Public Member Functions | Public Attributes | Protected Member Functions | Protected Attributes | Static Protected Attributes

CDynProg Class Reference

Detailed Description

Dynamic Programming Class.

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

Definition at line 76 of file DynProg.h.

Inheritance diagram for CDynProg:
Inheritance graph
[legend]

List of all members.

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
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 ()
void unset_generic ()
virtual void print_serializable (const char *prefix="")
virtual bool save_serializable (CSerializableFile *file, const char *prefix="", int32_t param_version=VERSION_PARAMETER)
virtual bool load_serializable (CSerializableFile *file, const char *prefix="", int32_t param_version=VERSION_PARAMETER)
DynArray< TParameter * > * load_file_parameters (const SGParamInfo *param_info, int32_t file_version, CSerializableFile *file, const char *prefix="")
DynArray< TParameter * > * load_all_file_parameters (int32_t file_version, int32_t current_version, CSerializableFile *file, const char *prefix="")
void map_parameters (DynArray< TParameter * > *param_base, int32_t &base_version, DynArray< const SGParamInfo * > *target_param_infos)
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_parameter_dictionary (CMap< TParameter *, CSGObject * > &dict)

Public Attributes

SGIO * io
Parallel * parallel
Version * version
Parameter * m_parameters
Parameter * m_model_selection_parameters
ParameterMap * m_parameter_map
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 TParameter * migrate (DynArray< TParameter * > *param_base, const SGParamInfo *target)
virtual void one_to_one_migration_prepare (DynArray< TParameter * > *param_base, const SGParamInfo *target, TParameter *&replacement, TParameter *&to_migrate, char *old_name=NULL)
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)
virtual bool update_parameter_hash ()

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
CDynamicObjectArray m_PEN
CDynamicObjectArray m_PEN_state_signals
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
CDynamicArray< int32_t > m_transition_matrix_a_id
 transition matrix
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
CDynamicArray< float64_t > m_initial_state_distribution_p_deriv
CDynamicArray< float64_t > m_end_state_distribution_q
 distribution of end-states
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 45 of file DynProg.cpp.

~CDynProg (  )  [virtual]

Definition at line 144 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 817 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 800 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 2054 of file DynProg.cpp.

void build_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 1201 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 603 of file DynProg.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 946 of file DynProg.cpp.

void create_word_string (  ) 

create word string from char* Jonas

Definition at line 363 of file DynProg.cpp.

virtual CSGObject* deep_copy (  )  const [virtual, inherited]

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

Definition at line 131 of file SGObject.h.

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 895 of file DynProg.cpp.

int32_t find_frame ( const int32_t  from_state  )  [protected]

find frame

Parameters:
from_state from state
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 445 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 456 of file DynProg.h.

SGIO * get_global_io (  )  [inherited]

get the io object

Returns:
io object

Definition at line 224 of file SGObject.cpp.

Parallel * get_global_parallel (  )  [inherited]

get the parallel object

Returns:
parallel object

Definition at line 259 of file SGObject.cpp.

Version * get_global_version (  )  [inherited]

get the version object

Returns:
version object

Definition at line 272 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 412 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 1108 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 1132 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 1145 of file SGObject.cpp.

T_STATES get_N (  )  const

access function for number of states N

Definition at line 327 of file DynProg.h.

virtual const char* get_name (  )  const [protected, virtual]
Returns:
object name

Implements CSGObject.

Definition at line 565 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 681 of file DynProg.cpp.

int32_t get_num_states (  ) 

get num states

Definition at line 236 of file DynProg.cpp.

int32_t get_num_svms (  ) 

get num svms

Definition at line 192 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 386 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 396 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 879 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 865 of file DynProg.cpp.

SGMatrix< int32_t > get_positions (  ) 

best path get positions

Returns:
positions positions

Definition at line 855 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 366 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 376 of file DynProg.h.

SGVector< float64_t > get_scores (  ) 

best path get scores

Returns:
scores scores

Definition at line 837 of file DynProg.cpp.

CSegmentLoss* get_segment_loss_object (  ) 

get the segment loss object

Definition at line 469 of file DynProg.h.

SGMatrix< int32_t > get_states (  ) 

best path get states

Returns:
states states

Definition at line 845 of file DynProg.cpp.

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 271 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 581 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 241 of file DynProg.cpp.

bool is_generic ( EPrimitiveType *  generic  )  const [virtual, inherited]

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 278 of file SGObject.cpp.

DynArray< TParameter * > * load_all_file_parameters ( int32_t  file_version,
int32_t  current_version,
CSerializableFile *  file,
const char *  prefix = "" 
) [inherited]

maps all parameters of this instance to the provided file version and loads all parameter data from the file into an array, which is sorted (basically calls load_file_parameter(...) for all parameters and puts all results into a sorted array)

Parameters:
file_version parameter version of the file
current_version version from which mapping begins (you want to use VERSION_PARAMETER for this in most cases)
file file to load from
prefix prefix for members
Returns:
(sorted) array of created TParameter instances with file data

Definition at line 679 of file SGObject.cpp.

DynArray< TParameter * > * load_file_parameters ( const SGParamInfo *  param_info,
int32_t  file_version,
CSerializableFile *  file,
const char *  prefix = "" 
) [inherited]

loads some specified parameters from a file with a specified version The provided parameter info has a version which is recursively mapped until the file parameter version is reached. Note that there may be possibly multiple parameters in the mapping, therefore, a set of TParameter instances is returned

Parameters:
param_info information of parameter
file_version parameter version of the file, must be <= provided parameter version
file file to load from
prefix prefix for members
Returns:
new array with TParameter instances with the attached data

Definition at line 523 of file SGObject.cpp.

bool load_serializable ( CSerializableFile *  file,
const char *  prefix = "",
int32_t  param_version = VERSION_PARAMETER 
) [virtual, inherited]

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
param_version (optional) a parameter version different to (this is mainly for testing, better do not use)
Returns:
TRUE if done, otherwise FALSE

Reimplemented in CModelSelectionParameters.

Definition at line 354 of file SGObject.cpp.

void load_serializable_post (  )  throw (ShogunException) [protected, virtual, inherited]

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 occurres.

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

Definition at line 1033 of file SGObject.cpp.

void load_serializable_pre (  )  throw (ShogunException) [protected, virtual, inherited]

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 occurres.

Definition at line 1028 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 480 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 2484 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
void map_parameters ( DynArray< TParameter * > *  param_base,
int32_t &  base_version,
DynArray< const SGParamInfo * > *  target_param_infos 
) [inherited]

Takes a set of TParameter instances (base) with a certain version and a set of target parameter infos and recursively maps the base level wise to the current version using CSGObject::migrate(...). The base is replaced. After this call, the base version containing parameters should be of same version/type as the initial target parameter infos. Note for this to work, the migrate methods and all the internal parameter mappings have to match

Parameters:
param_base set of TParameter instances that are mapped to the provided target parameter infos
base_version version of the parameter base
target_param_infos set of SGParamInfo instances that specify the target parameter base

Definition at line 717 of file SGObject.cpp.

TParameter * migrate ( DynArray< TParameter * > *  param_base,
const SGParamInfo *  target 
) [protected, virtual, inherited]

creates a new TParameter instance, which contains migrated data from the version that is provided. The provided parameter data base is used for migration, this base is a collection of all parameter data of the previous version. Migration is done FROM the data in param_base TO the provided param info Migration is always one version step. Method has to be implemented in subclasses, if no match is found, base method has to be called.

If there is an element in the param_base which equals the target, a copy of the element is returned. This represents the case when nothing has changed and therefore, the migrate method is not overloaded in a subclass

Parameters:
param_base set of TParameter instances to use for migration
target parameter info for the resulting TParameter
Returns:
a new TParameter instance with migrated data from the base of the type which is specified by the target parameter

Definition at line 923 of file SGObject.cpp.

void one_to_one_migration_prepare ( DynArray< TParameter * > *  param_base,
const SGParamInfo *  target,
TParameter *&  replacement,
TParameter *&  to_migrate,
char *  old_name = NULL 
) [protected, virtual, inherited]

This method prepares everything for a one-to-one parameter migration. One to one here means that only ONE element of the parameter base is needed for the migration (the one with the same name as the target). Data is allocated for the target (in the type as provided in the target SGParamInfo), and a corresponding new TParameter instance is written to replacement. The to_migrate pointer points to the single needed TParameter instance needed for migration. If a name change happened, the old name may be specified by old_name. In addition, the m_delete_data flag of to_migrate is set to true. So if you want to migrate data, the only thing to do after this call is converting the data in the m_parameter fields. If unsure how to use - have a look into an example for this. (base_migration_type_conversion.cpp for example)

Parameters:
param_base set of TParameter instances to use for migration
target parameter info for the resulting TParameter
replacement (used as output) here the TParameter instance which is returned by migration is created into
to_migrate the only source that is used for migration
old_name with this parameter, a name change may be specified

Definition at line 864 of file SGObject.cpp.

void precompute_content_values (  ) 

create array of precomputed content svm values

Definition at line 394 of file DynProg.cpp.

void precompute_stop_codons (  ) 

precompute stop codons

Definition at line 197 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 314 of file DynProg.cpp.

void print_modsel_params (  )  [inherited]

prints all parameter registered for model selection and their type

Definition at line 1084 of file SGObject.cpp.

void print_serializable ( const char *  prefix = ""  )  [virtual, inherited]

prints registered parameters out

Parameters:
prefix prefix for members

Definition at line 290 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 2458 of file DynProg.cpp.

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 281 of file DynProg.cpp.

bool save_serializable ( CSerializableFile *  file,
const char *  prefix = "",
int32_t  param_version = VERSION_PARAMETER 
) [virtual, inherited]

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
param_version (optional) a parameter version different to (this is mainly for testing, better do not use)
Returns:
TRUE if done, otherwise FALSE

Reimplemented in CModelSelectionParameters.

Definition at line 296 of file SGObject.cpp.

void save_serializable_post (  )  throw (ShogunException) [protected, virtual, inherited]

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 occurres.

Reimplemented in CKernel.

Definition at line 1043 of file SGObject.cpp.

void save_serializable_pre (  )  throw (ShogunException) [protected, virtual, inherited]

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 occurres.

Reimplemented in CKernel.

Definition at line 1038 of file SGObject.cpp.

void set_a ( SGMatrix< float64_t >  a  ) 

set matrix a

Parameters:
a new matrix a

Definition at line 459 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 356 of file DynProg.h.

void set_a_id ( SGMatrix< int32_t >  a  ) 

set a id

Parameters:
a new a id

Definition at line 467 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 480 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 686 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 781 of file DynProg.cpp.

void set_gene_string ( SGVector< char >  genestr  ) 

set best path genesstr

Parameters:
genestr gene string

Definition at line 757 of file DynProg.cpp.

void set_generic< floatmax_t > (  )  [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 217 of file SGObject.cpp.

void set_global_parallel ( Parallel *  parallel  )  [inherited]

set the parallel object

Parameters:
parallel parallel object to use

Definition at line 230 of file SGObject.cpp.

void set_global_version ( Version *  version  )  [inherited]

set the version object

Parameters:
version version object to use

Definition at line 265 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 2537 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 425 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 773 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 765 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 220 of file DynProg.cpp.

void set_observation_matrix ( SGNDArray< float64_t >  seq  ) 

set best path seq

Parameters:
seq signal features

Definition at line 659 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 725 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 345 of file DynProg.h.

void set_p_vector ( SGVector< float64_t >  p  ) 

set vector p

Parameters:
p new vector p

Definition at line 444 of file DynProg.cpp.

void set_plif_matrices ( CPlifMatrix *  pm  ) 

set plif matrices

Parameters:
pm plif matrix object

Definition at line 748 of file DynProg.cpp.

void set_pos ( SGVector< int32_t >  pos  ) 

set best path pos

Parameters:
pos the position vector

Definition at line 719 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 336 of file DynProg.h.

void set_q_vector ( SGVector< float64_t >  q  ) 

set vector q

Parameters:
q new vector q

Definition at line 452 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 734 of file DynProg.cpp.

virtual CSGObject* shallow_copy (  )  const [virtual, inherited]

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

Reimplemented in CGaussianKernel.

Definition at line 122 of file SGObject.h.

void unset_generic (  )  [inherited]

unset generic type

this has to be called in classes specializing a template class

Definition at line 285 of file SGObject.cpp.

bool update_parameter_hash (  )  [protected, virtual, inherited]

Updates the hash of current parameter combination.

Returns:
bool if parameter combination has changed since last update.

Definition at line 237 of file SGObject.cpp.

Member Data Documentation

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

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 777 of file DynProg.h.

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

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

Definition at line 781 of file DynProg.h.

SGIO* io [inherited]

io

Definition at line 462 of file SGObject.h.

CDynamicArray<int32_t> m_cum_num_words [protected]

cum num words

Definition at line 630 of file DynProg.h.

int32_t* m_cum_num_words_array [protected]

cum num words array

Definition at line 632 of file DynProg.h.

CDynamicArray<float64_t> m_dict_weights [protected]

dict weights

Definition at line 694 of file DynProg.h.

CDynamicArray<float64_t> m_end_state_distribution_q [protected]

distribution of end-states

Definition at line 617 of file DynProg.h.

CDynamicArray<float64_t> m_end_state_distribution_q_deriv [protected]

Definition at line 618 of file DynProg.h.

CDynamicArray<char> m_genestr [protected]

a single string (to be segmented)

Definition at line 677 of file DynProg.h.

CDynamicArray<bool> m_genestr_stop [protected]

storeage of stop codons array of size length(sequence)

Definition at line 732 of file DynProg.h.

uint32_t m_hash [inherited]

Hash of parameter values

Definition at line 480 of file SGObject.h.

CDynamicArray<float64_t> m_initial_state_distribution_p [protected]

initial distribution of states

Definition at line 613 of file DynProg.h.

CDynamicArray<float64_t> m_initial_state_distribution_p_deriv [protected]

Definition at line 614 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 736 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 745 of file DynProg.h.

int32_t m_long_transition_threshold [protected]

threshold for transitions that are computed the traditional way

Definition at line 762 of file DynProg.h.

bool m_long_transitions [protected]

use long transition approximation

Definition at line 759 of file DynProg.h.

int32_t m_max_a_id [protected]

max a id

Definition at line 657 of file DynProg.h.

CDynamicArray<int32_t> m_mod_words [protected]

mod words

Definition at line 638 of file DynProg.h.

int32_t* m_mod_words_array [protected]

mod words array

Definition at line 640 of file DynProg.h.

Parameter* m_model_selection_parameters [inherited]

model selection parameters

Definition at line 474 of file SGObject.h.

CDynamicArray<float64_t> m_my_losses [protected]

my losses

Definition at line 708 of file DynProg.h.

CDynamicArray<int32_t> m_my_pos_seq [protected]

my position sequence

Definition at line 704 of file DynProg.h.

CDynamicArray<float64_t> m_my_scores [protected]

my scores

Definition at line 706 of file DynProg.h.

CDynamicArray<int32_t> m_my_state_seq [protected]

my state seq

Definition at line 702 of file DynProg.h.

int32_t m_N [protected]

number of states

Definition at line 605 of file DynProg.h.

int32_t m_num_degrees [protected]

number of degress

Definition at line 623 of file DynProg.h.

int32_t m_num_intron_plifs [protected]

number of intron features and plifs

Definition at line 739 of file DynProg.h.

int32_t* m_num_lin_feat_plifs_cum [protected]

num lin feat plifs cum

Definition at line 754 of file DynProg.h.

int32_t* m_num_probes_cum [protected]

number of probes

Definition at line 752 of file DynProg.h.

int32_t m_num_raw_data [protected]

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

Definition at line 756 of file DynProg.h.

int32_t m_num_svms [protected]

number of SVMs

Definition at line 625 of file DynProg.h.

CDynamicArray<int32_t> m_num_unique_words [protected]

SVM start position number of unique words

Definition at line 653 of file DynProg.h.

CDynamicArray<int32_t> m_num_words [protected]

num words

Definition at line 634 of file DynProg.h.

int32_t* m_num_words_array [protected]

num words array

Definition at line 636 of file DynProg.h.

CDynamicArray<float64_t> m_observation_matrix [protected]

sequence

Definition at line 661 of file DynProg.h.

CDynamicArray<int32_t> m_orf_info [protected]

orf info

Definition at line 667 of file DynProg.h.

ParameterMap* m_parameter_map [inherited]

map for different parameter versions

Definition at line 477 of file SGObject.h.

Parameter* m_parameters [inherited]

parameters

Definition at line 471 of file SGObject.h.

CDynamicObjectArray m_PEN [protected]

PEN

Definition at line 673 of file DynProg.h.

CDynamicObjectArray m_PEN_state_signals [protected]

PEN state signals

Definition at line 675 of file DynProg.h.

CDynamicObjectArray m_plif_list [protected]

Plif list

Definition at line 671 of file DynProg.h.

CPlifMatrix* m_plif_matrices [protected]

plif matrices

Definition at line 727 of file DynProg.h.

CDynamicArray<int32_t> m_pos [protected]

candidate position

Definition at line 663 of file DynProg.h.

CDynamicArray<int32_t> m_positions [protected]

positions

Definition at line 720 of file DynProg.h.

int32_t* m_probe_pos [protected]

probe position

Definition at line 750 of file DynProg.h.

float64_t* m_raw_intensities [protected]

raw intensities

Definition at line 748 of file DynProg.h.

CDynamicArray<float64_t> m_scores [protected]

scores

Definition at line 716 of file DynProg.h.

CSegmentLoss* m_seg_loss_obj [protected]

segment loss object containing the functions to compute the segment loss

Definition at line 712 of file DynProg.h.

CDynamicArray<int32_t> m_segment_ids [protected]

segment IDs

Definition at line 698 of file DynProg.h.

CDynamicArray<float64_t> m_segment_loss [protected]

segment loss

Definition at line 696 of file DynProg.h.

CDynamicArray<float64_t> m_segment_mask [protected]

segment mask

Definition at line 700 of file DynProg.h.

CDynamicArray<float64_t> m_segment_sum_weights [protected]

segment sum weights

Definition at line 669 of file DynProg.h.

int32_t m_seq_len [protected]

number of candidate positions

Definition at line 665 of file DynProg.h.

CSparseFeatures<float64_t>* m_seq_sparse1 [protected]

sparse feature matrix dim1

Definition at line 723 of file DynProg.h.

CSparseFeatures<float64_t>* m_seq_sparse2 [protected]

sparse feature matrix dim2

Definition at line 725 of file DynProg.h.

CDynamicArray<bool> m_sign_words [protected]

sign words

Definition at line 642 of file DynProg.h.

bool* m_sign_words_array [protected]

sign words array

Definition at line 644 of file DynProg.h.

CDynamicArray<int32_t> m_states [protected]

states

Definition at line 718 of file DynProg.h.

CDynamicArray<int32_t> m_string_words [protected]

string words

Definition at line 646 of file DynProg.h.

int32_t* m_string_words_array [protected]

string words array

Definition at line 648 of file DynProg.h.

bool m_svm_arrays_clean [protected]

SVM arrays clean

Definition at line 655 of file DynProg.h.

CDynamicArray<float64_t> m_transition_matrix_a [protected]

Definition at line 609 of file DynProg.h.

CDynamicArray<float64_t> m_transition_matrix_a_deriv [protected]

Definition at line 610 of file DynProg.h.

CDynamicArray<int32_t> m_transition_matrix_a_id [protected]

transition matrix

Definition at line 608 of file DynProg.h.

CDynamicArray<int32_t> m_word_degree [protected]

word degree

Definition at line 628 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 692 of file DynProg.h.

int32_t mod_words_default [static, protected]
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 788 of file DynProg.h.

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

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

Definition at line 785 of file DynProg.h.

Parallel* parallel [inherited]

parallel

Definition at line 465 of file SGObject.h.

bool sign_words_default [static, protected]
Initial value:
 {true,true,true,true,true,true,true,true,
                                      false,false,false,false,false,false,false,false}

default values

Definition at line 791 of file DynProg.h.

int32_t string_words_default [static, protected]
Initial value:
 {0,0,0,0,0,0,0,0,
                                       1,1,1,1,1,1,1,1}

default values

Definition at line 794 of file DynProg.h.

Version* version [inherited]

version

Definition at line 468 of file SGObject.h.

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

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 772 of file DynProg.h.

The documentation for this class was generated from the following files:
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Defines
SHOGUN Machine Learning Toolbox - Documentation