Index of values

add h k v adds value v to the entry indexed by k in the hashnlist h.

add_connection i1 i2 v adds a new connection between the two interfaces i1 and i2, which have been previously obtained using the get_interf function above.

add_domain d p adds a new domain defined by the constructor d to the protein p, and returns an opaque handle to the new domain which may be used to extract interfaces.

Each matching can be further tagged with a strength, called the affinity.

all_matches r s 0 returns a list of pairs (len, pos) where len is the length of a match of the regular expression r in the string s, and pos is the character position at which it occurs.

Argument parsing stuff

allmatches m l returns a list of intervals where matcher m matches ligand l.

allpairs l1 l2 calculates the list of all pairs (e1, e2) of elements where e1 is from l1 and e2 is from l2.

Given a weight function f : 'a -> int and a list l of elements of type 'a, this function creates the corresponding list of weighted elements, obtained by applying the function, and sorts it.

array_add a e appends the element e at the end of the array a and returns the resulting array.

array_filteri f a returns the array of indices of elements of a which satisfy the boolean filter f.

array_fold_lefti f cumul a computes f (... (f (f cumul 0 a.(0)) 1 a.(1)) ...) (n-1) a.(n-1), where n is the length of the array a.

basic_interval start length creates an interval based on the original string.

bind l i attempts to bind the ligand l from i.start to i.start + i.len - 1.

change_length e q n sets the length of the reserved extend e in the assocext q to n, shifting all the other extents if necessary (if the length changes).

Performs the same checks that bind above would perform, but does not bind anything.

check e start len returns true if the range of length len starting at start does not overlap with any reserved range, false otherwise.

choosepairmap f l applies f to all pairs (e1, e2) of elements of l as returned by choosepairs l above.

choosepairs l returns a list of all pairs (e1, e2) of elements of l, where e1 is not equal to e2 and all the pairs are distinct regardless of order.

clear h removes all keys and values from the hashnlist h.

Do not use.

collapse_interval i returns (start, length), where the start and length parameters correspond to the accounting introduced by the original string from which the ligand was created.

Calls the standard compare function between the weights of two weighted elements.

compare i1 i2 returns -1 if i1 precedes i2 on the ligand, 1 if i1 follows i2 and 0 if they're equal.

Transform an abstract protein into an optimized protein

count q returns the number of cells in the dllist q.

Ligand constructor.

create n creates a new associative extent of length n.

Creates a new doubly-linked list.

create n creates a new hashnlist object of initial size n.

Used to set the current logging level.

Returns the value associated with a cell.

Do not use.

find h k returns the list of values attached to the key k in the hashnlist h.

Returns the first extent in the assocext.

first d returns the first cell in the dllist d.

free e q returns the previously reserved extent e in the associative extent queue q to the free state.

fst3 a b c = a

Return the list of maximal non-bound intervals.

Return the list of bound frags.

FIXME: ...

Use get_interf dp id to obtain an opaque handle to the interface identified by id of the domain referenced by dp.

Returns the character of each interface.

Domain has no state, and no initial state

Get the interval of an opaque frag type.

Get the interval of an opaque extent type.

Return the length of the interval.

get_interval_string l i returns the base string associated to the interval i in the ligand l.

get_length q returns the total length of the assocext q.

get_pos_extent q pos returns either the reserved extent or the free interval which contains the array entry (of length one!) at position pos, or throws Illegal_position if the position does not fit within the extent.

Extract the string from a ligand.

Get the value attached to an opaque extent type.

Returns the ligand which contains the specified frag.

indexlist h returns a list of all the keys which have a non-empty list of values associated to them in the hashnlist h.

Maps initial states to states.

Gives the defaults values attached to each expressor interface.

insert_before v c inserts a new cell with value v just before cell c in the dllist in which c exists, and returns the newly created cell.

insert_end v q inserts a new cell with value v at the end of the dllist q, and returns the newly created cell.

iter f q applies the function f to each extent e of q, in the order in which they appear, starting from the first to the last.

iter f q applies f e for each entry e of the dllist q.

join f1 f2 joins two ligands into one.

Returns the last extent in the assocext.

last d returns the last cell in the dllist d.

linter f l1 l2 calculates the list of pairs (e1, e2) which are such that f e1 e2 is true.

Returns the list of reserved extents.

Returns a list of free intervals.

list_repeat n x creates a list of length n where all the elements are equal to x.

A slightly more sophisticated version of linter.

Set the cur_log_level according to the string passed as parameter, which should be a representation of the log levels defined above.

The channel where we print the log messages.

Factory method.

Create an abstract protein from the configuration given.

make () returns a new abstract protein which does not contain any domain or any connection.

make withstats op creates a concrete instance of the optimized protein op.

Quick shortcut to create a matcher object.

Swarm constructor function.

...

Constructor for distinguished typeA processing units.

Use matcher_compare m1 m2 to decide whether two matchers are equal.

matcher_concat l returns a new matcher which corresponds to the concatenation of all the matchers in the list l.

The central role of an EXPOSURE module is to calculate the matchings between a pair of makers, which is what this function does.

mem h k return true if there is at least one value associated to the key k in h, or false otherwise.

Handily create a multi-element.

next c returns the next cell in the dllist in which c is contained.

next_extent e q returns the extent which follows e in the assocext q.

The fixed number of ligand bind projections this flavor of domain exports.

The fixed number of structural binding projections this flavor of domain exports.

pairmap f l1 l2 calculates the result of applying f to all the pairs (e1, e2) where e1 is from l1 and e2 is from l2.

Will raise Not_found if the strings don't match the permuter.

pilemap f l is very much like List.map f l except that f may throw the exception Skip, in which case the result of that application is not included in the result.

prev c returns the previous cell in the dllist in which c is contained.

Assocext.next_extent.

Do not use - it is referenced only through the logifier.pl preprocessing script.

Will raise Invalid_frag if the frag is stale or otherwise not registered.

remove c removes the cell c from dllist where it exists.

remove h k v removes value v from the entry indexed by k in the hashnlist h.

From List2 in CDK

From List2 in CDK

From List2 in CDK

From List2 in CDK

Replace, in place, the bound frag with the new basestring.

reserve q v start len will allocate value v to a new reserved extent ranging from start to start + len and return that extent, if that range does not overlap with an existing reserved extent.

trd3 a b c = c

snipmatch s1 s2 returns true if the two snippets match.

split f pos splits a ligand into two parts.

Extract the string out from a matcher.

swap (a,b) returns (b,a).

sym_assoc e l searches the list l for a pair where either the first or the second element matches e, and returns the other member of the pair.

sym_assoc_elem e l searches the list l for a pair where either the first or the second element matches e, and returns a pair consisting of the matched pair with the other member of the pair.

This reverses the order...

to_pu opi is a processing unit which can be fed to the Incubator layer.

verify_match_interval m l i verifies whether matcher m matches ligand l at interval i - in other words, whether interval i appears in allmatches m l.