endrow, seqnr, 1..endx], color); Aligncol[endrow, seqnr] := part.Aligncol[endrow, seqnr, endx+1..length(Aligncol[endrow, seqnr])]; else part := HTMLColor(Aligncol[startrow, seqnr, startx..endx], color); Aligncol[startrow, seqnr] := Aligncol[startrow, seqnr, 1..startx-1].part.Aligncol[startrow, seqnr, endx+1..-1] ; fi; fi; od; return([ot[1], Aligncol]); end: #---------------------------- OutTable := proc(msa: MultiAlign); Align := msa['ma']: Ref := msa['labels']: sc := msa['Score']: sec := GetSecondary(msa); width := 80; sup := msa['sup']; times:=round(length(Align[1])/width+0.5); outtab := CreateArray(1..2, 1..times, 1..length(Align)+length(sup)+1); for i to times do for j to length(Ref) do outtab[1, i, j] := sprintf('%d', j); od; outtab[1, i, j] := 'Score'; for j to length(Align) do outtab[2, i, j] := sprintf('%s', Align[j,width*(i-1)+1 .. min(width*i,length(Align[j]))] ); od; if msa[7] <> 0 then outtab[2, i, j] := sprintf('%s',sc[1, width*(i-1)+1 .. min(width*i,length(sc[1]))] ); fi; m := 0; for k to length(sup) do su := sup[k]; if su <> 0 and su[2] <> 0 then m := m + 1; outtab[1, i, j+m] := sprintf('%s',su[1]); outtab[2, i, j+m] := sprintf('%s\n', su[2, width*(i-1)+1 .. min(width*i,length(su[2]))] ); else outtab[1, i, j+m] := 0; outtab[2, i, j+m] := 0; fi; od; od; return(outtab); end: ShowRef := proc(msa: MultiAlign); ref := msa['Ref']; n := length(ref); ent := 0; f1 := ''; f2:= ''; out := '

'; if type(ent, Entry) then out := out.''; else out := out.''; fi; out := out.''; for i to n do out := out.''; od; out := out.'
Nr ID DescOCOSNumberID
'; if type(ent, Entry) then e := Entry(ent[i]); out := out.sprintf(' %4d %s %s %s %s',i, op(e['ID']), f1.e['DE'].f2, f1.GetEntryInfo(e, 'OC')[2].f2, f1.GetEntryInfo(e, 'OS')[2].f2); else out := out.sprintf(' %4d %s',i, ref[i]); fi; out := out.'

'; print('Show Ref called'); # for testing # CallSystem('rm -f '.dir.file.'.html'); # HTMLprint(out, dir, file); return(out); end: PosinHTML := proc(gapseq: string, x: integer); i := 0; posx := 0; while posx < x and i < length(gapseq) do i := i + 1; if gapseq[i] <>'<' then posx := posx + 1; else while gapseq[i]<>'>' do i := i + 1; od; fi; od; i; end: PrintMsaList := proc( msa: MultiAlign, DP: DomainParameter, dir: string, file: string, limit0:integer, Colors0: array); if nargs < 6 then Colors := ['red', 'green', 'blue', 'orange', 'light green', 'brown', 'yellow', 'pink', 'light blue', 'olive green','white', 'blue green', 'gray', 'black blue']; if nargs < 5 then limit := 5; else limit := limit0; fi: else Colors := Colors1; fi: ML := msa['ML']: msalist := ML['msalist']: n := length(msalist); Posscore := CreateArray(1..n, 1..2); for i from 1 to n do if msalist[i] <> [] then sc := msalist[i, 'score'][2]; if sc > limit then Posscore[i, 1] := msalist[i,'pos']; Posscore[i, 2] := sc; fi; fi; od; CallSystem('rm -f '.dir.file.'.html'); out := HTMLColorprint(msa, dir, file, Posscore, Colors); for i from 1 to n do if msalist[i, 'score'][2] > limit then HTMLColorprint(msalist[i], dir, file, [], Colors, i); fi; od; end: