LocARNA-1.8.11
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Classes | |
class | Aligner |
Implements locarna alignment algorithm. More... | |
class | AlignerImpl |
Implementation of Aligner. More... | |
class | AlignerN |
Implements SPARSE, next generation alignment algorithm for locarna. More... | |
class | AlignerNParams |
parameters for AlignerN More... | |
class | AlignerP |
Computes partition function of alignment, arc match and base match probabilities. More... | |
class | AlignerParams |
Parameter for alignment by Aligner. More... | |
class | AlignerPParams |
parameters for AlignerP More... | |
class | AlignerRestriction |
Restricts range of an alignment in Aligner. More... | |
class | Alignment |
Represents a structure-annotated sequence alignment. More... | |
class | AlignmentEdges |
pair of vector of alignment edges More... | |
class | AlignmentImpl |
Implementation of Alignment. More... | |
class | Alphabet |
Specifies an alphabet. More... | |
class | AnchorConstraints |
Represents anchor constraints between two sequences. More... | |
class | ArcMatch |
Represents a match of two base pairs (arc match) More... | |
class | ArcMatches |
Maintains the relevant arc matches and their scores. More... | |
class | ArcMatchesIndexed |
class ArcMatches with additional mapping More... | |
class | BasePairs |
Describes sequence and structure ensemble of an RNA. More... | |
class | BasePairs__Arc |
Represents a base pair. More... | |
class | ConfusionMatrix |
Compare RNA secondary structure by their confusion matrix. More... | |
class | DiscreteDistribution |
class | EdgeEnd |
end of an alignment edge More... | |
class | EPM |
a class for the representation of exact pattern matches (EPM) More... | |
class | ExactMatcher |
Computes exact pattern matchings (EPM) between two RNA sequences. More... | |
class | ExtRnaData |
represent sparsified data of RNA ensemble extended by in loop probabilities More... | |
class | ExtRnaDataImpl |
Implementation of ExtRnaData. More... | |
class | failure |
Simple exception class that supports a text message. More... | |
class | FiniteInt |
class | FitOnOff |
Implements fitting of a two-step function to a number sequence. More... | |
class | FreeEndgapsDescription |
Description of free end gaps. More... | |
class | Gap |
"enum class" of gaps in alignment edges More... | |
class | greater_second |
Implements comparison by member second. More... | |
class | InftyInt |
class | LCSEPM |
computes the best chain of EPMs, the LCS-EPM More... | |
class | MatchController |
abstract class that declares the method is_valid_match() More... | |
class | MatchProbs |
Provides probabilities for each match. More... | |
class | Matrix |
simple 2D matrix class, provides access via operator (int,int) More... | |
class | McC_ali_matrices_t |
Alifold-McCaskill matrices. More... | |
class | McC_matrices_base |
class | McC_matrices_t |
McCaskill matrices. More... | |
class | MultipleAlignment |
Represents a multiple alignment. More... | |
class | OMatrix |
Simple matrix class with offset. More... | |
struct | option_def |
Definition structure of an option. More... | |
struct | pair_of_size_t_hash |
Function class definining hash function for pairs of size_t. More... | |
class | PatternPair |
is able to manage an EPM, consists of 2 singlepatterns, one in each RNA More... | |
class | PatternPairMap |
manage a set of EPMs (PatternPair) More... | |
class | PFoldParams |
Parameters for partition folding. More... | |
class | plusvector |
Implements a vector with += operator. More... | |
class | quadruple |
Represents a 4-tuple. More... | |
class | quintuple |
Represents a 5-tuple. More... | |
class | Ribofit |
Family of Ribofit matrices. More... | |
class | Ribofit_will2014 |
class | Ribosum |
Represents ribosum similarity matrices. More... | |
class | RibosumFreq |
Represents ribosum similarity matrices including raw frequencies. More... | |
class | RMatrix |
Simple matrix class with restriction to a range. More... | |
class | RnaData |
represent sparsified data of RNA ensemble More... | |
class | RnaDataImpl |
Implementation of RnaData. More... | |
class | RnaEnsemble |
Represents the raw structure ensemble data for an RNA. More... | |
class | RnaEnsembleImpl |
Implementation of RnaEnsemble. More... | |
class | RnaStructure |
An RNA secondary structure. More... | |
class | RotMatrix |
A matrix class with rotation. More... | |
class | Scoring |
Provides methods for the scoring of alignments. More... | |
class | ScoringParams |
Parameters for scoring. More... | |
class | Sequence |
"Sequence View" of multiple alignment as array of column vectors More... | |
class | SequenceAnnotation |
Annotation of a sequence. More... | |
class | SinglePattern |
stores a Pattern in one sequence More... | |
class | SparseMatrix |
Represents a sparse 2D matrix. More... | |
class | SparseTraceController |
combines the TraceController with the Mapper for both sequences More... | |
class | SparseVector |
Represents a sparse vector. More... | |
class | SparsificationMapper |
Represents the mapping for sparsification. More... | |
class | StopWatch |
control a set of named stop watch like timers More... | |
class | StralScore |
Implements the stral-like scoring function. More... | |
class | string1 |
A simple 1-based string. More... | |
struct | syntax_error_failure |
thrown, when the format is recognized but syntax is incorrect More... | |
class | TaintedInftyInt |
class | TraceController |
Controls the matrix cells valid for traces. More... | |
class | TraceRange |
Represents a range of traces. More... | |
class | triple |
Represents a 3-tuple. More... | |
class | type_wrapper |
generic type_wrapper class More... | |
struct | unordered_map |
struct | unordered_set |
struct | wrong_format_failure |
thrown, when reading data that is not in the supposed format More... | |
Typedefs | |
typedef std::pair< AlignerRestriction, infty_score_t > | task_t |
type of a task (used in computing k-best alignment) | |
typedef Matrix< double > | ProbMatrix |
matrix for storing probabilities More... | |
typedef SparseMatrix< double > | SparseProbMatrix |
sparse matrix for storing probabilities | |
typedef SparseMatrix< pf_score_t > | SparsePFScoreMatrix |
sparse matrix for storing partition functions | |
typedef AlignerRestriction | AlignerPRestriction |
restriction of AlignerP ( same as for Aligner ) | |
typedef std::vector< EdgeEnd > | Alignment__edge_ends_t |
vector of alignment edge ends | |
typedef std::vector< ArcMatch > | ArcMatchVec |
Vector of arc matches. | |
typedef std::vector< ArcMatch::idx_type > | ArcMatchIdxVec |
Vector of arc match indices. | |
typedef size_t | size_type |
general size type | |
typedef size_type | pos_type |
type of a sequence position | |
typedef double | FLT_OR_DBL |
select FLT_OR_DBL More... | |
typedef std::vector< unsigned int > | intVec |
typedef std::pair< unsigned int, unsigned int > | intPair |
typedef std::pair< intPair, intPair > | intPPair |
typedef const intPPair * | intPPairPTR |
typedef std::vector< intPPair >::const_iterator | IntPPairCITER |
typedef std::vector< double > | numseq_t |
typedef long double | pf_t |
typedef std::vector< infty_score_t > | ScoreVector |
matrix of scores supporting infinity | |
typedef std::vector< pf_score_t > | PFScoreVector |
Vector of partition functions. | |
typedef Matrix< infty_score_t > | ScoreMatrix |
matrix of scores supporting infinity | |
typedef Matrix< pf_score_t > | PFScoreMatrix |
Matrix of partition functions. | |
typedef long int | score_t |
type of the locarna score as defined by the class Scoring | |
typedef InftyInt | infty_score_t |
typedef TaintedInftyInt | tainted_infty_score_t |
typedef double | pf_score_t |
type of partition functions | |
Functions | |
std::ostream & | operator<< (std::ostream &out, AlignerRestriction r) |
template<class T > | |
std::ostream & | operator<< (std::ostream &out, Alphabet< T > a) |
bool | is_gap_symbol (char c) |
Test for gap symbol. More... | |
char | gap_symbol (Gap gap) |
simplified symbols of gaps | |
char | special_gap_symbol (Gap gap) |
special symbols of gaps | |
Gap | gap_code (char symbol) |
code of a gap symbol | |
void | transform_toupper (std::string &s) |
void | normalize_rna_sequence (std::string &seq) |
Transform an RNA sequence string. More... | |
bool | has_prefix (const std::string &s, const std::string &p, size_t start=0) |
Test string prefix. More... | |
void | split_at_separator (const std::string &s, char sep, std::vector< std::string > &v) |
Tokenize string at separator symbol. More... | |
std::vector< std::string > | split_at_separator (const std::string &s, char sep) |
Tokenize string at separator symbol. More... | |
std::string | concat_with_separator (const std::vector< std::string > &v, char sep) |
Tokenize string at separator symbol. More... | |
bool | get_nonempty_line (std::istream &in, std::string &line) |
Get next non-empty/non-comment line. More... | |
double | sequence_identity (const string1 &seqA, const string1 &seqB) |
double | prob_exp_f (int seqlen) |
expected probability of a base pair (null-model) More... | |
bool | frag_len_geq (size_t i, size_t j, size_t minlen) |
size_t | frag_len (size_t i, size_t j) |
bool | operator< (const BasePairs::LeftAdjEntry &e1, const BasePairs::LeftAdjEntry &e2) |
bool | operator< (const BasePairs::RightAdjEntry &e1, const BasePairs::RightAdjEntry &e2) |
std::ostream & | operator<< (std::ostream &out, const BasePairs::Arc &arc) |
std::ostream & | operator<< (std::ostream &out, const PatternPairMap::patListTYPE &pat_pair_map) |
write pattern list of the PatternPairMap to stream More... | |
bool | operator< (const EPM &epm1, const EPM &epm2) |
std::ostream & | operator<< (std::ostream &out, const EPM &epm) |
template<class T1 > | |
T1 | max3 (const T1 &first, const T1 &second, const T1 &third) |
template<class T1 > | |
T1 | max4 (const T1 &first, const T1 &second, const T1 &third, const T1 &fourth) |
double | sqdiff (double x, double y) |
square difference | |
std::ostream & | operator<< (std::ostream &out, const TaintedInftyInt &x) |
TaintedInftyInt | operator+ (const TaintedInftyInt &x, const FiniteInt &y) |
TaintedInftyInt | operator- (const TaintedInftyInt &x, const FiniteInt &y) |
TaintedInftyInt | operator+ (const InftyInt &x, const InftyInt &y) |
TaintedInftyInt | operator- (const InftyInt &x, const InftyInt &y) |
InftyInt | operator+ (const InftyInt &x, const FiniteInt &y) |
InftyInt | operator- (const InftyInt &x, const FiniteInt &y) |
FiniteInt | operator+ (const FiniteInt &x, const FiniteInt &y) |
FiniteInt | operator- (const FiniteInt &x, const FiniteInt &y) |
bool | operator== (const TaintedInftyInt &x, const TaintedInftyInt &y) |
TaintedInftyInt | min (const TaintedInftyInt &x, const TaintedInftyInt &y) |
TaintedInftyInt | max (const TaintedInftyInt &x, const TaintedInftyInt &y) |
bool | operator> (const TaintedInftyInt &x, const TaintedInftyInt &y) |
bool | operator< (const TaintedInftyInt &x, const TaintedInftyInt &y) |
bool | operator>= (const TaintedInftyInt &x, const TaintedInftyInt &y) |
bool | operator<= (const TaintedInftyInt &x, const TaintedInftyInt &y) |
template<class T > | |
std::ostream & | operator<< (std::ostream &out, Matrix< T > mat) |
template<class T > | |
std::istream & | operator>> (std::istream &in, Matrix< T > &mat) |
std::ostream & | operator<< (std::ostream &out, const MultipleAlignment &ma) |
Write multiple alignment to stream. More... | |
bool | decode_argument (void *argument, int arg_type, const std::string &optarg) |
decode a string according to arg_type, for internal use More... | |
int | count_opts (option_def *options) |
char * | sprint_option_name (char *buf, option_def *options, int i) |
char * | sprint_option_xml (char *buf, option_def *options, int i) |
char * | sprint_option_name_opt (char *buf, option_def *options, int i) |
bool | process_options (int argc, char *argv[], option_def *options) |
process options More... | |
const char * | convert_arg_type (int arg_type) |
void | print_options (option_def options[]) |
void | print_usage (char *progname, option_def options[]) |
void | print_galaxy_xml (char *progname, option_def options[]) |
prints a galaxy wrapper in xml format More... | |
void | print_help (char *progname, option_def options[]) |
bool | process_options (int argc, char *argv[], option_def options[]) |
std::ostream & | operator<< (std::ostream &out, const Ribosum &ribosum) |
bool | is_blank (std::string &s) |
std::ostream & | operator<< (std::ostream &out, const RibosumFreq &ribosum) |
std::string | read_pp_in_loop_block (const std::string &firstline, std::istream &in) |
std::string | format_prob (double prob) |
output format for probabilities in pp files use limited precision; use scientific notation if it is shorter | |
template<class T > | |
std::ostream & | operator<< (std::ostream &out, const SparseMatrix< T > &m) |
Output operator. More... | |
template<class T > | |
std::ostream & | operator<< (std::ostream &out, const SparseVector< T > &v) |
Output operator. More... | |
std::ostream & | operator<< (std::ostream &out, const std::vector< SparsificationMapper::InfoForPosVec > &pos_vecs_) |
std::ostream & | operator<< (std::ostream &out, const SparsificationMapper::InfoForPosVec &pos_vec_) |
template<class T1 , class T2 > | |
std::ostream & | operator<< (std::ostream &out, const std::pair< T1, T2 > &pair) |
template<class T > | |
std::ostream & | operator<< (std::ostream &out, const std::vector< T > &vec) |
template<class T > | |
std::ostream & | operator<< (std::ostream &out, const type_wrapper< T > &x) |
Variables | |
bool | trace_debugging_output =false |
a static switch to enable generating debugging logs | |
const std::string | the_gap_symbols = "-_~." |
const std::string | simplified_gap_symbols = "---." |
StopWatch | stopwatch |
global StopWatch object | |
char | O_error_msg_buffer [MYBUFSIZ] |
string buffer for error message | |
char * | O_error_msg =O_error_msg_buffer |
pointer to string buffer for error message | |
char | buf [MYBUFSIZ] |
buffer used for constructing small strings | |
std::vector< double > | punA_tab |
std::vector< double > | punB_tab |
auxilliary types and global constants for use in locarna
typedef double LocARNA::FLT_OR_DBL |
select FLT_OR_DBL
typedef InftyInt LocARNA::infty_score_t |
an extended score_t that can store and calculate with infinite values (i.p. we use -infty for invalid matrix entries)
typedef Matrix< double > LocARNA::ProbMatrix |
matrix for storing probabilities
Matrix of probabilities.
std::string LocARNA::concat_with_separator | ( | const std::vector< std::string > & | v, |
char | sep | ||
) |
Tokenize string at separator symbol.
Split at seperator symbol and write to output vector of strings.
s | string |
sep | separator |
v[out] | vector of strings |
int LocARNA::count_opts | ( | option_def * | options | ) |
Counts the options in (null-terminated) array
options | array of options |
bool LocARNA::decode_argument | ( | void * | argument, |
int | arg_type, | ||
const std::string & | optarg | ||
) |
decode a string according to arg_type, for internal use
decode an argument according to specified type
argument | |
arg_type | |
optarg |
decode the string optarg according to the type of argument arg_type and write the result to argument
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inline |
Number of bases in a fragment
i | left end of fragment |
j | right end of fragment |
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inline |
Test for sufficient fragment length
i | left end of fragment |
j | right end of fragment |
minlen | minimum length of fragment |
bool LocARNA::get_nonempty_line | ( | std::istream & | in, |
std::string & | line | ||
) |
Get next non-empty/non-comment line.
in | input stream | |
[out] | line | line |
Get the next line of stream in that is neither emtpy nor starts with white space (the latter is considered a comment in pp and (our variant of) clustalw files).
While newline is quoted concatenate lines. (note: this is kept simple, such that we cannot quote quotes)
bool LocARNA::has_prefix | ( | const std::string & | s, |
const std::string & | p, | ||
size_t | start = 0 |
||
) |
Test string prefix.
s | string |
p | prefix |
start | optional start position |
bool LocARNA::is_blank | ( | std::string & | s | ) |
Test for only blank characters
s | string to be tested |
bool LocARNA::is_gap_symbol | ( | char | c | ) |
Test for gap symbol.
c | character to be tested |
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inline |
x | operand 1 |
y | operand 2 |
T1 LocARNA::max3 | ( | const T1 & | first, |
const T1 & | second, | ||
const T1 & | third | ||
) |
computes the maximum of three values
first | first value |
second | second value |
third | third value |
T1 LocARNA::max4 | ( | const T1 & | first, |
const T1 & | second, | ||
const T1 & | third, | ||
const T1 & | fourth | ||
) |
computes the maximum of four values
first | first value |
second | second value |
third | third value |
fourth | value |
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inline |
x | operand 1 |
y | operand 2 |
void LocARNA::normalize_rna_sequence | ( | std::string & | seq | ) |
Transform an RNA sequence string.
Transform, such that all characters are upper case and Ts are translated to Us
seq | sequence string |
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inline |
x | operand 1 |
y | operand 2 |
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inline |
x | operand 1 |
y | operand 2 |
Add
x | operand 1 |
y | operand 2 |
x | operand 1 |
y | operand 2 |
|
inline |
x | operand 1 |
y | operand 2 |
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inline |
x | operand 1 |
y | operand 2 |
Subtract
x | operand 1 |
y | operand 2 |
x | operand 1 |
y | operand 2 |
bool LocARNA::operator< | ( | const BasePairs::LeftAdjEntry & | e1, |
const BasePairs::LeftAdjEntry & | e2 | ||
) |
compare right ends of arcs (for sorting)
bool LocARNA::operator< | ( | const BasePairs::RightAdjEntry & | e1, |
const BasePairs::RightAdjEntry & | e2 | ||
) |
compare left ends of arcs (for sorting)
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inline |
Less than operator
x | operand 1 |
y | operand 2 |
std::ostream& LocARNA::operator<< | ( | std::ostream & | out, |
const TaintedInftyInt & | x | ||
) |
Output operator for writing object of TaintedInftyInt to output stream
out | the output stream |
x | the object to be written |
std::ostream& LocARNA::operator<< | ( | std::ostream & | out, |
Alphabet< T > | a | ||
) |
Output operator writing alphabet to output stream
out | the output stream |
a | the alphabet |
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inline |
Output operator for objects of AlignerRestrictions
out | output stream |
r | object of AlignerRestriction to be written to stream |
std::ostream & LocARNA::operator<< | ( | std::ostream & | out, |
const std::vector< SparsificationMapper::InfoForPosVec > & | pos_vecs_ | ||
) |
prints all valid sequence positions with additional information for all indices
out | output stream object |
pos_vecs_ | input vector |
std::ostream & LocARNA::operator<< | ( | std::ostream & | out, |
const SparsificationMapper::InfoForPosVec & | pos_vec_ | ||
) |
prints all valid sequence positions with additional information for one index
out | output stream object |
pos_vec_ | input vector |
std::ostream& LocARNA::operator<< | ( | std::ostream & | out, |
const Ribosum & | ribosum | ||
) |
Output operator
out | output stream |
ribosum | Ribosum to be written to stream |
std::ostream & LocARNA::operator<< | ( | std::ostream & | out, |
const BasePairs::Arc & | arc | ||
) |
Output operator for writing arc to output stream
out | the output stream |
arc | the arc to be written |
std::ostream& LocARNA::operator<< | ( | std::ostream & | out, |
Matrix< T > | mat | ||
) |
Output operator for writing (templated) matrix to output stream
out | the output stream |
mat | the matrix to be written |
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inline |
Output operator.
out | output stream |
m | sparse vector to be writing to stream |
std::ostream& LocARNA::operator<< | ( | std::ostream & | out, |
const RibosumFreq & | ribosum | ||
) |
Output operator
out | output stream |
ribosum | Ribosum to be written to stream |
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inline |
Output operator.
out | output stream |
m | sparse matrix to be writing to stream |
std::ostream& LocARNA::operator<< | ( | std::ostream & | out, |
const std::vector< T > & | vec | ||
) |
prints a vector
out | output stream object |
vec | vector |
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inline |
std::ostream & LocARNA::operator<< | ( | std::ostream & | out, |
const MultipleAlignment & | ma | ||
) |
Write multiple alignment to stream.
out | output stream |
ma | multiple alignment |
std::ostream & LocARNA::operator<< | ( | std::ostream & | out, |
const PatternPairMap::patListTYPE & | pat_pair_map | ||
) |
write pattern list of the PatternPairMap to stream
out | output stream object |
the | pattern list of the PatternPairMap |
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inline |
Less or equal than operator
x | operand 1 |
y | operand 2 |
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inline |
x | operand 1 (tainted) |
y | operand 2 (tainted) |
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inline |
Greater than operator
x | operand 1 |
y | operand 2 |
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inline |
Greater or equal than operator
x | operand 1 |
y | operand 2 |
std::istream& LocARNA::operator>> | ( | std::istream & | in, |
Matrix< T > & | mat | ||
) |
Input operator for reading (templated) matrix from input stream
in | the input stream | |
[out] | mat | the matrix to be read |
void LocARNA::print_galaxy_xml | ( | char * | progname, |
option_def | options[] | ||
) |
prints a galaxy wrapper in xml format
progname | Name of program |
options | Options array |
void LocARNA::print_help | ( | char * | progname, |
option_def | options[] | ||
) |
prints a standard help string suited for short help output
progname | Name of program |
options | Options array |
void LocARNA::print_options | ( | option_def | options[] | ) |
Print all options and their settings to standard out
options | options array |
void LocARNA::print_usage | ( | char * | progname, |
option_def | options[] | ||
) |
prints a standard usage string suited for short help output
progname | Name of program |
options | Options array |
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inline |
expected probability of a base pair (null-model)
bool LocARNA::process_options | ( | int | argc, |
char * | argv[], | ||
option_def | options[] | ||
) |
process options
bool LocARNA::process_options | ( | int | argc, |
char * | argv[], | ||
option_def * | options | ||
) |
process options
Processes an argument string as given to main() according to an array of options descriptions of type option_def.
argc | argument counter from main() |
argv | argument vector from main() |
options | array describing the options |
void LocARNA::split_at_separator | ( | const std::string & | s, |
char | sep, | ||
std::vector< std::string > & | v | ||
) |
Tokenize string at separator symbol.
Split at seperator symbol and write to output vector of strings. Output vector is overwritten.
s | string |
sep | separator |
v[out] | vector of strings |
std::vector< std::string > LocARNA::split_at_separator | ( | const std::string & | s, |
char | sep | ||
) |
Tokenize string at separator symbol.
Split at seperator symbol and write to output vector of strings. Output vector is overwritten.
s | string |
sep | separator |
char * LocARNA::sprint_option_name | ( | char * | buf, |
option_def * | options, | ||
int | i | ||
) |
Print option name to string buffer
buf | String buffer |
options | options array |
i | index of option to be printed |
char * LocARNA::sprint_option_name_opt | ( | char * | buf, |
option_def * | options, | ||
int | i | ||
) |
Print option name to string buffer, marking whether it is optional by []
buf | String buffer |
options | options array |
i | index of option to be printed |
char * LocARNA::sprint_option_xml | ( | char * | buf, |
option_def * | options, | ||
int | i | ||
) |
Print an option as xml in Galaxy Wrapper format to string buffer
buf | String buffer |
options | options array |
i | index of option to be printed |
void LocARNA::transform_toupper | ( | std::string & | s | ) |
Convert string to all upper case
[in,out] | s | string |
std::vector<double> LocARNA::punA_tab |
vector for unpaired probabilities temporarily required by sigma_
std::vector<double> LocARNA::punB_tab |
vector for unpaired probabilities