Index of values

arg_m cmp f l return the element (and value) which gives the minimum value for the result of applying f with respect to cmp where cmp x y should return 0 if x and y are equal, -1 if x < y and 1 otherwise.

arg_m cmp arr return the element number with the minimum value with respect to cmp.

arg_max f x y compares f x and f y and gives the argument: x or y which gives Pervasives.max (f x) (f y)

return the element (and value) which gives the maximum value for the result of applying a function.

return the element number with the maximum value.

arg_min f x y compares f x and f y and gives the argument: x or y which gives Pervasives.min (f x) (f y)

return the element (and value) which gives the minimum value for the result of applying a function.

return the element number with the minimum value.

argsort comp a returns an array consisting of indices of a sorted array a.

auxiliary function for array mean array -> initial value of sum, addition function, division function (always divide by a float value)

returns the median, w/ respect to compare, of an array

returns the median, w/ respect to a comparison function, of an array

sum for array

Return match matrix mismatch_allowance -> text -> pattern -> match matrix of patterns in the string

mismatch_allowance -> text -> pattern -> bool

Return match matrix mismatch_type -> text -> pattern -> min_mismatch table

  mismatch_type -> text -> pattern ->
  minimum mismatch * (text_beginx, textend, pat_beginy)
  text_begnix: a value from 0 to String.length text (inclusive)
                where in the text the match starts (text starts from 1)
                a 0 means that the first (few) letters of the pattern
                were deleted so that the suffix of the pattern matches
                the prefix of the test.
  pat_beginy: either 0 or 1. a 0 means that the first letter
               of the pattern was deleted when matching from text_beginx.
               1 means otherwise. note that this value and text_beginx cannot 
               be 0 at the same time.

convert a boolean tree to a string.

bdtree spec matcher creates a function for classification.

bern p is the function same as bernoulli p.

bernoulli p returns a random integer value either 0 or 1, that has Bernoulli distribution with success probablitiy p.

ID3 algorithm (Quinlan, 19??) for binary classes.

binomial n p returns a random integer value that has Binomial distrituion with index n and success probability p.

creates a CDAWG from a string.

close the file

combination lst k generates all combinations consisting of k elements in lst, and return them as a list.

Combine two frequences

array version of List.combine.

Return a fresh string that has been mapped with BC_NA.comp_to_dna_char

Return the complement base.

Return a fresh string that has been mapped with BC_NA.comp_to_rna_char

Return the complement base.

return the DNA reverse complement for ambiguous DNA

return the DNA reverse complement

convert a string according to an indexing

Convert a character to integer using the conversion table.

Convert an integer to a character.

return function: char -> char corresponding to the indexing

count p lst counts elements in list lst which satisfy predicate p

count elements in array which satisfy predicate p

Return the frequency count in a given string.

create a indexing with indexing alphabet size, and list of classifications e.g: create 2 [("ab", 0); ("def", 1)] creates a indexing of indexing alphabet size 2 which maps "ab" to 0, and "def" to 1, and other characters to 2.

create a random indexing from alphabet and indexing size string should contain letters of the original alphabet indexing size greater than 0 and less than 10, otherwise raises Invalid_argument

cross_sample k n randomly divides the set : {0, 1, ..., n-1} into k sets (s_{0} ..

cross_sample_list k l randomly divides the list l into k lists (s_{0} ..

cross_validate k data sampler learner evaluator runs a k-cross validation on the data.

text -> DASG

alphabet -> character map -> text -> DASG

DASG -> pattern -> bool

conversion of EDASG to DASG

delimit_eval outch before after f evaluates function: f () and returns its results.

diff lst1 lst2 returns new list containing all elements in lst1 but not in lst2.

Subtract two frequencies

dna_to_int ch converts a DNA character into a correspoinding integer value.

text -> EDASG

alphabet character map -> text -> EDASG

threshold -> text(EDASG) -> if match length was less than threshold

text(EDASG) -> pattern -> minimum threshold for match

conversion of EDASG to DASG

entropy gain score function: for ID3

text -> pattern -> minimum size window threshold

threshold -> text -> pattern -> minwindow > threshold?

exists p a returns true if at least one element of array a satisfies the predicate p, and false otherwise.

filter f str returns a new string whose characters return true with respect to f : char -> bool

a filter on a stream.

find str pat pos searches string pat in str, then return the position at which pat is found.

finds the best threshold for a given string, for dividing two sets of strings with episode matching, according to some score function.

finds the best mismatch for a given string, for dividing two sets of strings according to some score function.

branch-bound algorithm for finding best pattern two divide two lists with pattern based on strings

  'a: type of text1
  'b: type of text2
  'c: type of pattern
  a pattern is some data type which is based on a string. 
           (e.g.: Approximate pattern: (mismatch,string))
  pd  : positive data  nd: negative data
  alph: a string containing all characters of the alphabet to generate patterns from
  maxlen: maximum length of pattern
  scoref: score function which calculates a score (float) and is given arguments:
          let pdy: the list of elements of pd, which matches with matcher
          let ndy: the list of elements of pd, which matches with matcher
          the length of lists in order: pd nd pdy ndy.
          A higher score is judged to be better.
  comppat: comparison function for a pattern, used in case the score is the same (e.g. shorter patterns are better)
  copypat: copy function for a pattern (it should copy any non-persistent data types contained (e.g.: String.copy))
  makepat: a function which takes a string and makes the best pattern which distinguishes the given texts. returns (pdmatchcount, ndmatchcount, score, pattern)

returns a random floating-point number between 0 (inclusive) and `bound' (exclusive).

average of an array of floats

sum of an array of floats

the variance of values in the array.

average of a list of floats

standard deviation of values in a list of floats

sum of an list of floats

the variance of values in a list of floats

a fold for streams.

a fold_left for string.

a fold left for streams.

fold left for cached array.

a fold_left for string.

same as fold_left, but the function is applied to the index of the element as first argument, the cummulative value as the second argument, and the element itself as the third argument.

same as fold_left, but the function is applied to the index of the element as first argument, the cummulative value as the second argument, and the element itself as the third argument

same as fold_right, but the function is applied to the index of the element as first argument, and the element itself as the second argument, and the cumulative value as the thir argument.

same as fold_right, but the function is applied to the index of the element as first argument, and the element itself as the second argument, and the cummulative value as the third argument.

Checks if all elements of the string satisfy the predicate `p'.

returns frequency list of a given int list.

Return the frequency of a given character.

freq_to_cmap freq alph returns a Map which gives an integer for a given character in alph.

generate random float

generate random integer

Get an element from the array.

group lst n f.

group compare lst groups the list of elements into a list of lists, according to a compare function.

group_setsz lst n f.

return indexing alphabet "0...8"

Init for string.

similar to Array.init.

Initialize a new cached array.

two dimensional cached arrays.

same as input_char but return 8-bit integer representing the character

read a single character from in_channel

read a line from in_channel

Same as input_line except ignoring lines that start with '#' and empty.

returns a random integer between 0 (inclusive) and `bound' (exclusive).

average of an array of ints

sum of an array of ints

the variance of values in the array.

average of a list of ints

standard deviation of values in a list of ints

sum of an list of ints

the variance of values in a list of ints

ind_to_dna ch converts a integer value into a correspoinding DNA character.

returns true if the character is 'a', 't', 'c', or 'g' (case insensitive)

returns true if all characters in the string returns true for BC_NA.is_dna_char

returns true if the character is one of "acgtumrwsykvhdbxn" (case insensitive)

returns true if all characters in the string returns true for BC_NA.is_na_char

returns true if the character is 'a', 'u', 'c', or 'g' (case insensitive)

returns true if all characters in the string returns true for BC_NA.is_rna_char

run function for each line of input until End of file is read

an iteri for string.

Same as Stream.iter, but the function is applied to the index of the element as first argument, and the element itself as second argument.

similar to Array.iteri.

return the length of the cached array.

auxiliary function for list mean list -> initial value of sum, addition function, division function (always divide by a float value)

returns the median, w/ respect to compare, of a list.

returns the median, w/ respect to a comparison function, of a list

helper function for calculating the standard deviation of values in a list

auxiliary function for list sum

helper function for calculating the variance of values in a list

run local seaerch starting at initparam.

log base 2

m cmp l return the element of list l that is minimum, with respect to cmp.

m cmp a return the element of array a that is minimum, with respect to cmp.

make n v makes a cached array of size n filled with value v.

Make a table for the bijection (one-to-one correspondance) between each character of the string, and its position.

Make conversion table of char -> int from a string array.

Make conversion table of int -> char from a string.

apply function char -> char to each element of string, and return a string

a map on a stream.

Map on cached arrays.

apply a function 'a -> char to each element of array, and return the result as a string

apply a function 'a -> char to each element of a list, and return the result as a string

map on a two dimensional cached array.

map_snapshot f a creates a snapshot of a cached array.

apply a function to each char of a string, and return the result as an array

map_to_array f lst is the same as Array.map f (Array.of_list lst) but doesn't create the intermediate array.

map and then convert the results to a normal array.

apply a function to each char of a string, and return the result as a list

map and return the result as a list.

creates a MASCDAWG from a string.

get an element from a two dimensional cached array.

Assign a new value to an element of a two dimensional cached array.

return the maximum element of a list.

return the maximum element of an array.

Matthews correlation coefficient

return the minimum element of a list.

return the minimum element of an array.

Initialize everything.

Return a fresh mysql object.

Re-initialize a mysql object.

returns the set of nucleic acids represented by a single character: e.g.

neg_binomial r p returns a random integer value that has Negative Binomial distribution with index r and success probability p.

generate the neighborhood of a given indexing

nhd lst n returns the first n elements of list lst.

normal m v returns a normal random value N(m, v^2)

return a fresh string from an array of characters

Build a stream from an array.

convert the array to a cached array.

a stream of each line of a file.

The same as of_file_lines, except for ignoring comments and empty lines.

conversion to Pervasives.in_channel

a stream made with input_line on an input channel.

return a fresh string from a list of characters

open a file for input stream

partition p a returns pair of arrays (a1, a2) where a1 is the array of all elements of a which satisfy p, and a2 is the array of all elements of a which do not satisfy p.

posneg_cross_validate k posdata negdata sampler learner evaluator similar to cross_validate: runs a k-cross validation on the data, but the data consists of two sets, which should be equally sampled.

prune useless branches from a tree

qf v1 v2 f returns cumulative probablitiy of F distribution with digree of freedom v1, v2.

read a string Stream.t where each string in the stream represents one line of a Fasta format file.

Read an entire fasta format file.

reverse a string

return a fresh array with the elements in reverse order

reverse map.

map and return the result as list.

rev_nhd lst n returns the first n elements of list lst in reverse order.

create a fresh array from a list.

remove redundant consecutive elements of a list (similar to UNIX command uniq), but the result is in reverse order.

Return a fresh string representing the reverse complement of the input.

Return a fresh string representing the reverse complement of the input.

sample k n randomly selects k integers from the set : {0, 1, ..., n-1}.

sample_array k a randomly selects k elements from array a of n elements (Floyd's Algorithm?).

sample_list k l randomly selects k elements from list l of n elements (Floyd's Algorithm?).

search neighborhood of a solution, and return the best neighbor (depending on comp and evaluator) return option type of Some (param, (score, solution) or None if there are no good neighbors

  'a: type of score (evaluation)
  'b: type of search space parameter
  'c: type of solution
  'd: type of neighborhood search parameters (should be equal to 'b to be of any use)
  'e: type of data
  'f: evaluator (parameter passed to solver: should influence score)
  solver: data -> evaluator -> score compare -> solution compare -> searchspace parameter -> (score * solution)
  evaluator: 'f (evaluator (any parameter) passed to solver to (perhaps) influence score)
  compscore : compare function for evaluation (scores)
  compsol  : compare function for solutions (e.g. smaller solutions are better)

create internal representation of indexing.

convert binary decision trees to strings which can be used as internal representation first arg: tree, second arg: conversion function for parameters at Nodes ('a -> string), third arg: conversion function for Leaves ('b -> string)

set arr i f sets the value at the ith position to f ().

set seed (!=0) for float integer generator

set seed (!= 0) for random integer generator

shows a histogram.

snormal () returns a random value based on standard normal distribution (i.e.

array version of List.split.

A fold on rows of results which were obtained by mysql_store_result.

An iter on rows of results which were obtained by mysql_store_result.

A map on rows of results which were obtained by mysql_store_result.

Return a stream of fasta entries from a file.

convert the mismatch type to string

Substring matching.

Substring matching text -> pattern -> (position != -1)

sub_fold_left b l f init a computes f (... (f (f init a.(b)) a.(b+1)) ...) a.(b+l-1) It is equivalent to Array.fold_left f (Array.sub arr b l) init a (if f does not modify the array) but should be more efficient in that a fresh array is not created

text -> pattern -> bool

substrings str pos len sublen generates all substrings whose lengths are sublen from str.

creates a suffix_tree from a string (a dummy function which is not implemented)

convert each character of the string to a fresh array of characters

convert the cached array to a normal array.

convert a string to a DNA sequence.

convert a character to a DNA character.

conversion from Pervasives.in_channel

convert each character of the string to a list of characters

convert a string to an RNA sequence.

convert a character to an RNA character.

create string of indexing

return total frequency of all characters

trim str removes all white spaces in both ends of given string.

`push back' a byte to in_channel.

`push back' a character to in_channel.

`push back' a line to in_channel.

`push back' a line to in_channel.

remove redundant consecutive elements of a list (similar to UNIX command uniq).

uniq_base lst comp removes redundant consecutive elements of a list using a comparator comp.

A fold on rows of results which were obtained by mysql_store_result.

An iter on rows of results which were obtained by mysql_store_result.

A map on rows of results which were obtained by mysql_store_result.

vldc_match mascdawg pattern returns true if the pattern matches (substring matching with wildcard) the text represented by mascdawg.

Write a list of (header, sequence) to a file in FASTA format.