Detailed Description

Dynamic Programming Class.

Structure and Function collection. This Class implements a Dynamic Programming functions.

Definition at line 74 of file DynProg.h.

Inheritance diagram for CDynProg:

Public Member Functions
	CDynProg (int32_t p_num_svms=8)

virtual	~CDynProg ()

void	set_num_states (int32_t N)

int32_t	get_num_states ()

int32_t	get_num_svms ()

void	init_content_svm_value_array (const int32_t p_num_svms)

void	init_tiling_data (int32_t probe_pos, float64_t intensities, const int32_t num_probes)

void	precompute_tiling_plifs (CPlif *PEN, const int32_t tiling_plif_ids, const int32_t num_tiling_plifs)

void	resize_lin_feat (int32_t num_new_feat)

void	set_p_vector (SGVector< float64_t > p)

void	set_q_vector (SGVector< float64_t > q)

void	set_a (SGMatrix< float64_t > a)

void	set_a_id (SGMatrix< int32_t > a)

void	set_a_trans_matrix (SGMatrix< float64_t > a_trans)

void	init_mod_words_array (SGMatrix< int32_t > p_mod_words_array)

bool	check_svm_arrays ()

void	set_observation_matrix (SGNDArray< float64_t > seq)

int32_t	get_num_positions ()

void	set_content_type_array (SGMatrix< float64_t > seg_path)

void	set_pos (SGVector< int32_t > pos)

void	set_orf_info (SGMatrix< int32_t > orf_info)

void	set_gene_string (SGVector< char > genestr)

void	set_dict_weights (SGMatrix< float64_t > dictionary_weights)

void	best_path_set_segment_loss (SGMatrix< float64_t > segment_loss)

void	best_path_set_segment_ids_mask (int32_t segment_ids, float64_t segment_mask, int32_t m)

void	set_sparse_features (CSparseFeatures< float64_t > seq_sparse1, CSparseFeatures< float64_t > seq_sparse2)

void	set_plif_matrices (CPlifMatrix *pm)

SGVector< float64_t >	get_scores ()

SGMatrix< int32_t >	get_states ()

SGMatrix< int32_t >	get_positions ()

void	compute_nbest_paths (int32_t max_num_signals, bool use_orf, int16_t nbest, bool with_loss, bool with_multiple_sequences)

void	best_path_trans_deriv (int32_t my_state_seq, int32_t my_pos_seq, int32_t my_seq_len, const float64_t *seq_array, int32_t max_num_signals)

void	set_my_state_seq (int32_t *my_state_seq)

void	set_my_pos_seq (int32_t *my_pos_seq)

void	get_path_scores (float64_t *my_scores, int32_t seq_len)

void	get_path_losses (float64_t *my_losses, int32_t seq_len)

T_STATES	get_N () const
	access function for number of states N More...

void	set_q (T_STATES offset, float64_t value)

void	set_p (T_STATES offset, float64_t value)

void	set_a (T_STATES line_, T_STATES column, float64_t value)

float64_t	get_q (T_STATES offset) const

float64_t	get_q_deriv (T_STATES offset) const

float64_t	get_p (T_STATES offset) const

float64_t	get_p_deriv (T_STATES offset) const

void	precompute_content_values ()

float64_t *	get_lin_feat (int32_t &dim1, int32_t &dim2)

void	set_lin_feat (float64_t *p_lin_feat, int32_t p_num_svms, int32_t p_seq_len)

void	create_word_string ()

void	precompute_stop_codons ()

float64_t	get_a (T_STATES line_, T_STATES column) const

float64_t	get_a_deriv (T_STATES line_, T_STATES column) const

void	set_intron_list (CIntronList *intron_list, int32_t num_plifs)

CSegmentLoss *	get_segment_loss_object ()

void	long_transition_settings (bool use_long_transitions, int32_t threshold, int32_t max_len)

virtual CSGObject *	shallow_copy () const

virtual CSGObject *	deep_copy () const

virtual bool	is_generic (EPrimitiveType *generic) const

template<class T >
void	set_generic ()

template<>
void	set_generic ()

template<>
void	set_generic ()

template<>
void	set_generic ()

template<>
void	set_generic ()

template<>
void	set_generic ()

template<>
void	set_generic ()

template<>
void	set_generic ()

template<>
void	set_generic ()

template<>
void	set_generic ()

template<>
void	set_generic ()

template<>
void	set_generic ()

template<>
void	set_generic ()

template<>
void	set_generic ()

template<>
void	set_generic ()

template<>
void	set_generic ()

void	unset_generic ()

virtual void	print_serializable (const char *prefix="")

virtual bool	save_serializable (CSerializableFile file, const char prefix="")

virtual bool	load_serializable (CSerializableFile file, const char prefix="")

void	set_global_io (SGIO *io)

SGIO *	get_global_io ()

void	set_global_parallel (Parallel *parallel)

Parallel *	get_global_parallel ()

void	set_global_version (Version *version)

Version *	get_global_version ()

SGStringList< char >	get_modelsel_names ()

void	print_modsel_params ()

char *	get_modsel_param_descr (const char *param_name)

index_t	get_modsel_param_index (const char *param_name)

void	build_gradient_parameter_dictionary (CMap< TParameter , CSGObject > *dict)

bool	has (const std::string &name) const

template<typename T >
bool	has (const Tag< T > &tag) const

template<typename T , typename U = void>
bool	has (const std::string &name) const

template<typename T >
void	set (const Tag< T > &_tag, const T &value)

template<typename T , typename U = void>
void	set (const std::string &name, const T &value)

template<typename T >
T	get (const Tag< T > &_tag) const

template<typename T , typename U = void>
T	get (const std::string &name) const

virtual void	update_parameter_hash ()

virtual bool	parameter_hash_changed ()

virtual bool	equals (CSGObject *other, float64_t accuracy=0.0, bool tolerant=false)

virtual CSGObject *	clone ()

Public Attributes
SGIO *	io

Parallel *	parallel

Version *	version

Parameter *	m_parameters

Parameter *	m_model_selection_parameters

Parameter *	m_gradient_parameters

uint32_t	m_hash

Protected Member Functions
void	lookup_content_svm_values (const int32_t from_state, const int32_t to_state, const int32_t from_pos, const int32_t to_pos, float64_t *svm_values, int32_t frame)

void	lookup_tiling_plif_values (const int32_t from_state, const int32_t to_state, const int32_t len, float64_t *svm_values)

int32_t	find_frame (const int32_t from_state)

int32_t	raw_intensities_interval_query (const int32_t from_pos, const int32_t to_pos, float64_t *intensities, int32_t type)

bool	extend_orf (int32_t orf_from, int32_t orf_to, int32_t start, int32_t &last_pos, int32_t to)

virtual const char *	get_name () const

virtual void	load_serializable_pre () throw (ShogunException)

virtual void	load_serializable_post () throw (ShogunException)

virtual void	save_serializable_pre () throw (ShogunException)

virtual void	save_serializable_post () throw (ShogunException)

template<typename T >
void	register_param (Tag< T > &_tag, const T &value)

template<typename T >
void	register_param (const std::string &name, const T &value)

Protected Attributes
int32_t	m_num_degrees

int32_t	m_num_svms

CDynamicArray< int32_t >	m_word_degree

CDynamicArray< int32_t >	m_cum_num_words

int32_t *	m_cum_num_words_array

CDynamicArray< int32_t >	m_num_words

int32_t *	m_num_words_array

CDynamicArray< int32_t >	m_mod_words

int32_t *	m_mod_words_array

CDynamicArray< bool >	m_sign_words

bool *	m_sign_words_array

CDynamicArray< int32_t >	m_string_words

int32_t *	m_string_words_array

CDynamicArray< int32_t >	m_num_unique_words

bool	m_svm_arrays_clean

int32_t	m_max_a_id

CDynamicArray< float64_t >	m_observation_matrix

CDynamicArray< int32_t >	m_pos

int32_t	m_seq_len

CDynamicArray< int32_t >	m_orf_info

CDynamicArray< float64_t >	m_segment_sum_weights

CDynamicObjectArray	m_plif_list

CDynamicArray< char >	m_genestr

uint16_t ***	m_wordstr

CDynamicArray< float64_t >	m_dict_weights

CDynamicArray< float64_t >	m_segment_loss

CDynamicArray< int32_t >	m_segment_ids

CDynamicArray< float64_t >	m_segment_mask

CDynamicArray< int32_t >	m_my_state_seq

CDynamicArray< int32_t >	m_my_pos_seq

CDynamicArray< float64_t >	m_my_scores

CDynamicArray< float64_t >	m_my_losses

CSegmentLoss *	m_seg_loss_obj

CDynamicArray< float64_t >	m_scores

CDynamicArray< int32_t >	m_states

CDynamicArray< int32_t >	m_positions

CSparseFeatures< float64_t > *	m_seq_sparse1

CSparseFeatures< float64_t > *	m_seq_sparse2

CPlifMatrix *	m_plif_matrices

CDynamicArray< bool >	m_genestr_stop

CIntronList *	m_intron_list

int32_t	m_num_intron_plifs

CDynamicArray< float64_t >	m_lin_feat

float64_t *	m_raw_intensities

int32_t *	m_probe_pos

int32_t *	m_num_probes_cum

int32_t *	m_num_lin_feat_plifs_cum

int32_t	m_num_raw_data

bool	m_long_transitions

int32_t	m_long_transition_threshold

model specific variables.
these are p,q,a,b,N,M etc
int32_t	m_N
	number of states More...

CDynamicArray< int32_t >	m_transition_matrix_a_id
	transition matrix More...

CDynamicArray< float64_t >	m_transition_matrix_a

CDynamicArray< float64_t >	m_transition_matrix_a_deriv

CDynamicArray< float64_t >	m_initial_state_distribution_p
	initial distribution of states More...

CDynamicArray< float64_t >	m_initial_state_distribution_p_deriv

CDynamicArray< float64_t >	m_end_state_distribution_q
	distribution of end-states More...

CDynamicArray< float64_t >	m_end_state_distribution_q_deriv

Static Protected Attributes
static int32_t	word_degree_default [4] ={3,4,5,6}

static int32_t	cum_num_words_default [5] ={0,64,320,1344,5440}

static int32_t	frame_plifs [3] ={4,5,6}

static int32_t	num_words_default [4] = {64,256,1024,4096}

static int32_t	mod_words_default [32]

static bool	sign_words_default [16]

static int32_t	string_words_default [16]

Constructor & Destructor Documentation

CDynProg ( int32_t p_num_svms = 8 )

constructor

Parameters

p_num_svms number of SVMs

Definition at line 46 of file DynProg.cpp.

~CDynProg ( )

virtual

Definition at line 142 of file DynProg.cpp.

Member Function Documentation

void best_path_set_segment_ids_mask	(	int32_t *	segment_ids,
		float64_t *	segment_mask,
		int32_t	m
	)

set best path segmend ids mask

Parameters

segment_ids	segment ids
segment_mask	segment mask
m	dimension m

Definition at line 815 of file DynProg.cpp.

void best_path_set_segment_loss ( SGMatrix< float64_t > segment_loss )

set best path segment loss

Parameters

segment_loss segment loss

Definition at line 798 of file DynProg.cpp.

void best_path_trans_deriv	(	int32_t *	my_state_seq,
		int32_t *	my_pos_seq,
		int32_t	my_seq_len,
		const float64_t *	seq_array,
		int32_t	max_num_signals
	)

given a path though the state model and the corresponding positions compute the features. This can be seen as the derivative of the score (output of dynamic program) with respect to the parameters

Parameters

my_state_seq	state sequence of the path
my_pos_seq	sequence of positions
my_seq_len	length of state and position sequences
seq_array	array of features
max_num_signals	maximal number of signals

Definition at line 2052 of file DynProg.cpp.

void build_gradient_parameter_dictionary ( CMap< TParameter *, CSGObject * > * dict )

inherited

Builds a dictionary of all parameters in SGObject as well of those of SGObjects that are parameters of this object. Dictionary maps parameters to the objects that own them.

Parameters

dict	dictionary of parameters to be built.

Definition at line 630 of file SGObject.cpp.

bool check_svm_arrays ( )

check SVM arrays call this function to check consistency

Returns: whether arrays are ok

Definition at line 601 of file DynProg.cpp.

CSGObject * clone ( )

virtualinherited

Creates a clone of the current object. This is done via recursively traversing all parameters, which corresponds to a deep copy. Calling equals on the cloned object always returns true although none of the memory of both objects overlaps.

Returns: an identical copy of the given object, which is disjoint in memory. NULL if the clone fails. Note that the returned object is SG_REF'ed

Definition at line 747 of file SGObject.cpp.

void compute_nbest_paths	(	int32_t	max_num_signals,
		bool	use_orf,
		int16_t	nbest,
		bool	with_loss,
		bool	with_multiple_sequences
	)

run the viterbi algorithm to compute the n best viterbi paths

Parameters

max_num_signals	maximal number of signals for a single state
use_orf	whether orf shall be used
nbest	number of best paths (n)
with_loss	use loss
with_multiple_sequences	!!!not functional set to false!!!

Definition at line 944 of file DynProg.cpp.

void create_word_string ( )

create word string from char* Jonas

Definition at line 361 of file DynProg.cpp.

CSGObject * deep_copy ( ) const

virtualinherited

A deep copy. All the instance variables will also be copied.

Definition at line 231 of file SGObject.cpp.

bool equals	(	CSGObject *	other,
		float64_t	accuracy = `0.0`,
		bool	tolerant = `false`
	)

virtualinherited

Recursively compares the current SGObject to another one. Compares all registered numerical parameters, recursion upon complex (SGObject) parameters. Does not compare pointers!

May be overwritten but please do with care! Should not be necessary in most cases.

Parameters

other	object to compare with
accuracy	accuracy to use for comparison (optional)
tolerant	allows linient check on float equality (within accuracy)

Returns: true if all parameters were equal, false if not

Definition at line 651 of file SGObject.cpp.

bool extend_orf	(	int32_t	orf_from,
		int32_t	orf_to,
		int32_t	start,
		int32_t &	last_pos,
		int32_t	to
	)

protected

extend orf

Parameters

orf_from	orf from
orf_to	orf to
start	start
last_pos	last position
to	to

Definition at line 893 of file DynProg.cpp.

int32_t find_frame ( const int32_t from_state )

protected

find frame

Parameters

from_state from state

T get ( const Tag< T > & _tag ) const

inherited

Getter for a class parameter, identified by a Tag. Throws an exception if the class does not have such a parameter.

Parameters

_tag	name and type information of parameter

Returns: value of the parameter identified by the input tag

Definition at line 367 of file SGObject.h.

T get ( const std::string & name ) const

inherited

Getter for a class parameter, identified by a name. Throws an exception if the class does not have such a parameter.

Parameters

name	name of the parameter

Returns: value of the parameter corresponding to the input name and type

Definition at line 388 of file SGObject.h.

float64_t get_a	(	T_STATES	line_,
		T_STATES	column
	)		const

access function for matrix a

Parameters

line_	row in matrix 0...N-1
column	column in matrix 0...N-1

Returns: value at position line colum

Definition at line 443 of file DynProg.h.

float64_t get_a_deriv	(	T_STATES	line_,
		T_STATES	column
	)		const

access function for matrix a derivated

Parameters

line_	row in matrix 0...N-1
column	column in matrix 0...N-1

Returns: value at position line colum

Definition at line 454 of file DynProg.h.

SGIO * get_global_io ( )

inherited

get the io object

Returns: io object

Definition at line 268 of file SGObject.cpp.

Parallel * get_global_parallel ( )

inherited

get the parallel object

Returns: parallel object

Definition at line 310 of file SGObject.cpp.

Version * get_global_version ( )

inherited

get the version object

Returns: version object

Definition at line 323 of file SGObject.cpp.

float64_t* get_lin_feat	(	int32_t &	dim1,
		int32_t &	dim2
	)

return array of precomputed linear features like content predictions and PLiFed tiling array data Jonas

Returns: lin_feat_array

Definition at line 410 of file DynProg.h.

SGStringList< char > get_modelsel_names ( )

inherited

Returns: vector of names of all parameters which are registered for model selection

Definition at line 531 of file SGObject.cpp.

char * get_modsel_param_descr ( const char * param_name )

inherited

Returns description of a given parameter string, if it exists. SG_ERROR otherwise

Parameters

param_name name of the parameter

Returns: description of the parameter

Definition at line 555 of file SGObject.cpp.

index_t get_modsel_param_index ( const char * param_name )

inherited

Returns index of model selection parameter with provided index

Parameters

param_name name of model selection parameter

Returns: index of model selection parameter with provided name, -1 if there is no such

Definition at line 568 of file SGObject.cpp.

T_STATES get_N ( ) const

access function for number of states N

Definition at line 325 of file DynProg.h.

virtual const char* get_name ( ) const

protectedvirtual

Returns: object name

Implements CSGObject.

Definition at line 563 of file DynProg.h.

int32_t get_num_positions ( )

get number of positions; the dynamic program is sparse encoded and this function gives the number of positions that can actually be part of a predicted path

Returns: number of positions

Definition at line 679 of file DynProg.cpp.

int32_t get_num_states ( )

get num states

Definition at line 234 of file DynProg.cpp.

int32_t get_num_svms ( )

get num svms

Definition at line 191 of file DynProg.cpp.

float64_t get_p ( T_STATES offset ) const

access function for probability of initial states

Parameters

offset index 0...N-1

Returns: value at offset

Definition at line 384 of file DynProg.h.

float64_t get_p_deriv ( T_STATES offset ) const

access function for derivated probability of initial states

Parameters

offset index 0...N-1

Returns: value at offset

Definition at line 394 of file DynProg.h.

void get_path_losses	(	float64_t **	my_losses,
		int32_t *	seq_len
	)

get path losses

best_path_trans_deriv result retrieval functions

Parameters

my_losses	my losses
seq_len	length of sequence

Definition at line 877 of file DynProg.cpp.

void get_path_scores	(	float64_t **	my_scores,
		int32_t *	seq_len
	)

get path scores

best_path_trans_deriv result retrieval functions

Parameters

my_scores	scores
seq_len	length of sequence

Definition at line 863 of file DynProg.cpp.

SGMatrix< int32_t > get_positions ( )

best path get positions

Returns: positions positions

Definition at line 853 of file DynProg.cpp.

float64_t get_q ( T_STATES offset ) const

access function for probability of end states

Parameters

offset index 0...N-1

Returns: value at offset

Definition at line 364 of file DynProg.h.

float64_t get_q_deriv ( T_STATES offset ) const

access function for derivated probability of end states

Parameters

offset index 0...N-1

Returns: value at offset

Definition at line 374 of file DynProg.h.

SGVector< float64_t > get_scores ( )

best path get scores

Returns: scores scores

Definition at line 835 of file DynProg.cpp.

CSegmentLoss* get_segment_loss_object ( )

get the segment loss object

Definition at line 467 of file DynProg.h.

SGMatrix< int32_t > get_states ( )

best path get states

Returns: states states

Definition at line 843 of file DynProg.cpp.

bool has ( const std::string & name ) const

inherited

Checks if object has a class parameter identified by a name.

Parameters

name	name of the parameter

Returns: true if the parameter exists with the input name

Definition at line 289 of file SGObject.h.

bool has ( const Tag< T > & tag ) const

inherited

Checks if object has a class parameter identified by a Tag.

Parameters

tag	tag of the parameter containing name and type information

Returns: true if the parameter exists with the input tag

Definition at line 301 of file SGObject.h.

bool has ( const std::string & name ) const

inherited

Checks if a type exists for a class parameter identified by a name.

Parameters

name	name of the parameter

Returns: true if the parameter exists with the input name and type

Definition at line 312 of file SGObject.h.

void init_content_svm_value_array ( const int32_t p_num_svms )

init CDynamicArray for precomputed content svm values with size seq_len x num_svms

Parameters

p_num_svms number of svm weight vectors for content prediction

Definition at line 269 of file DynProg.cpp.

void init_mod_words_array ( SGMatrix< int32_t > p_mod_words_array )

init mod words array

Parameters

p_mod_words_array new mod words array

Definition at line 579 of file DynProg.cpp.

void init_tiling_data	(	int32_t *	probe_pos,
		float64_t *	intensities,
		const int32_t	num_probes
	)

init CDynamicArray for precomputed tiling intensitie-plif-values with size seq_len x num_svms

Parameters

probe_pos	local positions of probes
intensities	intensities of probes
num_probes	number of probes

Definition at line 239 of file DynProg.cpp.

bool is_generic ( EPrimitiveType * generic ) const

virtualinherited

If the SGSerializable is a class template then TRUE will be returned and GENERIC is set to the type of the generic.

Parameters

generic set to the type of the generic if returning TRUE

Returns: TRUE if a class template.

Definition at line 329 of file SGObject.cpp.

bool load_serializable	(	CSerializableFile *	file,
		const char *	prefix = `""`
	)

virtualinherited

Load this object from file. If it will fail (returning FALSE) then this object will contain inconsistent data and should not be used!

Parameters

file	where to load from
prefix	prefix for members

Returns: TRUE if done, otherwise FALSE

Definition at line 402 of file SGObject.cpp.

void load_serializable_post	(		)
throw	(	ShogunException
	)

protectedvirtualinherited

Can (optionally) be overridden to post-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::LOAD_SERIALIZABLE_POST is called.

Exceptions

ShogunException will be thrown if an error occurs.

Reimplemented in CKernel, CWeightedDegreePositionStringKernel, CList, CAlphabet, CLinearHMM, CGaussianKernel, CInverseMultiQuadricKernel, CCircularKernel, and CExponentialKernel.

Definition at line 459 of file SGObject.cpp.

void load_serializable_pre	(		)
throw	(	ShogunException
	)

protectedvirtualinherited

Can (optionally) be overridden to pre-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::LOAD_SERIALIZABLE_PRE is called.

Exceptions

ShogunException will be thrown if an error occurs.

Reimplemented in CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool >, and CDynamicObjectArray.

Definition at line 454 of file SGObject.cpp.

void long_transition_settings	(	bool	use_long_transitions,
		int32_t	threshold,
		int32_t	max_len
	)

settings for long transition handling

Parameters

use_long_transitions	use the long transition approximation
threshold	use long transition for segments larger than
max_len	allow transitions up to

Definition at line 478 of file DynProg.h.

void lookup_content_svm_values	(	const int32_t	from_state,
		const int32_t	to_state,
		const int32_t	from_pos,
		const int32_t	to_pos,
		float64_t *	svm_values,
		int32_t	frame
	)

protected

lookup content SVM values

Parameters

from_state	from state
to_state	to state
from_pos	from position
to_pos	to position
svm_values	SVM values
frame	frame

Definition at line 2482 of file DynProg.cpp.

void lookup_tiling_plif_values	(	const int32_t	from_state,
		const int32_t	to_state,
		const int32_t	len,
		float64_t *	svm_values
	)

protected

lookup tiling Plif values

Parameters

from_state	from state
to_state	to state
len	length
svm_values	SVM values

bool parameter_hash_changed ( )

virtualinherited

Returns: whether parameter combination has changed since last update

Definition at line 295 of file SGObject.cpp.

void precompute_content_values ( )

create array of precomputed content svm values

Definition at line 392 of file DynProg.cpp.

void precompute_stop_codons ( )

precompute stop codons

Definition at line 196 of file DynProg.cpp.

void precompute_tiling_plifs	(	CPlif **	PEN,
		const int32_t *	tiling_plif_ids,
		const int32_t	num_tiling_plifs
	)

precompute tiling Plifs

Parameters

PEN	Plif PEN
tiling_plif_ids	tiling plif id's
num_tiling_plifs	number of tiling plifs

Definition at line 312 of file DynProg.cpp.

void print_modsel_params ( )

inherited

prints all parameter registered for model selection and their type

Definition at line 507 of file SGObject.cpp.

void print_serializable ( const char * prefix = "" )

virtualinherited

prints registered parameters out

Parameters

prefix prefix for members

Definition at line 341 of file SGObject.cpp.

int32_t raw_intensities_interval_query	(	const int32_t	from_pos,
		const int32_t	to_pos,
		float64_t *	intensities,
		int32_t	type
	)

protected

raw intensities interval query

Parameters

from_pos	from position
to_pos	to position
intensities	intensities
type	type

Returns: an integer

Definition at line 2456 of file DynProg.cpp.

void register_param	(	Tag< T > &	_tag,
		const T &	value
	)

protectedinherited

Registers a class parameter which is identified by a tag. This enables the parameter to be modified by set() and retrieved by get(). Parameters can be registered in the constructor of the class.

Parameters

_tag	name and type information of parameter
value	value of the parameter

Definition at line 439 of file SGObject.h.

void register_param	(	const std::string &	name,
		const T &	value
	)

protectedinherited

Registers a class parameter which is identified by a name. This enables the parameter to be modified by set() and retrieved by get(). Parameters can be registered in the constructor of the class.

Parameters

name	name of the parameter
value	value of the parameter along with type information

Definition at line 452 of file SGObject.h.

void resize_lin_feat ( int32_t num_new_feat )

append rows to linear features array

Parameters

num_new_feat number of new rows to add

Definition at line 279 of file DynProg.cpp.

bool save_serializable	(	CSerializableFile *	file,
		const char *	prefix = `""`
	)

virtualinherited

Save this object to file.

Parameters

file	where to save the object; will be closed during returning if PREFIX is an empty string.
prefix	prefix for members

Returns: TRUE if done, otherwise FALSE

Definition at line 347 of file SGObject.cpp.

void save_serializable_post	(		)
throw	(	ShogunException
	)

protectedvirtualinherited

Can (optionally) be overridden to post-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::SAVE_SERIALIZABLE_POST is called.

Exceptions

ShogunException will be thrown if an error occurs.

Reimplemented in CKernel.

Definition at line 469 of file SGObject.cpp.

void save_serializable_pre	(		)
throw	(	ShogunException
	)

protectedvirtualinherited

Can (optionally) be overridden to pre-initialize some member variables which are not PARAMETER::ADD'ed. Make sure that at first the overridden method BASE_CLASS::SAVE_SERIALIZABLE_PRE is called.

Exceptions

ShogunException will be thrown if an error occurs.

Reimplemented in CKernel, CDynamicArray< T >, CDynamicArray< float64_t >, CDynamicArray< float32_t >, CDynamicArray< int32_t >, CDynamicArray< char >, CDynamicArray< bool >, and CDynamicObjectArray.

Definition at line 464 of file SGObject.cpp.

void set	(	const Tag< T > &	_tag,
		const T &	value
	)

inherited

Setter for a class parameter, identified by a Tag. Throws an exception if the class does not have such a parameter.

Parameters

_tag	name and type information of parameter
value	value of the parameter

Definition at line 328 of file SGObject.h.

void set	(	const std::string &	name,
		const T &	value
	)

inherited

Setter for a class parameter, identified by a name. Throws an exception if the class does not have such a parameter.

Parameters

name	name of the parameter
value	value of the parameter along with type information

Definition at line 354 of file SGObject.h.

void set_a ( SGMatrix< float64_t > a )

set matrix a

Parameters

a	new matrix a

Definition at line 457 of file DynProg.cpp.

void set_a	(	T_STATES	line_,
		T_STATES	column,
		float64_t	value
	)

access function for matrix a

Parameters

line_	row in matrix 0...N-1
column	column in matrix 0...N-1
value	value to be set

Definition at line 354 of file DynProg.h.

void set_a_id ( SGMatrix< int32_t > a )

set a id

Parameters

a new a id

Definition at line 465 of file DynProg.cpp.

void set_a_trans_matrix ( SGMatrix< float64_t > a_trans )

set a transition matrix

Parameters

a_trans transition matrix a

Definition at line 478 of file DynProg.cpp.

void set_content_type_array ( SGMatrix< float64_t > seg_path )

set an array of length #(candidate positions) which specifies the content type of each pos and a mask that determines to which extend the loss should be applied to this position; this is a way to encode label confidence via weights between zero and one

Parameters

seg_path seg path

Definition at line 684 of file DynProg.cpp.

void set_dict_weights ( SGMatrix< float64_t > dictionary_weights )

set best path dict weights

Parameters

dictionary_weights dictionary weights

Definition at line 779 of file DynProg.cpp.

void set_gene_string ( SGVector< char > genestr )

set best path genesstr

Parameters

genestr gene string

Definition at line 755 of file DynProg.cpp.

void set_generic ( )

inherited

Definition at line 74 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 79 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 84 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 89 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 94 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 99 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 104 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 109 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 114 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 119 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 124 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 129 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 134 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 139 of file SGObject.cpp.

void set_generic ( )

inherited

Definition at line 144 of file SGObject.cpp.

void set_generic ( )

inherited

set generic type to T

void set_global_io ( SGIO * io )

inherited

set the io object

Parameters

io	io object to use

Definition at line 261 of file SGObject.cpp.

void set_global_parallel ( Parallel * parallel )

inherited

set the parallel object

Parameters

parallel parallel object to use

Definition at line 274 of file SGObject.cpp.

void set_global_version ( Version * version )

inherited

set the version object

Parameters

version version object to use

Definition at line 316 of file SGObject.cpp.

void set_intron_list	(	CIntronList *	intron_list,
		int32_t	num_plifs
	)

set intron list

Parameters

intron_list
num_plifs	number of intron plifs

Definition at line 2535 of file DynProg.cpp.

void set_lin_feat	(	float64_t *	p_lin_feat,
		int32_t	p_num_svms,
		int32_t	p_seq_len
	)

set your own array of precomputed linear features like content predictions and PLiFed tiling array data Jonas

Parameters

p_lin_feat	array of features
p_num_svms	number of tracks
p_seq_len	number of candidate positions

Definition at line 423 of file DynProg.h.

void set_my_pos_seq ( int32_t * my_pos_seq )

set best path my position sequence

Parameters

my_pos_seq my position sequence

Definition at line 771 of file DynProg.cpp.

void set_my_state_seq ( int32_t * my_state_seq )

set best path my state sequence

Parameters

my_state_seq my state sequence

Definition at line 763 of file DynProg.cpp.

void set_num_states ( int32_t N )

set number of states use this to set N first

Parameters

N new N

Definition at line 219 of file DynProg.cpp.

void set_observation_matrix ( SGNDArray< float64_t > seq )

set best path seq

Parameters

seq	signal features

Definition at line 657 of file DynProg.cpp.

void set_orf_info ( SGMatrix< int32_t > orf_info )

set best path orf info only for compute_nbest_paths

Parameters

orf_info the orf info

Definition at line 723 of file DynProg.cpp.

void set_p	(	T_STATES	offset,
		float64_t	value
	)

access function for probability of first state

Parameters

offset	index 0...N-1
value	value to be set

Definition at line 343 of file DynProg.h.

void set_p_vector ( SGVector< float64_t > p )

set vector p

Parameters

p	new vector p

Definition at line 442 of file DynProg.cpp.

void set_plif_matrices ( CPlifMatrix * pm )

set plif matrices

Parameters

pm	plif matrix object

Definition at line 746 of file DynProg.cpp.

void set_pos ( SGVector< int32_t > pos )

set best path pos

Parameters

pos	the position vector

Definition at line 717 of file DynProg.cpp.

void set_q	(	T_STATES	offset,
		float64_t	value
	)

access function for probability of end states

Parameters

offset	index 0...N-1
value	value to be set

Definition at line 334 of file DynProg.h.

void set_q_vector ( SGVector< float64_t > q )

set vector q

Parameters

q	new vector q

Definition at line 450 of file DynProg.cpp.

void set_sparse_features	(	CSparseFeatures< float64_t > *	seq_sparse1,
		CSparseFeatures< float64_t > *	seq_sparse2
	)

set sparse feature matrices

Definition at line 732 of file DynProg.cpp.

CSGObject * shallow_copy ( ) const

virtualinherited

A shallow copy. All the SGObject instance variables will be simply assigned and SG_REF-ed.

Reimplemented in CGaussianKernel.

Definition at line 225 of file SGObject.cpp.

void unset_generic ( )

inherited

unset generic type

this has to be called in classes specializing a template class

Definition at line 336 of file SGObject.cpp.

void update_parameter_hash ( )

virtualinherited

Updates the hash of current parameter combination

Definition at line 281 of file SGObject.cpp.

Member Data Documentation

int32_t cum_num_words_default ={0,64,320,1344,5440}

staticprotected

default values storing the cumulative sum of the number of kmers that exist for the different degrees e.g. matlab spoken: cumsum(4.^[3 4 5 6])

Definition at line 771 of file DynProg.h.

int32_t frame_plifs ={4,5,6}

staticprotected

default values defining which of the plif are the frame specific plifs

Definition at line 775 of file DynProg.h.

SGIO* io

inherited

io

Definition at line 537 of file SGObject.h.

CDynamicArray<int32_t> m_cum_num_words

protected

cum num words

Definition at line 628 of file DynProg.h.

int32_t* m_cum_num_words_array

protected

cum num words array

Definition at line 630 of file DynProg.h.

CDynamicArray<float64_t> m_dict_weights

protected

dict weights

Definition at line 688 of file DynProg.h.

CDynamicArray<float64_t> m_end_state_distribution_q

protected

distribution of end-states

Definition at line 615 of file DynProg.h.

CDynamicArray<float64_t> m_end_state_distribution_q_deriv

protected

Definition at line 616 of file DynProg.h.

CDynamicArray<char> m_genestr

protected

a single string (to be segmented)

Definition at line 671 of file DynProg.h.

CDynamicArray<bool> m_genestr_stop

protected

storeage of stop codons array of size length(sequence)

Definition at line 726 of file DynProg.h.

Parameter* m_gradient_parameters

inherited

parameters wrt which we can compute gradients

Definition at line 552 of file SGObject.h.

uint32_t m_hash

inherited

Hash of parameter values

Definition at line 555 of file SGObject.h.

CDynamicArray<float64_t> m_initial_state_distribution_p

protected

initial distribution of states

Definition at line 611 of file DynProg.h.

CDynamicArray<float64_t> m_initial_state_distribution_p_deriv

protected

Definition at line 612 of file DynProg.h.

CIntronList* m_intron_list

protected

administers a list of introns and quality scores and provides functions for fast access

Definition at line 730 of file DynProg.h.

CDynamicArray<float64_t> m_lin_feat

protected

array for storage of precomputed linear features linge content svm values or pliffed tiling data Jonas

Definition at line 739 of file DynProg.h.

int32_t m_long_transition_threshold

protected

threshold for transitions that are computed the traditional way

Definition at line 756 of file DynProg.h.

bool m_long_transitions

protected

use long transition approximation

Definition at line 753 of file DynProg.h.

int32_t m_max_a_id

protected

max a id

Definition at line 655 of file DynProg.h.

CDynamicArray<int32_t> m_mod_words

protected

mod words

Definition at line 636 of file DynProg.h.

int32_t* m_mod_words_array

protected

mod words array

Definition at line 638 of file DynProg.h.

Parameter* m_model_selection_parameters

inherited

model selection parameters

Definition at line 549 of file SGObject.h.

CDynamicArray<float64_t> m_my_losses

protected

my losses

Definition at line 702 of file DynProg.h.

CDynamicArray<int32_t> m_my_pos_seq

protected

my position sequence

Definition at line 698 of file DynProg.h.

CDynamicArray<float64_t> m_my_scores

protected

my scores

Definition at line 700 of file DynProg.h.

CDynamicArray<int32_t> m_my_state_seq

protected

my state seq

Definition at line 696 of file DynProg.h.

int32_t m_N

protected

number of states

Definition at line 603 of file DynProg.h.

int32_t m_num_degrees

protected

number of degress

Definition at line 621 of file DynProg.h.

int32_t m_num_intron_plifs

protected

number of intron features and plifs

Definition at line 733 of file DynProg.h.

int32_t* m_num_lin_feat_plifs_cum

protected

num lin feat plifs cum

Definition at line 748 of file DynProg.h.

int32_t* m_num_probes_cum

protected

number of probes

Definition at line 746 of file DynProg.h.

int32_t m_num_raw_data

protected

number of additional data tracks like tiling, RNA-Seq, ...

Definition at line 750 of file DynProg.h.

int32_t m_num_svms

protected

number of SVMs

Definition at line 623 of file DynProg.h.

CDynamicArray<int32_t> m_num_unique_words

protected

SVM start position number of unique words

Definition at line 651 of file DynProg.h.

CDynamicArray<int32_t> m_num_words

protected

num words

Definition at line 632 of file DynProg.h.

int32_t* m_num_words_array

protected

num words array

Definition at line 634 of file DynProg.h.

CDynamicArray<float64_t> m_observation_matrix

protected

sequence

Definition at line 659 of file DynProg.h.

CDynamicArray<int32_t> m_orf_info

protected

orf info

Definition at line 665 of file DynProg.h.

Parameter* m_parameters

inherited

parameters

Definition at line 546 of file SGObject.h.

CDynamicObjectArray m_plif_list

protected

Plif list

Definition at line 669 of file DynProg.h.

CPlifMatrix* m_plif_matrices

protected

plif matrices

Definition at line 721 of file DynProg.h.

CDynamicArray<int32_t> m_pos

protected

candidate position

Definition at line 661 of file DynProg.h.

CDynamicArray<int32_t> m_positions

protected

positions

Definition at line 714 of file DynProg.h.

int32_t* m_probe_pos

protected

probe position

Definition at line 744 of file DynProg.h.

float64_t* m_raw_intensities

protected

raw intensities

Definition at line 742 of file DynProg.h.

CDynamicArray<float64_t> m_scores

protected

scores

Definition at line 710 of file DynProg.h.

CSegmentLoss* m_seg_loss_obj

protected

segment loss object containing the functions to compute the segment loss

Definition at line 706 of file DynProg.h.

CDynamicArray<int32_t> m_segment_ids

protected

segment IDs

Definition at line 692 of file DynProg.h.

CDynamicArray<float64_t> m_segment_loss

protected

segment loss

Definition at line 690 of file DynProg.h.

CDynamicArray<float64_t> m_segment_mask

protected

segment mask

Definition at line 694 of file DynProg.h.

CDynamicArray<float64_t> m_segment_sum_weights

protected

segment sum weights

Definition at line 667 of file DynProg.h.

int32_t m_seq_len

protected

number of candidate positions

Definition at line 663 of file DynProg.h.

CSparseFeatures<float64_t>* m_seq_sparse1

protected

sparse feature matrix dim1

Definition at line 717 of file DynProg.h.

CSparseFeatures<float64_t>* m_seq_sparse2

protected

sparse feature matrix dim2

Definition at line 719 of file DynProg.h.

CDynamicArray<bool> m_sign_words

protected

sign words

Definition at line 640 of file DynProg.h.

bool* m_sign_words_array

protected

sign words array

Definition at line 642 of file DynProg.h.

CDynamicArray<int32_t> m_states

protected

states

Definition at line 712 of file DynProg.h.

CDynamicArray<int32_t> m_string_words

protected

string words

Definition at line 644 of file DynProg.h.

int32_t* m_string_words_array

protected

string words array

Definition at line 646 of file DynProg.h.

bool m_svm_arrays_clean

protected

SVM arrays clean

Definition at line 653 of file DynProg.h.

CDynamicArray<float64_t> m_transition_matrix_a

protected

Definition at line 607 of file DynProg.h.

CDynamicArray<float64_t> m_transition_matrix_a_deriv

protected

Definition at line 608 of file DynProg.h.

CDynamicArray<int32_t> m_transition_matrix_a_id

protected

transition matrix

Definition at line 606 of file DynProg.h.

CDynamicArray<int32_t> m_word_degree

protected

word degree

Definition at line 626 of file DynProg.h.

uint16_t*** m_wordstr

protected

wordstr is a vector of L n-gram indices, with wordstr(i) representing a number betweeen 0 and 4095 corresponding to the 6-mer in genestr(i-5:i) pos is a vector of candidate transition positions (it is input to compute_nbest_paths) t_end is some index in pos

svs has been initialized by init_svm_values

At the end of this procedure, svs.svm_values[i+s*svs.seqlen] has the value of the s-th SVM on genestr(pos(t_end-i):pos(t_end)) for every i satisfying pos(t_end)-pos(t_end-i) <= svs.maxlookback

The SVM weights are precomputed in m_dict_weights

Definition at line 686 of file DynProg.h.

int32_t mod_words_default

staticprotected

Initial value:

= {1,1,1,1,1,1,1,1,
                                    1,1,1,1,1,1,1,1,
                                    0,0,0,0,0,0,0,0,
                                    0,0,0,0,0,0,0,0}

default values

Definition at line 782 of file DynProg.h.

int32_t num_words_default = {64,256,1024,4096}

staticprotected

default values like cum_num_words_default but not cumsumed: e.g. 4.^[3 4 5 6]

Definition at line 779 of file DynProg.h.

Parallel* parallel

inherited

parallel

Definition at line 540 of file SGObject.h.

bool sign_words_default

staticprotected

Initial value:

= {true,true,true,true,true,true,true,true,

false,false,false,false,false,false,false,false}

default values

Definition at line 785 of file DynProg.h.

int32_t string_words_default

staticprotected

Initial value:

= {0,0,0,0,0,0,0,0,

1,1,1,1,1,1,1,1}

default values

Definition at line 788 of file DynProg.h.

Version* version

inherited

version

Definition at line 543 of file SGObject.h.

int32_t word_degree_default ={3,4,5,6}

staticprotected

maximal length of a long transition Note: is ignored in the current implementation => arbitrarily long transitions can be decodeddefault values defining the k-mer degrees used for content type prediction

Definition at line 766 of file DynProg.h.

The documentation for this class was generated from the following files:

Detailed Description

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Static Protected Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation