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Of course, your program's commands -might be different; for a GUI interface, you would use an "about box". - - You should also get your employer (if you work as a programmer) or school, -if any, to sign a "copyright disclaimer" for the program, if necessary. -For more information on this, and how to apply and follow the GNU GPL, see -<http://www.gnu.org/licenses/>. - - The GNU General Public License does not permit incorporating your program -into proprietary programs. If your program is a subroutine library, you -may consider it more useful to permit linking proprietary applications with -the library. If this is what you want to do, use the GNU Lesser General -Public License instead of this License. But first, please read -<http://www.gnu.org/philosophy/why-not-lgpl.html>. - diff --git a/src/nbc/NEWS b/src/nbc/NEWS deleted file mode 100644 index 501c1bb..0000000 --- a/src/nbc/NEWS +++ /dev/null @@ -1,3 +0,0 @@ -score and tabulate have been rewritten in Standard ML, to take advantage -of certain optimizations that the MLton compiler performs, and improve -performance. Their behavior should be unchanged, except for some speedup. diff --git a/src/nbc/binary.sml b/src/nbc/binary.sml deleted file mode 100644 index af5acd5..0000000 --- a/src/nbc/binary.sml +++ /dev/null @@ -1,26 +0,0 @@ -signature BINARY = sig - val fromInt32: int -> Word8Vector.vector - val fromInt16: int -> Word8Vector.vector - val fromReal: real -> Word8Vector.vector -end - -structure Binary :> BINARY = struct - val word8VectorFromArray = Word8ArraySlice.vector o Word8ArraySlice.full - fun fromInt32 i = - let - val array = Word8Array.array (PackWord32Little.bytesPerElem, 0w0) - val word = LargeWord.fromInt i - in - PackWord32Little.update (array, 0, word) - ; word8VectorFromArray array - end - fun fromInt16 i = - let - val array = Word8Array.array (PackWord16Little.bytesPerElem, 0w0) - val word = LargeWord.fromInt i - in - PackWord16Little.update (array, 0, word) - ; word8VectorFromArray array - end - val fromReal = PackRealLittle.toBytes -end diff --git a/src/nbc/build.sh b/src/nbc/build.sh deleted file mode 100644 index 3328271..0000000 --- a/src/nbc/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#! /bin/sh -v -mllex substitution.lex -mlyacc substitution.grm -mlton -link-opt -lJudy -link-opt -lz score.mlb gzip.c diff --git a/src/nbc/clean.sh b/src/nbc/clean.sh deleted file mode 100644 index 58d95bf..0000000 --- a/src/nbc/clean.sh +++ /dev/null @@ -1,2 +0,0 @@ -#! /bin/sh -v -rm substitution.lex.sml substitution.grm.sig substitution.grm.sml score diff --git a/src/nbc/count.ml b/src/nbc/count.ml deleted file mode 100644 index bd97b7b..0000000 --- a/src/nbc/count.ml +++ /dev/null @@ -1,60 +0,0 @@ -module ExtArray = ExtArray.Array -let (|>) a b = b a - -module Options = struct - let parser = OptParse.OptParser.make ~version:"1.0" () - let per_word = - let option = OptParse.StdOpt.str_option ~metavar:"file" () in - OptParse.OptParser.add parser ~short_name:'w' ~long_name:"per-word" - ~help:"file to store per-word counts in" option; - (fun () -> match OptParse.Opt.opt option with - Some x -> x - | None -> - OptParse.OptParser.usage parser (); - exit 1 - ) - let total = - let option = OptParse.StdOpt.str_option ~metavar:"file" () in - OptParse.OptParser.add parser ~short_name:'t' ~long_name:"total" - ~help:"file to store total count in" option; - (fun () -> match OptParse.Opt.opt option with - Some x -> x - | None -> - OptParse.OptParser.usage parser (); - exit 1 - ) - let order = - let option = OptParse.StdOpt.int_option ~default:15 () in - OptParse.OptParser.add parser ~short_name:'r' ~long_name:"order" option; - (fun () -> OptParse.Opt.get option) - let files = OptParse.OptParser.parse_argv parser - let total = total () - let per_word = per_word () - let order = order () -end - -let load_file order judy total name = - Misc.io_of_gzip name |> Fasta.enum_words order - |> Enum.fold (fun word total -> - Judy.bump judy word; - Judy.bump judy (Gene.reverse word); - total + 2 - ) total -let load_files order names = - let judy = Judy.create () in - List.fold_left (load_file order judy) 0 names, judy -let gzip_output_string c s = Gzip.output c s 0 (String.length s) -let () = - let total_words, judy = load_files Options.order Options.files in - ( - let c = open_out Options.total in - output_string c (string_of_int total_words ^ "\n"); - close_out c - ); ( - let c = Gzip.open_out Options.per_word in - Judy.iter (fun word count -> - gzip_output_string c - (String.concat "" [string_of_int count; " "; word; "\n"]) - ) judy; - Gzip.close_out c - ) diff --git a/src/nbc/fail.sml b/src/nbc/fail.sml deleted file mode 100644 index f3d324c..0000000 --- a/src/nbc/fail.sml +++ /dev/null @@ -1,10 +0,0 @@ -signature FAIL = sig - val fail: string -> 'a -end - -structure Fail :> FAIL = struct - fun fail why = ( - TextIO.output (TextIO.stdErr, why ^ "\n") - ; OS.Process.exit OS.Process.failure - ) -end diff --git a/src/nbc/fasta-test.mlb b/src/nbc/fasta-test.mlb deleted file mode 100644 index 564fd11..0000000 --- a/src/nbc/fasta-test.mlb +++ /dev/null @@ -1,9 +0,0 @@ -local - local - fasta-all.mlb - in - functor Test - end -in - test-generate.sml -end diff --git a/src/nbc/gene.mlb b/src/nbc/gene.mlb deleted file mode 100644 index 47261ff..0000000 --- a/src/nbc/gene.mlb +++ /dev/null @@ -1,5 +0,0 @@ -local - $(SML_LIB)/basis/basis.mlb -in - gene.sml -end diff --git a/src/nbc/gene.sml b/src/nbc/gene.sml deleted file mode 100644 index 738e3fe..0000000 --- a/src/nbc/gene.sml +++ /dev/null @@ -1,49 +0,0 @@ -signature GENE = sig - val reverse: string -> string - val first: int -> string - val next: string -> string option -end - -structure Gene :> GENE = struct - fun reverse s = - let - val n = size s - val m = n - 1 - fun opposite c = case c of - #"A" => #"T" - | #"T" => #"A" - | #"C" => #"G" - | #"G" => #"C" - | _ => c - in - CharVector.tabulate (n, fn i => opposite (String.sub (s, m - i))) - end - fun first order = CharVector.tabulate (order, fn _ => #"A") - fun next nmer = - let - val order = size nmer - fun finish (rightmostNonT, replacement) = CharVector.tabulate ( - order - , fn index => - case - Int.compare ( - index - , rightmostNonT - ) - of - LESS => String.sub (nmer, index) - | EQUAL => replacement - | GREATER => #"A" - ) - fun continue index = - if index < 0 then NONE - else case String.sub (nmer, index) of - #"A" => SOME (finish (index, #"C")) - | #"C" => SOME (finish (index, #"G")) - | #"G" => SOME (finish (index, #"T")) - | #"T" => continue (index - 1) - | _ => raise Fail "Invalid base" - in - continue (size nmer - 1) - end -end diff --git a/src/nbc/genome.sml b/src/nbc/genome.sml deleted file mode 100644 index 81f3183..0000000 --- a/src/nbc/genome.sml +++ /dev/null @@ -1,33 +0,0 @@ -signature GENOME = sig - exception Bad - type t - val load: string * int -> t - val get: t * string -> int option -end - -structure Genome :> GENOME = struct - exception Bad - fun |> (x, f) = f x - infix |> - - type t = (string, int) HashTable.hash_table - fun load (gname, order) = - let - val h = HashTable.mkTable - (HashString.hashString, op =) - (1024 * 1024, Fail "") - in - Options.genomeText (order, gname) |> Gzip.openIn |> Misc.sequenceLines - |> Sequence.map (fn s => ( - case Misc.split2 s of - SOME (count, nmer) => ( - nmer - , case Int.fromString count of - NONE => raise Bad - | SOME x => x - ) | NONE => raise Bad - )) |> Sequence.app (HashTable.insert h) - ; h - end - fun get (h, nmer) = HashTable.find h nmer -end diff --git a/src/nbc/gzip.c b/src/nbc/gzip.c deleted file mode 100644 index d2bf98f..0000000 --- a/src/nbc/gzip.c +++ /dev/null @@ -1,13 +0,0 @@ -#include <zlib.h> - -int -gzreadoffset(gzFile file, voidp buf, unsigned offset, unsigned len) -{ - return gzread(file, buf + offset, len); -} - -int -gzwriteoffset(gzFile file, voidpc buf, unsigned offset, unsigned len) -{ - return gzwrite(file, buf + offset, len); -} diff --git a/src/nbc/gzip.sml b/src/nbc/gzip.sml deleted file mode 100644 index fc6e5ff..0000000 --- a/src/nbc/gzip.sml +++ /dev/null @@ -1,164 +0,0 @@ -signature GZIP = sig - exception Failure - val openIn: string -> TextIO.instream - val openOut: string -> TextIO.outstream -end - -structure Gzip :> GZIP = struct - structure Primitive :> sig - eqtype gzFile - val null: gzFile - val gzopen: string * string -> gzFile - val gzread: gzFile * CharArray.array * word * word -> int - val gzwritea: gzFile * CharArray.array * word * word -> int - val gzwritev: gzFile * CharVector.vector * word * word -> int - val gzclose: gzFile -> int - end = struct - type gzFile = MLton.Pointer.t - val null = MLton.Pointer.null - val gzopen = _import "gzopen": string * string -> gzFile; - val gzread = _import "gzreadoffset": - gzFile * CharArray.array * word * word -> int; - val gzwritea = _import "gzwriteoffset": - gzFile * CharArray.array * word * word -> int; - val gzwritev = _import "gzwriteoffset": - gzFile * CharVector.vector * word * word -> int; - val gzclose = _import "gzclose": gzFile -> int; - end - - exception Failure - fun readArraySlice (g, slice) = - let - val (array, offset, length) = CharArraySlice.base slice - val wordoffset = Word.fromInt offset - val wordlength = Word.fromInt length - in - Primitive.gzread (g, array, wordoffset, wordlength) - end - fun readerFromPrimitive (name, g) = - let - val closed = ref false - fun error x = raise IO.Io { - name = name - , function = "readArr" - , cause = x - } - fun readArr slice = - if !closed then error IO.ClosedStream - else let - val r = readArraySlice (g, slice) - in - if r < 0 then error Failure - else r - end - fun close () = - if !closed then () - else ( - closed := true - ; ignore (Primitive.gzclose g) - ) - in - TextPrimIO.augmentReader (TextPrimIO.RD { - name = name - , chunkSize = 32 * 1024 - , readVec = NONE - , readArr = SOME readArr - , readVecNB = NONE - , readArrNB = NONE - , block = NONE - , canInput = NONE - , avail = fn () => NONE - , getPos = NONE - , setPos = NONE - , endPos = NONE - , verifyPos = NONE - , close = close - , ioDesc = NONE - }) - end - fun readerFromName name = - let - val path = name ^ "\000" - val g = Primitive.gzopen (path, "r\000") - in - if g = Primitive.null then NONE - else SOME (readerFromPrimitive (name, g)) - end - fun openIn name = - case readerFromName name of - SOME x => TextIO.mkInstream (TextIO.StreamIO.mkInstream (x, "")) - | NONE => raise IO.Io { - name = name - , function = "openIn" - , cause = Failure - } - fun writeSlice (base, write) (g, slice) = - let - val (vector, offset, length) = base slice - val wordoffset = Word.fromInt offset - val wordlength = Word.fromInt length - in - write (g, vector, wordoffset, wordlength) - end - val writeVectorSlice = writeSlice (CharVectorSlice.base, Primitive.gzwritev) - val writeArraySlice = writeSlice (CharArraySlice.base, Primitive.gzwritea) - fun writerFromPrimitive (name, g) = - let - val closed = ref false - fun error (function, x) = raise IO.Io { - name = name - , function = function - , cause = x - } - fun close () = - if !closed then () - else ( - closed := true - ; ignore (Primitive.gzclose g) - ) - fun write (name, realWrite) slice = - if !closed then error (name, IO.ClosedStream) - else let - val r = realWrite (g, slice) - in - if r <= 0 then error (name, Failure) - else r - end - val writeVec = write ("writeVec", writeVectorSlice) - val writeArr = write ("writeArr", writeArraySlice) - in - TextPrimIO.augmentWriter (TextPrimIO.WR { - name = name - , chunkSize = 32 * 1024 - , writeVec = SOME writeVec - , writeArr = SOME writeArr - , writeVecNB = NONE - , writeArrNB = NONE - , block = NONE - , canOutput = NONE - , getPos = NONE - , setPos = NONE - , endPos = NONE - , verifyPos = NONE - , close = close - , ioDesc = NONE - }) - end - fun writerFromName name = - let - val path = name ^ "\000" - val g = Primitive.gzopen (path, "w9") - in - if g = Primitive.null then NONE - else SOME (writerFromPrimitive (name, g)) - end - fun openOut name = - case writerFromName name of - SOME x => TextIO.mkOutstream (TextIO.StreamIO.mkOutstream (x, IO.NO_BUF)) - | NONE => raise IO.Io { - name = name - , function = "openOut" - , cause = Failure - } -end - diff --git a/src/nbc/history.mlb b/src/nbc/history.mlb deleted file mode 100644 index e7103cc..0000000 --- a/src/nbc/history.mlb +++ /dev/null @@ -1,5 +0,0 @@ -local - $(SML_LIB)/basis/basis.mlb -in - history.sml -end diff --git a/src/nbc/history.sml b/src/nbc/history.sml deleted file mode 100644 index 52c1bb2..0000000 --- a/src/nbc/history.sml +++ /dev/null @@ -1,74 +0,0 @@ -structure History :> sig - type history - val create: int -> history - val clear: history -> history - val push: history * char -> string option * history -end = struct - type history = {maximumSize: int, content: string} - fun create maximumSize = {maximumSize = maximumSize, content = ""} - fun clear {maximumSize, content = _} = - {maximumSize = maximumSize, content = ""} - fun addToString (string, newCharacter) = - let - val size = size string - in - CharVector.tabulate ( - size + 1 - , fn index => - if index = size then newCharacter - else String.sub (string, index) - ) - end - fun shiftIntoString (string, newCharacter) = - let - val size = size string - in - CharVector.tabulate ( - size - , fn index => - if index = size - 1 then newCharacter - else String.sub (string, index + 1) - ) - end - fun push ({maximumSize, content}, newCharacter) = - let - val currentSize = size content - in - if currentSize = maximumSize then - let - val newContent = shiftIntoString ( - content - , newCharacter - ) - in ( - SOME newContent - , { - maximumSize = maximumSize - , content = newContent - } - ) end - else if currentSize = maximumSize - 1 then - let - val newContent = addToString ( - content - , newCharacter - ) - in ( - SOME newContent - , { - maximumSize = maximumSize - , content = newContent - } - ) end - else ( - NONE - , { - maximumSize = maximumSize - , content = addToString ( - content - , newCharacter - ) - } - ) - end -end diff --git a/src/nbc/judy.sml b/src/nbc/judy.sml deleted file mode 100644 index 73e257b..0000000 --- a/src/nbc/judy.sml +++ /dev/null @@ -1,175 +0,0 @@ -signature JUDY = sig - exception OutOfMemory - type t - val create: unit -> t - val insert: t * string * int -> unit - val get: t * string -> int option - val bump: t * string -> unit - val first: t -> (string * int) option - val next: t * string -> (string * int) option - val sequence: t -> (string * int) Sequence.t - val app: (string * int -> unit) -> t -> unit -end -structure Judy :> JUDY = struct - structure Primitive :> sig - type judy - type errorDetail - type return - val judyNull: judy - val errorDetailNull: errorDetail - val get: judy * string * errorDetail -> return - val insert: judy ref * string * errorDetail -> return - val delete: judy ref * string * errorDetail -> int - val free: judy ref * errorDetail -> word - val first: judy * CharArray.array * errorDetail -> return - val next: judy * CharArray.array * errorDetail -> return - val returnIsError: return -> bool - val returnIsNull: return -> bool - val returnGet: return -> int - val returnSet: return * int -> unit - end = struct - type judy = MLton.Pointer.t - type errorDetail = MLton.Pointer.t - type return = MLton.Pointer.t - val judyNull = MLton.Pointer.null - val errorDetailNull = MLton.Pointer.null - val get = _import "JudySLGet": judy * string * errorDetail -> return; - val insert = _import "JudySLIns": judy ref * string * errorDetail -> return; - val delete = _import "JudySLDel": judy ref * string * errorDetail -> int; - val free = _import "JudySLFreeArray": judy ref * errorDetail -> word; - val first = _import "JudySLFirst": judy * CharArray.array * errorDetail -> return; - val next = _import "JudySLNext": judy * CharArray.array * errorDetail -> return; - local - val pjerr = MLton.Pointer.sub (MLton.Pointer.null, 0w1) - in - fun returnIsError return = return = pjerr - end - fun returnIsNull return = return = MLton.Pointer.null - fun returnGet return = Int32.toInt (MLton.Pointer.getInt32 (return, 0)) - fun returnSet (return, i) = MLton.Pointer.setInt32 (return, 0, Int32.fromInt i) - end - exception OutOfMemory - type t = {judy: Primitive.judy ref, max: int ref} - fun create () = {judy = ref Primitive.judyNull, max = ref 0} - fun insert ({judy, max}, key, value) = - let - val return = Primitive.insert ( - judy - , key ^ "\000" - , Primitive.errorDetailNull - ) - in - if Primitive.returnIsError return then raise OutOfMemory - else let - val n = size key - in - if !max < n then max := n else () - ; Primitive.returnSet (return, value) - end - end - fun get ({judy, max = _}, key) = - let - val return = Primitive.get ( - !judy - , key ^ "\000" - , Primitive.errorDetailNull - ) - in - if Primitive.returnIsNull return then NONE - else SOME (Primitive.returnGet return) - end - fun bump ({judy, max}, key) = - let - val return = Primitive.insert ( - judy - , key ^ "\000" - , Primitive.errorDetailNull - ) - in - if Primitive.returnIsError return then raise OutOfMemory - else let - val n = size key - in - if !max < n then max := n else () - ; Primitive.returnSet ( - return - , Primitive.returnGet return + 1 - ) - end - end - fun strlen array = - case CharArray.findi (fn (_, c) => c = #"\000") array of - NONE => raise Option - | SOME (i, _) => i - fun stringFromNullTerminatedArray array = - CharArraySlice.vector ( - CharArraySlice.slice (array, 0, SOME (strlen array)) - ) - fun first {judy, max} = - let - val array = CharArray.array (!max + 1, #"\000") - val return = Primitive.first ( - !judy - , array - , Primitive.errorDetailNull - ) - in - if Primitive.returnIsNull return then NONE - else SOME ( - stringFromNullTerminatedArray array - , Primitive.returnGet return - ) - end - fun next ({judy, max}, key) = - let - val size = size key - val array = CharArray.tabulate ( - !max + 1 - , fn i => - if i < size then String.sub (key, i) - else #"\000" - ) - val return = Primitive.next ( - !judy - , array - , Primitive.errorDetailNull - ) - in - if Primitive.returnIsNull return then NONE - else SOME ( - stringFromNullTerminatedArray array - , Primitive.returnGet return - ) - end - fun sequence t = - let - val last = ref NONE - fun get () = - case ( - case !last of - NONE => first t - | SOME key => next (t, key) - ) of - NONE => NONE - | SOME (return as (key, _)) => ( - last := SOME key - ; SOME return - ) - in - Sequence.from get - end - fun app f t = - let - fun apply (key, value) = ( - f (key, value) - ; fetch key - ) and fetch key = - case next (t, key) of - NONE => () - | SOME x => apply x - in - case first t of - NONE => () - | SOME x => apply x - end -end diff --git a/src/nbc/kahan.sml b/src/nbc/kahan.sml deleted file mode 100644 index 70c6b47..0000000 --- a/src/nbc/kahan.sml +++ /dev/null @@ -1,31 +0,0 @@ -(* Kahan summation *) - -signature KAHAN = sig - type t - val zero: t - val add: t * real -> t - val sum: t -> real - val sequence: real Sequence.t -> real - val list: real list -> real - val array: real array -> real -end - -structure Kahan :> KAHAN = struct - type t = real * real - val zero = (0.0, 0.0) - fun add ((s, c), x) = - let - val y = x - c - val t = s + y - in - (t, t - s - y) - end - fun sum (s, c) = s - local - fun swappedAdd (a, b) = add (b, a) - in - fun sequence e = sum (Sequence.fold swappedAdd zero e) - fun list l = sum (foldl swappedAdd zero l) - fun array a = sum (Array.foldl swappedAdd zero a) - end -end diff --git a/src/nbc/main.sml b/src/nbc/main.sml deleted file mode 100644 index 361d9ca..0000000 --- a/src/nbc/main.sml +++ /dev/null @@ -1,98 +0,0 @@ -structure Main = struct - -fun |> (x, f) = f x -infix |> - -val order = Options.order -val genomes = case Options.genomes of - SOME x => x |> TextIO.openIn |> Misc.sequenceLines - | NONE => Options.genomesDir |> Misc.sortedDirectoryNoPrefix |> Sequence.fromList -fun input () = - case Fasta.sequence (Gzip.openIn Options.input) of - NONE => Fail.fail "input file is not FASTA format" - | SOME x => - Sequence.map (fn (header, data) => - (header, String.map Char.toUpper data) - ) x -fun output genome = - let - fun inner format = case format of - Options.Matlab {variable, file} => - let - val matlab = Matlab.openOut file - val doubleArray = Matlab.beginDoubleArray (matlab, variable) - in { - write = fn (_, score) => - Matlab.writeDouble (doubleArray, score) - , close = fn () => ( - Matlab.concludeDoubleArray doubleArray - ; Matlab.closeOut matlab - ) - } end - | Options.Text filename => - let - val gzip = Gzip.openOut filename - in { - write = fn (header, score) => - TextIO.output ( - gzip - , Real.fmt (StringCvt.FIX (SOME 8)) score - ) - , close = fn () => TextIO.closeOut gzip - } end - | Options.Dual {text, matlab} => - let - val text = inner (Options.Text text) - val matlab = inner (Options.Matlab matlab) - in { - write = fn x => ( - #write text x - ; #write matlab x - ), close = fn () => ( - #close text () - ; #close matlab () - ) - } end - in - inner (Options.output genome) - end -fun totalWords (genome, order) = - let - val name = Options.totalWords (genome, order) - val input = TextIO.openIn name - in - (case Option.mapPartial Real.fromString (Misc.inputLine input) of - NONE => Fail.fail ("could not read number from " ^ name) - | SOME r => r - ) before TextIO.closeIn input - end - -val () = - Sequence.app (fn gname => - let - val {write, close} = output gname - val totalWords = totalWords (gname, order) - val genome = ( - Stopwatch.start ("Loading genome " ^ gname) - ; Genome.load (gname, order) - before Stopwatch.finish () - ) - in - Stopwatch.start ("Scoring fragments") - ; input () |> Sequence.app (fn (header, fragment) => - write ( - header - , Score.score ( - order - , Options.missConstant - , fn nmer => Genome.get (genome, nmer) - , totalWords - , fragment - ) - ) - ); Stopwatch.finish () - ; close () - end - ) genomes - -end diff --git a/src/nbc/matlab.sml b/src/nbc/matlab.sml deleted file mode 100644 index 65f532d..0000000 --- a/src/nbc/matlab.sml +++ /dev/null @@ -1,135 +0,0 @@ -signature MATLAB = sig - type t - val openOut: string -> t - type doubleArray - val beginDoubleArray: t * string -> doubleArray - val writeDouble: doubleArray * real -> unit - val concludeDoubleArray: doubleArray -> unit - val writeDoubleArray: t * string * real vector -> unit - val closeOut: t -> unit -end - -structure Matlab :> MATLAB = struct - fun outputReal (c, f) = BinIO.output (c, Binary.fromReal f) - fun outputInt32 (c, i) = BinIO.output (c, Binary.fromInt32 i) - fun outputInt16 (c, i) = BinIO.output (c, Binary.fromInt16 i) - type t = BinIO.outstream - type doubleArray = { - outstream: BinIO.outstream - , wholeSizePos: BinIO.StreamIO.out_pos - , paddedSize: int - , arraySizePos: BinIO.StreamIO.out_pos - , dataSizePos: BinIO.StreamIO.out_pos - , elements: int ref - } - fun pad n = - if n > 0 andalso n <= 4 then 4 - else (n + 7) div 8 * 8 - fun doubleArraySize (nameLength, arrayLength) = - 32 + nameLength + 4 + 8 + arrayLength * 8 - val s8Tag = 1 - val s32Tag = 5 - val u32Tag = 6 - val doubleTag = 9 - val doubleFlag = 6 - val matrixTag = 14 - fun lsl (x, y) = Word.toIntX (Word.<< (Word.fromInt x, Word.fromInt y)) - fun beginDoubleArray (c, name) = - let - val nameSize = Int.min (size name, 63) - val name = Word8VectorSlice.vector ( - Word8VectorSlice.slice (Byte.stringToBytes name, 0, SOME nameSize) - ) - val paddedSize = pad nameSize - val padding = Word8Vector.tabulate (paddedSize - nameSize, fn _ => 0w0) - val () = outputInt32 (c, matrixTag) - val wholeSizePos = BinIO.getPosOut c - val () = ( - outputInt32 (c, 0) - ; outputInt32 (c, u32Tag) - ; outputInt32 (c, 8) - ; outputInt32 (c, doubleFlag) - ; outputInt32 (c, 0) - ; outputInt32 (c, s32Tag) - ; outputInt32 (c, 8) - ; outputInt32 (c, 1) - ) - val arraySizePos = BinIO.getPosOut c - val () = ( - outputInt32 (c, 0) - ; if nameSize > 0 andalso nameSize <= 4 then - outputInt32 (c, lsl (nameSize, 16) + s8Tag) - else ( - outputInt32 (c, s8Tag) - ; outputInt32 (c, nameSize) - ); BinIO.output (c, name) - ; BinIO.output (c, padding) - ; outputInt32 (c, doubleTag) - ) - val dataSizePos = BinIO.getPosOut c - val () = outputInt32 (c, 0) - in - { - outstream = c - , wholeSizePos = wholeSizePos - , paddedSize = paddedSize - , arraySizePos = arraySizePos - , dataSizePos = dataSizePos - , elements = ref 0 - } - end - fun writeDouble (da, f) = ( - outputReal (#outstream da, f) - ; #elements da := !(#elements da) + 1 - ) - fun concludeDoubleArray da = - let - val saved = BinIO.getPosOut (#outstream da) - in - BinIO.setPosOut (#outstream da, #wholeSizePos da) - ; outputInt32 ( - #outstream da - , doubleArraySize (#paddedSize da, !(#elements da)) - ); BinIO.setPosOut (#outstream da, #arraySizePos da) - ; outputInt32 (#outstream da, !(#elements da)) - ; BinIO.setPosOut (#outstream da, #dataSizePos da) - ; outputInt32 (#outstream da, (!(#elements da) * 8)) - ; BinIO.setPosOut (#outstream da, saved) - end - fun writeDoubleArray (c, name, array) = - let - val da = beginDoubleArray (c, name) - in - Vector.app (fn x => writeDouble (da, x)) array - ; concludeDoubleArray da - end - fun writeHeader (c, software, version) = - let - val date = Date.fromTimeUniv (Time.now ()) - val text = concat [ - "MATLAB 5.0 MAT-file, written by " - , software, " ", version, ", " - , Date.fmt "%Y-%m-$d %H:%M:%S UTC" date - ] - val size = size text - val header = - CharVector.tabulate ( - 124 - , fn i => - if i < size then String.sub (text, i) - else #" " - ) - in - BinIO.output (c, Byte.stringToBytes header) - ; outputInt16 (c, 0x0100) - ; outputInt16 (c, 0x4d49) - end - fun openOut name = - let - val c = BinIO.openOut name - in - writeHeader (c, Program.name, Program.version) - ; c - end - val closeOut = BinIO.closeOut -end diff --git a/src/nbc/misc.sml b/src/nbc/misc.sml deleted file mode 100644 index 4790bbc..0000000 --- a/src/nbc/misc.sml +++ /dev/null @@ -1,125 +0,0 @@ -signature MISC = sig - val inputLine: TextIO.instream -> string option - val sequenceFromRead: (TextIO.instream -> 'a option) -> TextIO.instream -> 'a Sequence.t - val sequenceLines: TextIO.instream -> string Sequence.t - val sortedDirectoryNoPrefix: string -> string list - val sortedDirectory: string -> string list - val substitute: (string * string) list -> string -> string option - val basenameWithoutExtension: string -> string - val split2: string -> (string * string) option - val longestCommonSubstring: string list -> string -end - -structure Misc :> MISC = struct - fun |> (x, f) = f x - infix |> - fun \ f x y = f (x, y) - fun sequenceFromRead f ioc = Sequence.from (fn () => f ioc) - fun inputLine instream = case TextIO.inputLine instream of - NONE => NONE - | SOME x => SOME (String.substring (x, 0, size x - 1)) - val sequenceLines = sequenceFromRead inputLine - fun sortedDirectoryNoPrefix d = - let - val h = OS.FileSys.openDir d - fun loop l = - case OS.FileSys.readDir h of - NONE => ( - OS.FileSys.closeDir h - ; ListMergeSort.sort (op >) l - ) | SOME n => loop ( - if String.sub (n, 0) = #"." then l - else n :: l - ) - in - loop nil - end - fun sortedDirectory d = - map (\OS.Path.concat d) (sortedDirectoryNoPrefix d) - fun assoc list key = - case - List.find (fn (possibility, _) => possibility = key) list - of - NONE => NONE - | SOME (_, answer) => SOME answer - local - exception NotFound - in - fun substitute v s = - Substitution.substitute - (fn s => (case assoc v s of - NONE => raise NotFound - | SOME x => x - )) s - handle NotFound => NONE - end - fun basenameWithoutExtension s = OS.Path.base (OS.Path.file s) - local - fun index f (string, offset) = - let - val last = size string - fun loop i = - if i = last then ~1 - else if f (String.sub (string, i)) then i - else loop (i + 1) - in - loop offset - end - in - val indexWhitespace = index Char.isSpace - val indexNonWhitespace = index (not o Char.isSpace) - end - fun split2 s = - let - val f1b = indexNonWhitespace (s, 0) - in - if f1b = ~1 then NONE - else let - val f1e = indexWhitespace (s, f1b + 1) - in - if f1e = ~1 then NONE - else let - val f2b = indexNonWhitespace (s, f1e + 1) - in - if f2b = ~1 then NONE - else let - val f2e = indexWhitespace (s, f2b + 1) - in - if f2e = ~1 then SOME ( - substring (s, f1b, f1e - f1b) - , substring (s, f2b, size s - f2b) - ) else if indexNonWhitespace (s, f2e + 1) = ~1 then - SOME ( - substring (s, f1b, f1e - f1b) - , substring (s, f2b, f2e - f2b) - ) - else NONE - end - end - end - end - fun longestCommonSubstring strings = - case - foldl (fn (a, b) => (case b of - NONE => SOME a - | SOME b => if size a < size b then SOME a else SOME b - )) NONE strings - of - NONE => "" - | SOME shortest => let - val minimumSize = size shortest - fun loop (size, offset) = - let - fun next () = - if size + offset = minimumSize then - loop (size - 1, 0) - else loop (size, offset + 1) - val sub = substring (shortest, offset, size) - in - if List.all (String.isSubstring sub) strings then sub - else next () - end - in - loop (minimumSize, 0) - end -end diff --git a/src/nbc/nmer-test.mlb b/src/nbc/nmer-test.mlb deleted file mode 100644 index c363f4a..0000000 --- a/src/nbc/nmer-test.mlb +++ /dev/null @@ -1,9 +0,0 @@ -local - local - nmer-all.mlb - in - functor Test - end -in - test-generate.sml -end diff --git a/src/nbc/options.sml b/src/nbc/options.sml deleted file mode 100644 index 907c95a..0000000 --- a/src/nbc/options.sml +++ /dev/null @@ -1,202 +0,0 @@ -signature OPTIONS = sig - val order: int - val input: string - val genomesDir: string - val genomes: string option - val genomeText: int * string -> string - val totalWords: string * int -> string - val missConstant: real - datatype output = - Matlab of {variable: string, file: string} - | Text of string - | Dual of {text: string, matlab: {variable: string, file: string}} - val output: string -> output - val arguments: string list -end - -structure Options :> OPTIONS = struct - fun |> (x, f) = f x - infix |> - datatype outformat = Otext | Omatlab | Odual - local - val order = ref 15 - val fasta = ref NONE - val genomesDir = ref "/var/lib/genomes" - val genomes = ref NONE - val genomeText = ref "$genomes_dir/$genome/${order}perword.gz" - val totalWords = ref "$genomes_dir/$genome/${order}total" - val missConstant = ref (1.0 / 26067530.0 / 1000000.0) - val outFormat = ref Otext - val variable = ref "ps_g" - val outFile = ref "$input-$order-$genome.$extension" - fun withDefault (description, default) = concat ( - description - :: " (" - :: (case default of - NONE => ["no default)"] - | SOME x => ["default: ", x, ")"]) - ) - val options = [ - { - short = "r", long = ["order"] - , help = withDefault - ("Set the length of words used in matches", NONE) - , desc = GetOpt.ReqArg ( - fn x => case Int.fromString x of - NONE => Fail.fail - "given order is not a valid integer" - | SOME y => order := y - , "integer" - ) - }, { - short = "a", long = ["fasta-input"] - , help = "FASTA input file" - , desc = GetOpt.ReqArg (fn x => fasta := SOME x, "filename") - }, { - short = "j", long = ["genomes-dir"] - , help = withDefault ( - "Set the directory where genomes are stored" - , SOME (!genomesDir) - ), desc = GetOpt.ReqArg (fn x => genomesDir := x, "directory") - }, { - short = "g", long = ["genome-list"] - , help = withDefault ( - "Read genomes from this file, one per line" - , !genomes - ), desc = GetOpt.ReqArg (fn x => genomes := SOME x, "filename") - }, { - short = "w", long = ["genome-text"] - , help = withDefault ( - "Filename to read per-word counts from" - , SOME (!genomeText) - ), desc = GetOpt.ReqArg (fn x => genomeText := x, "filename") - }, { - short = "t", long = ["total-words"] - , help = withDefault ( - "Filename to read total word counts from" - , SOME (!totalWords) - ), desc = GetOpt.ReqArg (fn x => totalWords := x, "filename") - }, { - short = "k", long = ["miss-constant"] - , help = withDefault ( - "Set the constant used for scoring missing words" - , SOME (Real.toString (!missConstant)) - ), desc = GetOpt.ReqArg ( - fn x => (case Real.fromString x of - SOME y => missConstant := y - | NONE => Fail.fail - "given miss constant is not a valid number" - ), "number" - ) - }, { - short = "x", long = ["text"] - , help = "Select gzipped text output (default)" - , desc = GetOpt.NoArg (fn () => outFormat := Otext) - }, { - short = "m", long = ["matlab"] - , help = "Select Matlab binary output" - , desc = GetOpt.NoArg (fn () => outFormat := Omatlab) - }, { - short = "u", long = ["dual"] - , help = "Select both gzipped text and Matlab binary output" - , desc = GetOpt.NoArg (fn () => outFormat := Odual) - }, { - short = "v", long = ["variable"] - , help = withDefault ( - "Set Matlab output variable" - , SOME (!variable) - ), desc = GetOpt.ReqArg (fn x => variable := x, "name") - }, { - short = "o", long = ["output-file"] - , help = withDefault ( - "Set output filename(s)" - , SOME (!outFile) - ), desc = GetOpt.ReqArg (fn x => outFile := x, "filename") - } - ] - val optionsWithHelp = { - short = "h", long = ["help"] - , help = "Display help" - , desc = GetOpt.NoArg (fn () => ( - print ( - GetOpt.usageInfo { - header = "score <options>" - , options = options - } ^ "\n" - ); OS.Process.exit OS.Process.success - )) - } :: options - in - val (_, arguments) = GetOpt.getOpt { - argOrder = GetOpt.Permute - , options = optionsWithHelp - , errFn = print - } (CommandLine.arguments ()) - val order = !order - val input = case !fasta of - NONE => Fail.fail "No input file given" - | SOME x => x - val genomesDir = !genomesDir - val genomes = !genomes - val genomeText = fn (order, genome) => ( - case - Misc.substitute [ - ("genomes_dir", genomesDir) - , ("genome", genome) - , ("order", Int.toString order) - ] (!genomeText) - of - NONE => Fail.fail "bad per-word count filename syntax" - | SOME x => x - ) - val totalWords = fn (genome, order) => ( - case - Misc.substitute [ - ("genomes_dir", genomesDir) - , ("genome", genome) - , ("order", Int.toString order) - ] (!totalWords) - of - NONE => Fail.fail "bad total word count filename syntax" - | SOME x => x - ) - val missConstant = !missConstant - datatype output = - Matlab of {variable: string, file: string} - | Text of string - | Dual of {text: string, matlab: {variable: string, file: string}} - fun output genome = - let - val common = [ - ("input", Misc.basenameWithoutExtension input) - , ("order", Int.toString order) - , ("genome", genome) - ] - fun textName () = - case Misc.substitute - (("extension", "txt.gz") :: common) (!outFile) - of - NONE => Fail.fail "bad text output filename syntax" - | SOME x => x - fun matlabName () = - case Misc.substitute - (("extension", "mat") :: common) (!outFile) - of - NONE => Fail.fail "bad Matlab output filename syntax" - | SOME x => x - in - case !outFormat of - Otext => Text (textName ()) - | Omatlab => Matlab { - variable = !variable - , file = matlabName () - } | Odual => Dual { - text = textName () - , matlab = { - variable = !variable - , file = matlabName () - } - } - end - end -end diff --git a/src/nbc/program.sml b/src/nbc/program.sml deleted file mode 100644 index df787ad..0000000 --- a/src/nbc/program.sml +++ /dev/null @@ -1,9 +0,0 @@ -signature PROGRAM = sig - val version: string - val name: string -end - -structure Program :> PROGRAM = struct - val version = "2.0" - val name = "Naive Bayes Classifier - Score" -end diff --git a/src/nbc/score.mlb b/src/nbc/score.mlb deleted file mode 100644 index 662bb83..0000000 --- a/src/nbc/score.mlb +++ /dev/null @@ -1,27 +0,0 @@ -$(SML_LIB)/basis/basis.mlb -$(SML_LIB)/basis/mlton.mlb -$(SML_LIB)/smlnj-lib/Util/smlnj-lib.mlb -$(SML_LIB)/mlyacc-lib/mlyacc-lib.mlb -fail.sml -sequence.sml -ann "allowFFI true" in - judy.sml - gzip.sml -end -substitution.grm.sig -substitution.grm.sml -substitution.lex.sml -substitution.sml -misc.sml -options.sml -storejudy.sml -genome.sml -nmer.sml -kahan.sml -score.sml -binary.sml -program.sml -matlab.sml -stopwatch.sml -fasta.sml -main.sml diff --git a/src/nbc/score.sml b/src/nbc/score.sml deleted file mode 100644 index 90d569a..0000000 --- a/src/nbc/score.sml +++ /dev/null @@ -1,30 +0,0 @@ -signature SCORE = sig - val score: int * real * (string -> int option) * real * string -> real -end - -structure Score :> SCORE = struct - fun |> (x, f) = f x - infix |> - - fun addCount (hitsum, fcount, gcount, totalWords) = - Kahan.add (hitsum, Real.fromInt fcount * Math.ln (Real.fromInt gcount / totalWords)) - fun addNmer (totalWords, getGenomeCount) (nmer, ref fcount, (misses, anyhits, hitsum)) = - case getGenomeCount nmer of - NONE => (misses + 1, anyhits, hitsum) - | SOME gcount => ( - misses, true - , addCount (hitsum, fcount, gcount, totalWords) - ) - fun score (order, missConstant, getGenomeCount, totalWords, fragment) = - let - val add = addNmer (totalWords, getGenomeCount) - val seed = (0, false, Kahan.zero) - val (misses, anyhits, hitsum) = - Nmer.count (order, fragment) |> HashTable.foldi add seed - in - if anyhits then - Kahan.add (hitsum, Math.ln missConstant * Real.fromInt misses) - |> Kahan.sum - else Real.negInf - end -end diff --git a/src/nbc/sequence.sml b/src/nbc/sequence.sml deleted file mode 100644 index 73a3fbf..0000000 --- a/src/nbc/sequence.sml +++ /dev/null @@ -1,74 +0,0 @@ -signature SEQUENCE = sig - type 'a t - val fold: ('a * 'b -> 'b) -> 'b -> 'a t -> 'b - val from: (unit -> 'a option) -> 'a t - val map: ('a -> 'b) -> 'a t -> 'b t - val app: ('a -> unit) -> 'a t -> unit - val fromArray: 'a array -> 'a t - val fromList: 'a list -> 'a t - val toList: 'a t -> 'a list - val toArray: 'a t -> 'a array -end - -structure Sequence :> SEQUENCE = struct - type 'a t = unit -> 'a option - fun fold f seed t = - let - fun loop x = - case t () of - NONE => x - | SOME y => loop (f (y, x)) - in - loop seed - end - fun from t = t - fun map f t = - fn () => ( - case t () of - NONE => NONE - | SOME x => SOME (f x) - ) - fun app f t = - let - fun loop () = - case t () of - NONE => () - | SOME x => ( - f x - ; loop () - ) - in - loop () - end - fun fromArray a = - let - val i = ref 0 - fun f () = - if !i >= Array.length a then NONE - else - SOME (Array.sub (a, !i)) - before i := !i + 1 - in - from f - end - fun fromList l = - let - val c = ref l - fun f () = - case !c of - x :: y => (c := y; SOME x) - | nil => NONE - in - from f - end - fun toList t = - let - fun loop l = - case t () of - NONE => rev l - | SOME x => loop (x :: l) - in - loop nil - end - fun toArray t = Array.fromList (toList t) -end diff --git a/src/nbc/stopwatch.sml b/src/nbc/stopwatch.sml deleted file mode 100644 index 43547ed..0000000 --- a/src/nbc/stopwatch.sml +++ /dev/null @@ -1,24 +0,0 @@ -signature STOPWATCH = sig - exception FinishWithoutStart - val start: string -> unit - val finish: unit -> unit -end -structure Stopwatch :> STOPWATCH = struct - exception FinishWithoutStart - local - val time = ref NONE - in - fun start doing = ( - print (concat [doing, "..."]) - ; time := SOME (Time.now ()) - ) - fun finish () = case !time of - SOME t => ( - print (concat [ - " done in " - , Time.toString (Time.- (Time.now (), t)) - , " seconds.\n" - ]); time := NONE - ) | NONE => raise FinishWithoutStart - end -end diff --git a/src/nbc/storejudy.sml b/src/nbc/storejudy.sml deleted file mode 100644 index c6385be..0000000 --- a/src/nbc/storejudy.sml +++ /dev/null @@ -1,17 +0,0 @@ -signature STORE_JUDY = sig - type t - val load: (int * string) Sequence.t -> t - val get: t * string -> int option -end - -structure StoreJudy :> STORE_JUDY = struct - type t = Judy.t - fun load e = - let - val j = Judy.create () - in - Sequence.app (fn (count, nmer) => Judy.insert (j, nmer, count)) e - ; j - end - val get = Judy.get -end diff --git a/src/nbc/substitution.grm b/src/nbc/substitution.grm deleted file mode 100644 index 58505b5..0000000 --- a/src/nbc/substitution.grm +++ /dev/null @@ -1,50 +0,0 @@ -%% -%name SubstitutionGrm -%pos int -%arg (lookup): string -> string -%term - DOLLAR - | TEXT of string - | LEFT_PARENTHESIS - | LEFT_BRACE - | RIGHT_PARENTHESIS - | RIGHT_BRACE - | EOF -%nonterm - STRING of string - | LIST of string list - | PORTION of string - | VARIABLE of string - | PARENTHESIZED of string list - | INSIDE_PARENTHESES of string list - | BRACED of string list - | INSIDE_BRACES of string list -%eop EOF -%noshift EOF -%start STRING -%% -STRING: LIST (concat LIST) -LIST: - (nil) - | PORTION LIST (PORTION :: LIST) -PORTION: - TEXT (TEXT) - | VARIABLE (lookup VARIABLE) -VARIABLE: - DOLLAR TEXT (TEXT) - | PARENTHESIZED (concat PARENTHESIZED) - | BRACED (concat BRACED) -PARENTHESIZED: - LEFT_PARENTHESIS INSIDE_PARENTHESES RIGHT_PARENTHESIS (INSIDE_PARENTHESES) -INSIDE_PARENTHESES: - (nil) - | TEXT INSIDE_PARENTHESES (TEXT :: INSIDE_PARENTHESES) - | LEFT_PARENTHESIS INSIDE_PARENTHESES RIGHT_PARENTHESIS INSIDE_PARENTHESES - ("(" :: INSIDE_PARENTHESES1 @ ")" :: INSIDE_PARENTHESES2) -BRACED: - LEFT_BRACE INSIDE_BRACES RIGHT_BRACE (INSIDE_BRACES) -INSIDE_BRACES: - (nil) - | TEXT INSIDE_BRACES (TEXT :: INSIDE_BRACES) - | LEFT_BRACE INSIDE_BRACES RIGHT_BRACE INSIDE_BRACES - ("{" :: INSIDE_BRACES1 @ "}" :: INSIDE_BRACES2) diff --git a/src/nbc/substitution.lex b/src/nbc/substitution.lex deleted file mode 100644 index e460121..0000000 --- a/src/nbc/substitution.lex +++ /dev/null @@ -1,54 +0,0 @@ -type svalue = Tokens.svalue -type ('a, 'b) token = ('a, 'b) Tokens.token -type pos = int -type lexresult = (svalue, pos) token -type arg = int ref -fun eof _ = Tokens.EOF (~1, ~1) -%% -%full -%header (functor SubstitutionLexFun (structure Tokens: SubstitutionGrm_TOKENS)); -%arg (nesting); -%s VARIABLE PARENTHESIZED BRACED; -text = ([^$] | "\\$")+; -dollar = "$"; -leftparenthesis = "("; -rightparenthesis = ")"; -notparenthesis = [^()]+; -leftbrace = "{"; -rightbrace = "}"; -notbrace = [^{}]+; -other = [A-Za-z0-9_]+; -%% -<INITIAL>{text} => (Tokens.TEXT (yytext, yypos, yypos + size yytext)); -<INITIAL>{dollar} => (YYBEGIN VARIABLE; Tokens.DOLLAR (yypos, yypos + 1)); -<INITIAL>{dollar}{leftparenthesis} => ( - YYBEGIN PARENTHESIZED - ; nesting := !nesting + 1 - ; Tokens.LEFT_PARENTHESIS (yypos, yypos + 1) -); -<INITIAL>{dollar}{leftbrace} => ( - YYBEGIN BRACED - ; nesting := !nesting + 1 - ; Tokens.LEFT_BRACE (yypos, yypos + 1) -); -<VARIABLE>{other} => (YYBEGIN INITIAL; Tokens.TEXT (yytext, yypos, yypos + size yytext)); -<PARENTHESIZED>{notparenthesis} => (Tokens.TEXT (yytext, yypos, yypos + size yytext)); -<PARENTHESIZED>{leftparenthesis} => ( - nesting := !nesting + 1 - ; Tokens.LEFT_PARENTHESIS (yypos, yypos + 1) -); -<PARENTHESIZED>{rightparenthesis} => ( - nesting := !nesting - 1 - ; if !nesting = 0 then YYBEGIN INITIAL else () - ; Tokens.RIGHT_PARENTHESIS (yypos, yypos + 1) -); -<BRACED>{notbrace} => (Tokens.TEXT (yytext, yypos, yypos + size yytext)); -<BRACED>{leftbrace} => ( - nesting := !nesting + 1 - ; Tokens.LEFT_BRACE (yypos, yypos + 1) -); -<BRACED>{rightbrace} => ( - nesting := !nesting - 1 - ; if !nesting = 0 then YYBEGIN INITIAL else () - ; Tokens.RIGHT_BRACE (yypos, yypos + 1) -); diff --git a/src/nbc/substitution.sml b/src/nbc/substitution.sml deleted file mode 100644 index 57d55cf..0000000 --- a/src/nbc/substitution.sml +++ /dev/null @@ -1,26 +0,0 @@ -signature SUBSTITUTION = sig - val substitute: (string -> string) -> string -> string option -end - -structure Substitution :> SUBSTITUTION = struct - structure LrVals = SubstitutionGrmLrValsFun (structure Token = LrParser.Token) - structure Lex = SubstitutionLexFun (structure Tokens = LrVals.Tokens) - structure Parser = JoinWithArg ( - structure ParserData = LrVals.ParserData - structure Lex = Lex - structure LrParser = LrParser - ) - fun substitute lookup source = - let - val position = ref 0 - val instream = TextIO.openString source - fun read n = TextIO.inputN (instream, n) - val lexer = Parser.makeLexer read (ref 0) - fun error (_, _, _) = () - val (result, _) = Parser.parse (0, lexer, error, lookup) - val () = TextIO.closeIn instream - in - SOME result - end - handle Parser.ParseError => NONE -end diff --git a/src/nbc/tabulate.ml b/src/nbc/tabulate.ml deleted file mode 100644 index dbfbe43..0000000 --- a/src/nbc/tabulate.ml +++ /dev/null @@ -1,190 +0,0 @@ -let (|>) a b = b a -let car, cdr = fst, snd -let odd n = n land 1 = 1 -let even n = not (odd n) -module ExtArray = ExtArray.Array -module ExtList = ExtList.List -module ExtString = ExtString.String -module Program = struct - let name = "Naive Bayes Classifier - Tabulate" - let version = "1.0" -end -let chop_extra s = ExtString.strip ~chars:"_- " s -let any_alphanumeric s = - let e = String.length s in - let rec loop i = - if i = e then false - else match s.[i] with - 'a'..'z' | 'A'..'Z' | '0'..'9' -> true - | _ -> loop (i + 1) - in loop 0 -let guess_prefix filenames = - let s = - List.map Misc.basename_without_extension filenames - |> Misc.longest_common_substring |> chop_extra - in - if any_alphanumeric s then s - else "" -module Options = struct - let parser = OptParse.OptParser.make ~version:Program.version () - let genomes = - let option = OptParse.StdOpt.str_option ~metavar:"file" () in - OptParse.OptParser.add parser ~short_name:'g' ~long_name:"genome-list" option; - (fun () -> match OptParse.Opt.opt option with - Some x -> x - | None -> - OptParse.OptParser.usage parser (); - exit 1 - ) - let columns = - let option = OptParse.StdOpt.int_option ~default:200 () in - OptParse.OptParser.add parser ~short_name:'c' ~long_name:"columns" option; - (fun () -> OptParse.Opt.get option) - let template = - let option = OptParse.StdOpt.str_option ~metavar:"template" - ~default:"$prefix-$n.csv.gz" () in - OptParse.OptParser.add parser ~short_name:'t' ~long_name:"output-template" option; - (fun () -> OptParse.Opt.get option) - let given_prefix = - let x = ref None in - OptParse.StdOpt.str_callback ~metavar:"prefix" (fun s -> x := Some s) - |> OptParse.OptParser.add parser ~short_name:'p' - ~long_name:"output-prefix"; - (fun () -> !x) - let files = OptParse.OptParser.parse_argv parser - let prefix = match given_prefix () with - None -> ( - match guess_prefix files with - "" -> "table" - | s -> s - ) | Some x -> x - let string_of_int n = Printf.sprintf "%08u" n - let output n = template () |> Misc.substitute ["prefix", prefix; "n", string_of_int n] -end - -exception Collide of string * string * string -let match_files_to_genomes genomes files = - let g = Array.of_list genomes in - let gl = Array.length g in - let gi = Array.init gl (fun i -> i) in - Array.sort (fun ai bi -> compare (String.length g.(bi)) (String.length g.(ai))) gi; - let gf = Array.make gl None in - List.iter (fun file -> - try ( - let i = ExtArray.find (fun i -> ExtString.exists file g.(i)) gi in - match gf.(i) with - None -> gf.(i) <- Some file - | Some other_file -> raise (Collide (g.(i), other_file, file)) - ) with Not_found -> () (* file does not match any genomes *) - ) files; - let r = ref [] in - for i = gl - 1 downto 0 do - match gf.(i) with - None -> () (* no file matches a given genome *) - | Some file -> r := (g.(i), file) :: !r - done; - !r - -let columns = Options.columns () -let genomes, files = - let genomes = Misc.io_of_file (Options.genomes ()) |> Misc.enum_of_lines - |> ExtList.of_enum in - let g, f = match_files_to_genomes genomes Options.files |> List.split in - Array.of_list g, - f |> List.map (fun x -> x, x |> open_in |> IO.input_channel) |> Array.of_list - -let newfile, newline, cell, finish = - let i = ref 0 in - let open_file () = - i := !i + 1; - let filename = Options.output !i in - Gzip.open_out filename - in - let c = ref None in - let force_out () = - match !c with - None -> - let d = open_file () in - c := Some d; - d - | Some d -> d - in - let start_of_line = ref true in - (* newfile *) (fun () -> - (match !c with - Some c -> Gzip.close_out c - | None -> ()); - i := !i + 1; - c := None - ), - (* newline *) (fun () -> - let c = force_out () in - Gzip.output_char c '\n'; - start_of_line := true - ), - (* cell *) (fun s -> - let c = force_out () in - if not !start_of_line then Gzip.output_char c ','; - Gzip.output c s 0 (String.length s); - start_of_line := false - ), - (* finish *) (fun () -> - match !c with - Some c -> Gzip.close_out c - | None -> () - ) - -let read_two_fields (filename, c) = - let line = IO.read_line c in - match Misc.split2 line with - Some x -> x - | None -> - Printf.eprintf "\ - There is something wrong with the file %s. \ - The offending line is:\n%s\n" filename line; - exit 1 - -let output_file () = - newfile (); - let yes_we_have_input = - let x = ref false in - (fun () -> - if !x then () - else ( - cell "names"; - x := true - ) - ) - in - let a = Array.make columns "" in - let rec loop i = - if i < columns then ( - try ( - let name, datum = read_two_fields files.(0) in - yes_we_have_input (); - cell name; - a.(i) <- datum; - loop (i + 1) - ) with IO.No_more_input -> - if i > 0 then Array.sub a 0 i - else raise End_of_file - ) else a - in - let a = loop 0 in - let these_columns = Array.length a in - newline (); - cell genomes.(0); - for i = 0 to these_columns - 1 do cell a.(i) done; - newline (); - for i = 1 to Array.length genomes - 1 do - cell genomes.(i); - for j = 0 to these_columns - 1 do - let _, datum = read_two_fields files.(i) in - cell datum - done; - newline () - done - -let () = - try while true do output_file () done - with End_of_file -> finish () diff --git a/src/nbc/test-generate.sml b/src/nbc/test-generate.sml deleted file mode 100644 index 77cafd3..0000000 --- a/src/nbc/test-generate.sml +++ /dev/null @@ -1 +0,0 @@ -structure Test = Test () |