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
extent s.
|
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] |