| Overview |  |
Copyright © 2016-2017 Jörgen Brandt
Version: 0.1.0
Authors: Jörgen Brandt (joergen.brandt@onlinehome.de).
del() = {del, [term()]}
edit_script() = [{term(), term()}]
ins() = {ins, [term()]}
match() = {match, [term()]}
mismatch() = {mismatch, [term()], [term()]}
pos_pair() = {non_neg_integer(), non_neg_integer()}
score_lnk() = {number(), pos_pair() | undef}
score_table() = #{{pos_integer(), pos_integer()} => score_lnk()}
strategy() = global | global_endfree | local
subst_fun() = fun((term(), term()) -> number())
summary_script() = [match() | mismatch() | ins() | del()]
| editscr/4 | Constructs an edit script from two sequences and the Dynamic Programming score table. |
| extend_backward/4 | Extends a local alignment from a given position in backward direction. |
| extend_forward/4 | Extends a local alignment from a given position in forward direction. |
| find_horizontal_end/1 | Finds the optimal end in the second sequence in a global end-space free alignment. |
| find_local_matches/4 | |
| find_max_score/3 | Finds the position in a Dynamic Programming score table with the highest score. |
| find_vertical_end/1 | Finds the optimal end in the first sequence in a global end-space free alignment. |
| get_score/2 | |
| new/1 | A simplified version of the function new/3 to construct a stateful
module holding the parameters for the Dynamic Programming scheme. |
| new/3 | Constructs a new stateful module holding the parameters for the Dynamic Programming scheme. |
| print_tbl/1 | |
| scoretbl/3 | Creates the Dynamic Programming score table from two sequences. |
| sumscr/1 | Creates a summary script from an edit script. |
editscr(TLst1, TLst2, Tbl, ModArg) -> edit_script()
Constructs an edit script from two sequences and the Dynamic Programming score table.
extend_backward(Pos, ScopeStart, Tbl, ModArg) -> any()
Extends a local alignment from a given position in backward direction.
extend_forward(Pos, ScopeEnd, Tbl, ModArg) -> any()
Extends a local alignment from a given position in forward direction.
find_horizontal_end(Tbl::score_table()) -> {pos_pair(), number()}
Finds the optimal end in the second sequence in a global end-space free alignment.
The function produces a pair consisting of a position pair and its score.find_local_matches(ScopeStart, ScopeEnd, Tbl, ModArg) -> any()
find_max_score(ScopeStart, ScopeEnd, Tbl) -> {pos_pair(), number()}
Finds the position in a Dynamic Programming score table with the highest score.
find_vertical_end(Tbl::score_table()) -> {pos_pair(), number()}
Finds the optimal end in the first sequence in a global end-space free alignment.
The function produces a pair consisting of a position pair and its score.get_score(Tbl, Lib_dp) -> any()
new(Strategy::strategy()) -> #lib_dp{}
A simplified version of the function new/3 to construct a stateful
module holding the parameters for the Dynamic Programming scheme.
global,
global_endfree, or local.
new(Strategy, SubstFun, Indel) -> #lib_dp{}
Constructs a new stateful module holding the parameters for the Dynamic Programming scheme.
The stateful module is initialized withglobal for global alignment
(Needleman-Wunsch), global_endfree for global end-space free
alignment, or local for local alignment (Smith-Waterman).
A simpler initialization function where only the the strategy has to be
provided is new/1.
scoretbl/3 to create a score table from two sequences and
editscr/4 to construct an edit script from a score table.
print_tbl(Tbl) -> any()
scoretbl(TLst1, TLst2, ModArg) -> any()
Creates the Dynamic Programming score table from two sequences.
sumscr(T::edit_script()) -> summary_script()
Creates a summary script from an edit script.
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