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-rw-r--r--src/nbc/count.sml290
1 files changed, 0 insertions, 290 deletions
diff --git a/src/nbc/count.sml b/src/nbc/count.sml
deleted file mode 100644
index d036050..0000000
--- a/src/nbc/count.sml
+++ /dev/null
@@ -1,290 +0,0 @@
-datatype sides = Single | Double
-datatype labeled = Labeled | Unlabeled
-local
- (*
- val perWord = ref NONE
- val total = ref NONE
- *)
- val order = ref (SOME 15)
- val sides = ref Double
- val labeled = ref Labeled
- val optionsWithoutHelp = [
- (* {
- short = "w", long = ["per-word"]
- , desc = GetOpt.ReqArg (
- fn file => perWord := SOME file
- , "file"
- ), help = "file to store per-word counts in"
- }, {
- short = "t", long = ["total"]
- , desc = GetOpt.ReqArg (
- fn file => total := SOME file
- , "file"
- ), help = "file to store total count in"
- }, *) {
- short = "r", long = ["order"]
- , desc = GetOpt.ReqArg (
- fn size => order := Int.fromString size
- , "size"
- ), help = "word size"
- }, {
- short = "1", long = ["single"]
- , desc = GetOpt.NoArg (fn () => sides := Single)
- , help = "only count one side"
- }, {
- short = "u", long = ["unlabeled"]
- , desc = GetOpt.NoArg (fn () => labeled := Unlabeled)
- , help = "emit counts for every possible nmer, without labels"
- }
- ]
- fun usageString () = GetOpt.usageInfo {
- header = CommandLine.name () ^ " <options> <input FASTA file> ..."
- , options = optionsWithoutHelp
- } ^ "\n"
- datatype status = Success | Failure
- fun displayHelpAndExit status = (
- TextIO.output (
- TextIO.stdErr
- , usageString ()
- ); OS.Process.exit (case status of
- Success => OS.Process.success
- | Failure => OS.Process.failure
- )
- )
- val options = {
- short = "h", long = ["help"]
- , desc = GetOpt.NoArg (fn () => displayHelpAndExit Success)
- , help = "display help"
- } :: optionsWithoutHelp
-in
- val (_, files) = GetOpt.getOpt {
- argOrder = GetOpt.Permute
- , options = options
- , errFn = fn errorMessage => (
- TextIO.output (TextIO.stdErr, errorMessage ^ "\n")
- ; displayHelpAndExit Failure
- )
- } (CommandLine.arguments ())
- (*
- val perWordFileName = case !perWord of
- NONE => (
- TextIO.output (
- stdErr
- , "per-word file name required but not provided\n"
- ); displayHelpAndExit Failure
- ) | SOME fileName => fileName
- val totalFileName = case !total of
- NONE => (
- TextIO.output (
- stdErr
- , "total file name required but not provided\n"
- ); displayHelpAndExit Failure
- ) | SOME fileName => fileName
- *)
- val order = case !order of
- NONE => (
- TextIO.output (
- TextIO.stdErr
- , "invalid order\n"
- ); displayHelpAndExit Failure
- ) | SOME integer => integer
- val sides = !sides
- val labeled = !labeled
-end
-
-signature COLLECTION = sig
- type collection
- type nmer
- val empty: unit -> collection
- val add: collection * nmer -> unit
- val get: collection * nmer -> int
- val app: (nmer * int -> unit) -> collection -> unit
-end
-
-functor Collection (Nmer: NMER)
-:> COLLECTION where type nmer = Nmer.nmer = struct
- type nmer = Nmer.nmer
- structure Table = HashTableFn (
- type hash_key = nmer
- val hashVal = Nmer.hash
- val sameKey = Nmer.equal
- )
- type collection = int ref Table.hash_table
- exception NotFound
- fun empty () = Table.mkTable (256 * 1024, NotFound)
- fun add (table, nmer) = case Table.find table nmer of
- NONE => Table.insert table (nmer, ref 1)
- | SOME count => count := !count + 1
- fun get (table, nmer) = case Table.find table nmer of
- NONE => 0
- | SOME (ref count) => count
- fun app execute table = Table.appi (fn (nmer, ref count) =>
- execute (nmer, count)
- ) table
-end
-
-datatype result = Success | Failure
-
-signature OUTPUT = sig
- type collection
- val output: collection -> unit
-end
-
-functor Unlabeled (
- structure Nmer: NMER
- structure Collection: COLLECTION
- sharing type Collection.nmer = Nmer.nmer
-) :> OUTPUT
- where type collection = Collection.collection
-= struct
- type collection = Collection.collection
- fun put string = TextIO.output (TextIO.stdOut, string)
- fun single count = (
- put (Int.toString count)
- ; put "\n"
- )
- fun output collection =
- let
- fun continue nmer = (
- single (Collection.get (collection, nmer))
- ;
- if nmer = Nmer.maximum then ()
- else continue (Nmer.next nmer)
- )
- in
- continue (Nmer.minimum)
- end
-end
-
-functor Labeled (
- structure Nmer: NMER
- structure Collection: COLLECTION
- sharing type Collection.nmer = Nmer.nmer
-) :> OUTPUT
- where type collection = Collection.collection
-= struct
- type collection = Collection.collection
- fun put string = TextIO.output (TextIO.stdOut, string)
- fun single (nmer, count) = (
- put (Nmer.toString nmer)
- ; put " "
- ; put (Int.toString count)
- ; put "\n"
- )
- fun output collection = Collection.app single collection
-end
-
-functor File (
- structure Collection: COLLECTION
- structure Output: OUTPUT
- sharing type Collection.collection = Output.collection
-) :> FILE
- where type nmer = Collection.nmer
- where type result = result
- where type argument = unit
-= struct
- type argument = unit
- type file = Collection.collection
- type read = unit
- type nmer = Collection.nmer
- type result = result
- fun startFile _ = Collection.empty ()
- fun startRead _ = ()
- fun nmer (counts, (), nmer) = Collection.add (counts, nmer)
- fun stopRead (_, ()) = ()
- fun stopFile counts = (
- Output.output counts
- ; Success
- )
- fun invalidFormat file = Failure
-end
-
-functor Everything (Nmer: NMER) = struct
- structure Collection = Collection (Nmer)
- structure Unlabeled = File (
- structure Collection = Collection
- structure Output = Unlabeled (
- structure Nmer = Nmer
- structure Collection = Collection
- )
- )
- structure Labeled = File (
- structure Collection = Collection
- structure Output = Labeled (
- structure Nmer = Nmer
- structure Collection = Collection
- )
- )
- structure SingleSidedUnlabeled = SingleSidedFasta (
- structure Nmer = Nmer
- structure File = Unlabeled
- )
- structure DoubleSidedUnlabeled = DoubleSidedFasta (
- structure Nmer = Nmer
- structure File = Unlabeled
- )
- structure SingleSidedLabeled = SingleSidedFasta (
- structure Nmer = Nmer
- structure File = Labeled
- )
- structure DoubleSidedLabeled = DoubleSidedFasta (
- structure Nmer = Nmer
- structure File = Labeled
- )
-end
-
-structure Everything32 = Everything (
- Nmer (
- val order = order
- structure Word = Word32
- )
-)
-structure Everything64 = Everything (
- Nmer (
- val order = order
- structure Word = Word64
- )
-)
-
-val process =
- if order <= 32 then (case sides of
- Single => (case labeled of
- Unlabeled => Everything32.SingleSidedUnlabeled.process
- | Labeled => Everything32.SingleSidedLabeled.process
- ) | Double => (case labeled of
- Unlabeled => Everything32.DoubleSidedUnlabeled.process
- | Labeled => Everything32.DoubleSidedLabeled.process
- )
- ) else (case sides of
- Single => (case labeled of
- Unlabeled => Everything64.SingleSidedUnlabeled.process
- | Labeled => Everything64.SingleSidedLabeled.process
- ) | Double => (case labeled of
- Unlabeled => Everything64.DoubleSidedUnlabeled.process
- | Labeled => Everything64.DoubleSidedLabeled.process
- )
- )
-
-val () =
- let
- fun one name =
- let
- val instream = TextIO.openIn name
- val result = process ((), instream)
- in
- TextIO.closeIn instream
- ; case result of
- Success => true
- | Failure => (
- TextIO.output (
- TextIO.stdErr
- , name
- ^ ": invalid format\n"
- ); false
- )
- end
- fun all names = List.all one names
- in
- if all files then ()
- else OS.Process.exit OS.Process.failure
- end
generated by cgit v1.2.3 (git 2.39.1) at 2024-11-15 02:45:02 +0000