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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
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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_tget_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_tget_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)
CSegmentLossget_segment_loss_object ()
void long_transition_settings (bool use_long_transitions, int32_t threshold, int32_t max_len)
virtual CSGObjectshallow_copy () const
virtual CSGObjectdeep_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::get_version_parameter())
virtual bool load_serializable (CSerializableFile *file, const char *prefix="", int32_t param_version=Version::get_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)
SGIOget_global_io ()
void set_global_parallel (Parallel *parallel)
Parallelget_global_parallel ()
void set_global_version (Version *version)
Versionget_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)
virtual void update_parameter_hash ()
virtual bool parameter_hash_changed ()
virtual bool equals (CSGObject *other, float64_t accuracy=0.0, bool tolerant=false)
virtual CSGObjectclone ()

Public Attributes

SGIOio
Parallelparallel
Versionversion
Parameterm_parameters
Parameterm_model_selection_parameters
Parameterm_gradient_parameters
ParameterMapm_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 TParametermigrate (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)

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_tm_observation_matrix
CDynamicArray< int32_t > m_pos
int32_t m_seq_len
CDynamicArray< int32_t > m_orf_info
CDynamicArray< float64_tm_segment_sum_weights
CDynamicObjectArray m_plif_list
CDynamicArray< char > m_genestr
uint16_t *** m_wordstr
CDynamicArray< float64_tm_dict_weights
CDynamicArray< float64_tm_segment_loss
CDynamicArray< int32_t > m_segment_ids
CDynamicArray< float64_tm_segment_mask
CDynamicArray< int32_t > m_my_state_seq
CDynamicArray< int32_t > m_my_pos_seq
CDynamicArray< float64_tm_my_scores
CDynamicArray< float64_tm_my_losses
CSegmentLossm_seg_loss_obj
CDynamicArray< float64_tm_scores
CDynamicArray< int32_t > m_states
CDynamicArray< int32_t > m_positions
CSparseFeatures< float64_t > * m_seq_sparse1
CSparseFeatures< float64_t > * m_seq_sparse2
CPlifMatrixm_plif_matrices
CDynamicArray< bool > m_genestr_stop
CIntronListm_intron_list
int32_t m_num_intron_plifs
CDynamicArray< float64_tm_lin_feat
float64_tm_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_tm_transition_matrix_a
CDynamicArray< float64_tm_transition_matrix_a_deriv
CDynamicArray< float64_tm_initial_state_distribution_p
 initial distribution of states
CDynamicArray< float64_tm_initial_state_distribution_p_deriv
CDynamicArray< float64_tm_end_state_distribution_q
 distribution of end-states
CDynamicArray< float64_tm_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_svmsnumber of SVMs

Definition at line 45 of file DynProg.cpp.

~CDynProg ( )
virtual

Definition at line 141 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_idssegment ids
segment_masksegment mask
mdimension m

Definition at line 814 of file DynProg.cpp.

void best_path_set_segment_loss ( SGMatrix< float64_t segment_loss)

set best path segment loss

Parameters
segment_losssegment loss

Definition at line 797 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_seqstate sequence of the path
my_pos_seqsequence of positions
my_seq_lenlength of state and position sequences
seq_arrayarray of features
max_num_signalsmaximal number of signals

Definition at line 2051 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
dictdictionary of parameters to be built.

Definition at line 1243 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 600 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 1360 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_signalsmaximal number of signals for a single state
use_orfwhether orf shall be used
nbestnumber of best paths (n)
with_lossuse loss
with_multiple_sequences!!!not functional set to false!!!

Definition at line 943 of file DynProg.cpp.

void create_word_string ( )

create word string from char* Jonas

Definition at line 360 of file DynProg.cpp.

CSGObject * deep_copy ( ) const
virtualinherited

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

Definition at line 200 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
otherobject to compare with
accuracyaccuracy to use for comparison (optional)
tolerantallows linient check on float equality (within accuracy)
Returns
true if all parameters were equal, false if not

Definition at line 1264 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_fromorf from
orf_toorf to
startstart
last_poslast position
toto

Definition at line 892 of file DynProg.cpp.

int32_t find_frame ( const int32_t  from_state)
protected

find frame

Parameters
from_statefrom 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
columncolumn 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
columncolumn 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 237 of file SGObject.cpp.

Parallel * get_global_parallel ( )
inherited

get the parallel object

Returns
parallel object

Definition at line 278 of file SGObject.cpp.

Version * get_global_version ( )
inherited

get the version object

Returns
version object

Definition at line 291 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 1135 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_namename of the parameter
Returns
description of the parameter

Definition at line 1159 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_namename of model selection parameter
Returns
index of model selection parameter with provided name, -1 if there is no such

Definition at line 1172 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
protectedvirtual
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 678 of file DynProg.cpp.

int32_t get_num_states ( )

get num states

Definition at line 233 of file DynProg.cpp.

int32_t get_num_svms ( )

get num svms

Definition at line 190 of file DynProg.cpp.

float64_t get_p ( T_STATES  offset) const

access function for probability of initial states

Parameters
offsetindex 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
offsetindex 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_lossesmy losses
seq_lenlength of sequence

Definition at line 876 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_scoresscores
seq_lenlength of sequence

Definition at line 862 of file DynProg.cpp.

SGMatrix< int32_t > get_positions ( )

best path get positions

Returns
positions positions

Definition at line 852 of file DynProg.cpp.

float64_t get_q ( T_STATES  offset) const

access function for probability of end states

Parameters
offsetindex 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
offsetindex 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 834 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 842 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 268 of file DynProg.cpp.

void init_mod_words_array ( SGMatrix< int32_t >  p_mod_words_array)

init mod words array

Parameters
p_mod_words_arraynew mod words array

Definition at line 578 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_poslocal positions of probes
intensitiesintensities of probes
num_probesnumber of probes

Definition at line 238 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
genericset to the type of the generic if returning TRUE
Returns
TRUE if a class template.

Definition at line 297 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_versionparameter version of the file
current_versionversion from which mapping begins (you want to use Version::get_version_parameter() for this in most cases)
filefile to load from
prefixprefix for members
Returns
(sorted) array of created TParameter instances with file data

Definition at line 704 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_infoinformation of parameter
file_versionparameter version of the file, must be <= provided parameter version
filefile to load from
prefixprefix for members
Returns
new array with TParameter instances with the attached data

Definition at line 545 of file SGObject.cpp.

bool load_serializable ( CSerializableFile file,
const char *  prefix = "",
int32_t  param_version = Version::get_version_parameter() 
)
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
filewhere to load from
prefixprefix 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

Definition at line 374 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
ShogunExceptionwill be thrown if an error occurs.

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

Definition at line 1062 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
ShogunExceptionwill 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 1057 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_transitionsuse the long transition approximation
thresholduse long transition for segments larger than
max_lenallow 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_statefrom state
to_stateto state
from_posfrom position
to_posto position
svm_valuesSVM values
frameframe

Definition at line 2481 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_statefrom state
to_stateto state
lenlength
svm_valuesSVM 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_baseset of TParameter instances that are mapped to the provided target parameter infos
base_versionversion of the parameter base
target_param_infosset of SGParamInfo instances that specify the target parameter base

Definition at line 742 of file SGObject.cpp.

TParameter * migrate ( DynArray< TParameter * > *  param_base,
const SGParamInfo target 
)
protectedvirtualinherited

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_baseset of TParameter instances to use for migration
targetparameter 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 949 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 
)
protectedvirtualinherited

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_baseset of TParameter instances to use for migration
targetparameter info for the resulting TParameter
replacement(used as output) here the TParameter instance which is returned by migration is created into
to_migratethe only source that is used for migration
old_namewith this parameter, a name change may be specified

Definition at line 889 of file SGObject.cpp.

bool parameter_hash_changed ( )
virtualinherited
Returns
whether parameter combination has changed since last update

Definition at line 263 of file SGObject.cpp.

void precompute_content_values ( )

create array of precomputed content svm values

Definition at line 391 of file DynProg.cpp.

void precompute_stop_codons ( )

precompute stop codons

Definition at line 195 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
PENPlif PEN
tiling_plif_idstiling plif id's
num_tiling_plifsnumber of tiling plifs

Definition at line 311 of file DynProg.cpp.

void print_modsel_params ( )
inherited

prints all parameter registered for model selection and their type

Definition at line 1111 of file SGObject.cpp.

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

prints registered parameters out

Parameters
prefixprefix for members

Definition at line 309 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_posfrom position
to_posto position
intensitiesintensities
typetype
Returns
an integer

Definition at line 2455 of file DynProg.cpp.

void resize_lin_feat ( int32_t  num_new_feat)

append rows to linear features array

Parameters
num_new_featnumber of new rows to add

Definition at line 278 of file DynProg.cpp.

bool save_serializable ( CSerializableFile file,
const char *  prefix = "",
int32_t  param_version = Version::get_version_parameter() 
)
virtualinherited

Save this object to file.

Parameters
filewhere to save the object; will be closed during returning if PREFIX is an empty string.
prefixprefix 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

Definition at line 315 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
ShogunExceptionwill be thrown if an error occurs.

Reimplemented in CKernel.

Definition at line 1072 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
ShogunExceptionwill 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 1067 of file SGObject.cpp.

void set_a ( SGMatrix< float64_t a)

set matrix a

Parameters
anew matrix a

Definition at line 456 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
columncolumn in matrix 0...N-1
valuevalue to be set

Definition at line 356 of file DynProg.h.

void set_a_id ( SGMatrix< int32_t >  a)

set a id

Parameters
anew a id

Definition at line 464 of file DynProg.cpp.

void set_a_trans_matrix ( SGMatrix< float64_t a_trans)

set a transition matrix

Parameters
a_transtransition matrix a

Definition at line 477 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_pathseg path

Definition at line 683 of file DynProg.cpp.

void set_dict_weights ( SGMatrix< float64_t dictionary_weights)

set best path dict weights

Parameters
dictionary_weightsdictionary weights

Definition at line 778 of file DynProg.cpp.

void set_gene_string ( SGVector< char >  genestr)

set best path genesstr

Parameters
genestrgene string

Definition at line 754 of file DynProg.cpp.

void set_generic< complex128_t > ( )
inherited

set generic type to T

Definition at line 42 of file SGObject.cpp.

void set_global_io ( SGIO io)
inherited

set the io object

Parameters
ioio object to use

Definition at line 230 of file SGObject.cpp.

void set_global_parallel ( Parallel parallel)
inherited

set the parallel object

Parameters
parallelparallel object to use

Definition at line 243 of file SGObject.cpp.

void set_global_version ( Version version)
inherited

set the version object

Parameters
versionversion object to use

Definition at line 284 of file SGObject.cpp.

void set_intron_list ( CIntronList intron_list,
int32_t  num_plifs 
)

set intron list

Parameters
intron_list
num_plifsnumber of intron plifs

Definition at line 2534 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_featarray of features
p_num_svmsnumber of tracks
p_seq_lennumber 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_seqmy position sequence

Definition at line 770 of file DynProg.cpp.

void set_my_state_seq ( int32_t *  my_state_seq)

set best path my state sequence

Parameters
my_state_seqmy state sequence

Definition at line 762 of file DynProg.cpp.

void set_num_states ( int32_t  N)

set number of states use this to set N first

Parameters
Nnew N

Definition at line 218 of file DynProg.cpp.

void set_observation_matrix ( SGNDArray< float64_t seq)

set best path seq

Parameters
seqsignal features

Definition at line 656 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_infothe orf info

Definition at line 722 of file DynProg.cpp.

void set_p ( T_STATES  offset,
float64_t  value 
)

access function for probability of first state

Parameters
offsetindex 0...N-1
valuevalue to be set

Definition at line 345 of file DynProg.h.

void set_p_vector ( SGVector< float64_t p)

set vector p

Parameters
pnew vector p

Definition at line 441 of file DynProg.cpp.

void set_plif_matrices ( CPlifMatrix pm)

set plif matrices

Parameters
pmplif matrix object

Definition at line 745 of file DynProg.cpp.

void set_pos ( SGVector< int32_t >  pos)

set best path pos

Parameters
posthe position vector

Definition at line 716 of file DynProg.cpp.

void set_q ( T_STATES  offset,
float64_t  value 
)

access function for probability of end states

Parameters
offsetindex 0...N-1
valuevalue to be set

Definition at line 336 of file DynProg.h.

void set_q_vector ( SGVector< float64_t q)

set vector q

Parameters
qnew vector q

Definition at line 449 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 731 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 194 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 304 of file SGObject.cpp.

void update_parameter_hash ( )
virtualinherited

Updates the hash of current parameter combination

Definition at line 250 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 773 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 777 of file DynProg.h.

SGIO* io
inherited

io

Definition at line 496 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 690 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 673 of file DynProg.h.

CDynamicArray<bool> m_genestr_stop
protected

storeage of stop codons array of size length(sequence)

Definition at line 728 of file DynProg.h.

Parameter* m_gradient_parameters
inherited

parameters wrt which we can compute gradients

Definition at line 511 of file SGObject.h.

uint32_t m_hash
inherited

Hash of parameter values

Definition at line 517 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 732 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 741 of file DynProg.h.

int32_t m_long_transition_threshold
protected

threshold for transitions that are computed the traditional way

Definition at line 758 of file DynProg.h.

bool m_long_transitions
protected

use long transition approximation

Definition at line 755 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 508 of file SGObject.h.

CDynamicArray<float64_t> m_my_losses
protected

my losses

Definition at line 704 of file DynProg.h.

CDynamicArray<int32_t> m_my_pos_seq
protected

my position sequence

Definition at line 700 of file DynProg.h.

CDynamicArray<float64_t> m_my_scores
protected

my scores

Definition at line 702 of file DynProg.h.

CDynamicArray<int32_t> m_my_state_seq
protected

my state seq

Definition at line 698 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 735 of file DynProg.h.

int32_t* m_num_lin_feat_plifs_cum
protected

num lin feat plifs cum

Definition at line 750 of file DynProg.h.

int32_t* m_num_probes_cum
protected

number of probes

Definition at line 748 of file DynProg.h.

int32_t m_num_raw_data
protected

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

Definition at line 752 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 514 of file SGObject.h.

Parameter* m_parameters
inherited

parameters

Definition at line 505 of file SGObject.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 723 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 716 of file DynProg.h.

int32_t* m_probe_pos
protected

probe position

Definition at line 746 of file DynProg.h.

float64_t* m_raw_intensities
protected

raw intensities

Definition at line 744 of file DynProg.h.

CDynamicArray<float64_t> m_scores
protected

scores

Definition at line 712 of file DynProg.h.

CSegmentLoss* m_seg_loss_obj
protected

segment loss object containing the functions to compute the segment loss

Definition at line 708 of file DynProg.h.

CDynamicArray<int32_t> m_segment_ids
protected

segment IDs

Definition at line 694 of file DynProg.h.

CDynamicArray<float64_t> m_segment_loss
protected

segment loss

Definition at line 692 of file DynProg.h.

CDynamicArray<float64_t> m_segment_mask
protected

segment mask

Definition at line 696 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 719 of file DynProg.h.

CSparseFeatures<float64_t>* m_seq_sparse2
protected

sparse feature matrix dim2

Definition at line 721 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 714 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 688 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 784 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 781 of file DynProg.h.

Parallel* parallel
inherited

parallel

Definition at line 499 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 787 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 790 of file DynProg.h.

Version* version
inherited

version

Definition at line 502 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 768 of file DynProg.h.


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

SHOGUN Machine Learning Toolbox - Documentation