Index of values


A
add [Hashnlist]
add h k v adds value v to the entry indexed by k in the hashnlist h.
add_connection [Protein.Abstract]
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 [Protein.Abstract]
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.
affinity [Swarm.EXPOSURE]
Each matching can be further tagged with a strength, called the affinity.
all_domains [Genome.OldCompiled]
all_matches [Util]
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.
all_options [Main]
Argument parsing stuff
allmatches [Ligand.Matcher]
allmatches m l returns a list of intervals where matcher m matches ligand l.
allpairs [Util]
allpairs l1 l2 calculates the list of all pairs (e1, e2) of elements where e1 is from l1 and e2 is from l2.
anonymous [Main]
apply_weight_and_sort [Util]
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.
argparse [Main]
array_add [Util]
array_add a e appends the element e at the end of the array a and returns the resulting array.
array_filteri [Util]
array_filteri f a returns the array of indices of elements of a which satisfy the boolean filter f.
array_fold_lefti [Util]
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.

B
basic_interval [Ligand]
basic_interval start length creates an interval based on the original string.
bind [Ligand]
bind l i attempts to bind the ligand l from i.start to i.start + i.len - 1.

C
c_md [Genome.Compile]
c_sd [Genome.Compile]
change_length [Assocext]
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).
check [Ligand]
Performs the same checks that bind above would perform, but does not bind anything.
check [Assocext]
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 [Util]
choosepairmap f l applies f to all pairs (e1, e2) of elements of l as returned by choosepairs l above.
choosepairs [Util]
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 [Hashnlist]
clear h removes all keys and values from the hashnlist h.
cmp [Log]
Do not use.
collapse_interval [Ligand]
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.
compare_by_weight [Util]
Calls the standard compare function between the weights of two weighted elements.
compare_intervals [Ligand]
compare i1 i2 returns -1 if i1 precedes i2 on the ligand, 1 if i1 follows i2 and 0 if they're equal.
compile [Protein.Optimized]
Transform an abstract protein into an optimized protein
compile_domain [Genome.Compile]
contains_begin [Ligand]
contains_end [Ligand]
count [Dllist]
count q returns the number of cells in the dllist q.
create [Ligand]
Ligand constructor.
create [Assocext]
create n creates a new associative extent of length n.
create [Dllist]
Creates a new doubly-linked list.
create [Hashnlist]
create n creates a new hashnlist object of initial size n.
cur_log_level [Log]
Used to set the current logging level.

D
deref [Dllist]
Returns the value associated with a cell.

E
event [Log]
Do not use.

F
find [Hashnlist]
find h k returns the list of values attached to the key k in the hashnlist h.
first [Ligand]
first [Assocext]
Returns the first extent in the assocext.
first [Dllist]
first d returns the first cell in the dllist d.
free [Assocext]
free e q returns the previously reserved extent e in the associative extent queue q to the free state.
from_compact [Genome.Compile]
fst3 [Util]
fst3 a b c = a

G
getConfigRep [CheatParseRep]
get_active_interval_list [Ligand]
Return the list of maximal non-bound intervals.
get_frag_list [Ligand]
Return the list of bound frags.
get_frag_string [Ligand]
FIXME: ...
get_interf [Protein.Abstract]
Use get_interf dp id to obtain an opaque handle to the interface identified by id of the domain referenced by dp.
get_interf_character [Protein.Abstract.DOMDEF]
Returns the character of each interface.
get_interf_character [Protein.Abstract.LBDE]
get_interf_character [Protein.Abstract.LBDR]
get_interf_character [Protein.Abstract.PDMatcher]
Domain has no state, and no initial state
get_interf_character [Protein.Abstract.LID]
get_interf_character [Protein.Abstract.BMD]
get_interf_character [Protein.Abstract.SLBD]
get_interval [Ligand]
Get the interval of an opaque frag type.
get_interval [Assocext]
Get the interval of an opaque extent type.
get_interval_length [Ligand]
Return the length of the interval.
get_interval_string [Ligand]
get_interval_string l i returns the base string associated to the interval i in the ligand l.
get_length [Assocext]
get_length q returns the total length of the assocext q.
get_pos_extent [Assocext]
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.
get_stats [Protein]
get_string [Ligand]
Extract the string from a ligand.
get_value [Assocext]
Get the value attached to an opaque extent type.
get_whole [Ligand]
Returns the ligand which contains the specified frag.

I
indexlist [Hashnlist]
indexlist h returns a list of all the keys which have a non-empty list of values associated to them in the hashnlist h.
initmap [Protein.Abstract.DOMDEF]
Maps initial states to states.
input_defaults [Protein.Abstract.DOMDEF]
Gives the defaults values attached to each expressor interface.
insert_before [Dllist]
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 [Dllist]
insert_end v q inserts a new cell with value v at the end of the dllist q, and returns the newly created cell.
instantiate_domain [Genome.OldCompiled]
iter [Ligand]
iter [Assocext]
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 [Dllist]
iter f q applies f e for each entry e of the dllist q.

J
join [Ligand]
join f1 f2 joins two ligands into one.

L
last [Ligand]
last [Assocext]
Returns the last extent in the assocext.
last [Dllist]
last d returns the last cell in the dllist d.
linter [Util]
linter f l1 l2 calculates the list of pairs (e1, e2) which are such that f e1 e2 is true.
list_extents [Assocext]
Returns the list of reserved extents.
list_free_intervals [Assocext]
Returns a list of free intervals.
list_repeat [Util]
list_repeat n x creates a list of length n where all the elements are equal to x.
lmultinter [Util]
A slightly more sophisticated version of linter.
log_from_string [Log]
Set the cur_log_level according to the string passed as parameter, which should be a representation of the log levels defined above.
log_out [Log]
The channel where we print the log messages.

M
make [Testinter]
make [GenomeParser]
make [SingleCellHarness]
make [Cell]
Factory method.
make [Protein.Wizard]
Create an abstract protein from the configuration given.
make [Protein.Abstract]
make () returns a new abstract protein which does not contain any domain or any connection.
make [Protein]
make withstats op creates a concrete instance of the optimized protein op.
make [Ligand.Matcher]
Quick shortcut to create a matcher object.
make [Swarm.SWARM]
Swarm constructor function.
make_hash [Genome.Compile]
make_instance [Genome.OldCompiled]
make_string_permuter [Ligand.Matcher]
...
make_typeA_pu [Incubator.Procunit]
Constructor for distinguished typeA processing units.
matcher_compare [Ligand.Matcher]
Use matcher_compare m1 m2 to decide whether two matchers are equal.
matcher_concat [Ligand.Matcher]
matcher_concat l returns a new matcher which corresponds to the concatenation of all the matchers in the list l.
matchings [Swarm.EXPOSURE]
The central role of an EXPOSURE module is to calculate the matchings between a pair of makers, which is what this function does.
mem [Hashnlist]
mem h k return true if there is at least one value associated to the key k in h, or false otherwise.
multi [Util]
Handily create a multi-element.

N
next [Dllist]
next c returns the next cell in the dllist in which c is contained.
next_extent [Assocext]
next_extent e q returns the extent which follows e in the assocext q.
next_frag [Ligand]
num_lbprojs [Protein.Abstract.DOMDEF]
The fixed number of ligand bind projections this flavor of domain exports.
num_lbprojs [Protein.Abstract.LBDE]
num_lbprojs [Protein.Abstract.LBDR]
num_lbprojs [Protein.Abstract.PDMatcher]
num_lbprojs [Protein.Abstract.LID]
num_lbprojs [Protein.Abstract.BMD]
num_lbprojs [Protein.Abstract.SLBD]
num_sbprojs [Protein.Abstract.DOMDEF]
The fixed number of structural binding projections this flavor of domain exports.
num_sbprojs [Protein.Abstract.LBDE]
num_sbprojs [Protein.Abstract.LBDR]
num_sbprojs [Protein.Abstract.PDMatcher]
num_sbprojs [Protein.Abstract.LID]
num_sbprojs [Protein.Abstract.BMD]
num_sbprojs [Protein.Abstract.SLBD]

O
options [Cell_options]

P
pairmap [Util]
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.
permute_strings [Ligand.Matcher]
Will raise Not_found if the strings don't match the permuter.
pilemap [Util]
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 [Dllist]
prev c returns the previous cell in the dllist in which c is contained.
prev_extent [Assocext]
prev_frag [Ligand]
protect [Log]
Do not use - it is referenced only through the logifier.pl preprocessing script.

R
release [Ligand]
Will raise Invalid_frag if the frag is stale or otherwise not registered.
remove [Dllist]
remove c removes the cell c from dllist where it exists.
remove [Hashnlist]
remove h k v removes value v from the entry indexed by k in the hashnlist h.
remove [Util]
From List2 in CDK
remove_first [Util]
From List2 in CDK
removeq [Util]
From List2 in CDK
removeq_first [Util]
From List2 in CDK
replace [Ligand]
Replace, in place, the bound frag with the new basestring.
reserve [Assocext]
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.

S
set_log [Cell_options]
snd3 [Util]
trd3 a b c = c
snipmatch [Ligand.Matcher]
snipmatch s1 s2 returns true if the two snippets match.
split [Ligand]
split f pos splits a ligand into two parts.
stringform [Ligand.Matcher]
Extract the string out from a matcher.
swap [Util]
swap (a,b) returns (b,a).
sym_assoc [Util]
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 [Util]
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.

T
to_list [Dllist]
This reverses the order...
to_pu [Protein]
to_pu opi is a processing unit which can be fed to the Incubator layer.
trd3 [Util]

U
usage [Main]

V
verify_match_interval [Ligand.Matcher]
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.

W
weigh [Util]