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CTrie< Trie > Class Template Reference

Detailed Description

template<class Trie>
class shogun::CTrie< Trie >

Template class Trie implements a suffix trie, i.e. a tree in which all suffixes up to a certain length are stored.

It is excessively used in the CWeightedDegreeStringKernel and CWeightedDegreePositionStringKernel to construct the whole features space \(\Phi(x)\) and enormously helps here to speed up SVM training and evaluation.

Note that depending on the underlying structure used, a single symbol in the tree requires 20 bytes (DNATrie). It is also used to do the efficient recursion in computing positional oligomer importance matrices (POIMs) where the structure requires * 20+3*8 (POIMTrie) bytes.

Finally note that this tree may use compact internal nodes (for strings that appear without modifications, thus not requiring further branches), which may save a lot of memory on higher degree tries.

Definition at line 158 of file Trie.h.

Inheritance diagram for CTrie< Trie >:
Inheritance graph
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Public Member Functions

 CTrie ()
 CTrie (int32_t d, bool p_use_compact_terminal_nodes=true)
 CTrie (const CTrie &to_copy)
virtual ~CTrie ()
const CTrieoperator= (const CTrie &to_copy)
bool compare_traverse (int32_t node, const CTrie &other, int32_t other_node)
bool compare (const CTrie &other)
bool find_node (int32_t node, int32_t *trace, int32_t &trace_len) const
int32_t find_deepest_node (int32_t start_node, int32_t &deepest_node) const
void display_node (int32_t node) const
void destroy ()
void set_degree (int32_t d)
void create (int32_t len, bool p_use_compact_terminal_nodes=true)
void delete_trees (bool p_use_compact_terminal_nodes=true)
void add_to_trie (int32_t i, int32_t seq_offset, int32_t *vec, float32_t alpha, float64_t *weights, bool degree_times_position_weights)
float64_t compute_abs_weights_tree (int32_t tree, int32_t depth)
float64_tcompute_abs_weights (int32_t &len)
float64_t compute_by_tree_helper (int32_t *vec, int32_t len, int32_t seq_pos, int32_t tree_pos, int32_t weight_pos, float64_t *weights, bool degree_times_position_weights)
void compute_by_tree_helper (int32_t *vec, int32_t len, int32_t seq_pos, int32_t tree_pos, int32_t weight_pos, float64_t *LevelContrib, float64_t factor, int32_t mkl_stepsize, float64_t *weights, bool degree_times_position_weights)
void compute_scoring_helper (int32_t tree, int32_t i, int32_t j, float64_t weight, int32_t d, int32_t max_degree, int32_t num_feat, int32_t num_sym, int32_t sym_offset, int32_t offs, float64_t *result)
void add_example_to_tree_mismatch_recursion (int32_t tree, int32_t i, float64_t alpha, int32_t *vec, int32_t len_rem, int32_t degree_rec, int32_t mismatch_rec, int32_t max_mismatch, float64_t *weights)
void traverse (int32_t tree, const int32_t p, struct TreeParseInfo info, const int32_t depth, int32_t *const x, const int32_t k)
void count (const float64_t w, const int32_t depth, const struct TreeParseInfo info, const int32_t p, int32_t *x, const int32_t k)
int32_t compact_nodes (int32_t start_node, int32_t depth, float64_t *weights)
float64_t get_cumulative_score (int32_t pos, uint64_t seq, int32_t deg, float64_t *weights)
void fill_backtracking_table_recursion (Trie *tree, int32_t depth, uint64_t seq, float64_t value, DynArray< ConsensusEntry > *table, float64_t *weights)
void fill_backtracking_table (int32_t pos, DynArray< ConsensusEntry > *prev, DynArray< ConsensusEntry > *cur, bool cumulative, float64_t *weights)
void POIMs_extract_W (float64_t *const *const W, const int32_t K)
void POIMs_precalc_SLR (const float64_t *const distrib)
void POIMs_get_SLR (const int32_t parentIdx, const int32_t sym, const int32_t depth, float64_t *S, float64_t *L, float64_t *R)
void POIMs_add_SLR (float64_t *const *const poims, const int32_t K, const int32_t debug)
bool get_use_compact_terminal_nodes ()
void set_use_compact_terminal_nodes (bool p_use_compact_terminal_nodes)
int32_t get_num_used_nodes ()
void set_position_weights (float64_t *p_position_weights)
int32_t get_node (bool last_node=false)
void check_treemem ()
void set_weights_in_tree (bool weights_in_tree_)
bool get_weights_in_tree ()
void POIMs_extract_W_helper (const int32_t nodeIdx, const int32_t depth, const int32_t offset, const int32_t y0, float64_t *const *const W, const int32_t K)
void POIMs_calc_SLR_helper1 (const float64_t *const distrib, const int32_t i, const int32_t nodeIdx, int32_t left_tries_idx[4], const int32_t depth, int32_t const lastSym, float64_t *S, float64_t *L, float64_t *R)
void POIMs_calc_SLR_helper2 (const float64_t *const distrib, const int32_t i, const int32_t nodeIdx, int32_t left_tries_idx[4], const int32_t depth, float64_t *S, float64_t *L, float64_t *R)
void POIMs_add_SLR_helper1 (const int32_t nodeIdx, const int32_t depth, const int32_t i, const int32_t y0, float64_t *const *const poims, const int32_t K, const int32_t debug)
void POIMs_add_SLR_helper2 (float64_t *const *const poims, const int32_t K, const int32_t k, const int32_t i, const int32_t y, const float64_t valW, const float64_t valS, const float64_t valL, const float64_t valR, const int32_t debug)
virtual const char * get_name () const
template<>
void POIMs_extract_W_helper (const int32_t nodeIdx, const int32_t depth, const int32_t offset, const int32_t y0, float64_t *const *const W, const int32_t K)
template<>
void POIMs_extract_W (float64_t *const *const W, const int32_t K)
template<>
void POIMs_calc_SLR_helper1 (const float64_t *const distrib, const int32_t i, const int32_t nodeIdx, int32_t left_tries_idx[4], const int32_t depth, int32_t const lastSym, float64_t *S, float64_t *L, float64_t *R)
template<>
void POIMs_calc_SLR_helper2 (const float64_t *const distrib, const int32_t i, const int32_t nodeIdx, int32_t left_tries_idx[4], const int32_t depth, float64_t *S, float64_t *L, float64_t *R)
template<>
void POIMs_precalc_SLR (const float64_t *const distrib)
template<>
void POIMs_get_SLR (const int32_t parentIdx, const int32_t sym, const int32_t depth, float64_t *S, float64_t *L, float64_t *R)
template<>
void POIMs_add_SLR_helper2 (float64_t *const *const poims, const int32_t K, const int32_t k, const int32_t i, const int32_t y, const float64_t valW, const float64_t valS, const float64_t valL, const float64_t valR, const int32_t debug)
template<>
void POIMs_add_SLR_helper1 (const int32_t nodeIdx, const int32_t depth, const int32_t i, const int32_t y0, float64_t *const *const poims, const int32_t K, const int32_t debug)
template<>
void POIMs_add_SLR (float64_t *const *const poims, const int32_t K, const int32_t debug)
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

int32_t NUM_SYMS
SGIOio
Parallelparallel
Versionversion
Parameterm_parameters
Parameterm_model_selection_parameters
Parameterm_gradient_parameters
ParameterMapm_parameter_map
uint32_t m_hash

Protected Member Functions

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 length
int32_t * trees
int32_t degree
float64_tposition_weights
Trie * TreeMem
int32_t TreeMemPtr
int32_t TreeMemPtrMax
bool use_compact_terminal_nodes
bool weights_in_tree
int32_t * nofsKmers

Constructor & Destructor Documentation

CTrie ( )

default constructor

Definition at line 663 of file Trie.h.

CTrie ( int32_t  d,
bool  p_use_compact_terminal_nodes = true 
)

constructor

Parameters
ddegree
p_use_compact_terminal_nodesif compact terminal nodes shall be used

Definition at line 680 of file Trie.h.

CTrie ( const CTrie< Trie > &  to_copy)

copy constructor

Definition at line 696 of file Trie.h.

~CTrie ( )
virtual

Definition at line 1129 of file Trie.h.

Member Function Documentation

void add_example_to_tree_mismatch_recursion ( int32_t  tree,
int32_t  i,
float64_t  alpha,
int32_t *  vec,
int32_t  len_rem,
int32_t  degree_rec,
int32_t  mismatch_rec,
int32_t  max_mismatch,
float64_t weights 
)

add example to tree mismatch recursion

Parameters
treetree
ii
alphaalpha
vecvector
len_remlength of rem
degree_recdegree rec
mismatch_recmismatch rec
max_mismatchmaximum mismatch
weightsweights

Definition at line 1235 of file Trie.h.

void add_to_trie ( int32_t  i,
int32_t  seq_offset,
int32_t *  vec,
float32_t  alpha,
float64_t weights,
bool  degree_times_position_weights 
)

add to trie

Parameters
ii
seq_offsetsequence offset
vecvector
alphaalpha
weightsweights
degree_times_position_weightsif degree times position weights shall be applied

Definition at line 1497 of file Trie.h.

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.

void check_treemem ( )

check tree memory usage

Definition at line 519 of file Trie.h.

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.

int32_t compact_nodes ( int32_t  start_node,
int32_t  depth,
float64_t weights 
)

compact nodes

Parameters
start_nodestart node
depthdepth
weightsweights

Definition at line 815 of file Trie.h.

bool compare ( const CTrie< Trie > &  other)

compare

Parameters
otherother trie
Returns
if comparison was successful

Definition at line 1011 of file Trie.h.

bool compare_traverse ( int32_t  node,
const CTrie< Trie > &  other,
int32_t  other_node 
)

compare traverse

Parameters
nodenode
otherother trie
other_nodeother node
Returns
if comparison was successful

Definition at line 924 of file Trie.h.

float64_t * compute_abs_weights ( int32_t &  len)

compute absolute weights

Parameters
lenlength
Returns
computed absolute weights

Definition at line 1215 of file Trie.h.

float64_t compute_abs_weights_tree ( int32_t  tree,
int32_t  depth 
)

compute absolute weights tree

Parameters
treetree to compute for
depthdepth
Returns
computed absolute weights tree

Definition at line 1186 of file Trie.h.

float64_t compute_by_tree_helper ( int32_t *  vec,
int32_t  len,
int32_t  seq_pos,
int32_t  tree_pos,
int32_t  weight_pos,
float64_t weights,
bool  degree_times_position_weights 
)

compute by tree helper

Parameters
vecvector
lenlength
seq_possequence position
tree_postree position
weight_posweight position
weights
degree_times_position_weightsif degree times position weights shall be applied
Returns
a computed value

Definition at line 1723 of file Trie.h.

void compute_by_tree_helper ( int32_t *  vec,
int32_t  len,
int32_t  seq_pos,
int32_t  tree_pos,
int32_t  weight_pos,
float64_t LevelContrib,
float64_t  factor,
int32_t  mkl_stepsize,
float64_t weights,
bool  degree_times_position_weights 
)

compute by tree helper

Parameters
vecvector
lenlength
seq_possequence position
tree_postree position
weight_posweight position
LevelContriblevel contribution
factorfactor
mkl_stepsizeMKL stepsize
weights
degree_times_position_weightsif degree times position weights shall be applied

Definition at line 1798 of file Trie.h.

void compute_scoring_helper ( int32_t  tree,
int32_t  i,
int32_t  j,
float64_t  weight,
int32_t  d,
int32_t  max_degree,
int32_t  num_feat,
int32_t  num_sym,
int32_t  sym_offset,
int32_t  offs,
float64_t result 
)

compute scoring helper

Parameters
treetree
ii
jj
weightweight
ddegree
max_degreemaximum degree
num_featnumber of features
num_symnumber of symbols
sym_offsetsymbol offset
offsoffsets
resultresult

Definition at line 1348 of file Trie.h.

void count ( const float64_t  w,
const int32_t  depth,
const struct TreeParseInfo  info,
const int32_t  p,
int32_t *  x,
const int32_t  k 
)

count

Parameters
ww
depthdepth
infotree parse info
pp
xx
k

Definition at line 1443 of file Trie.h.

void create ( int32_t  len,
bool  p_use_compact_terminal_nodes = true 
)

create

Parameters
lenlength of new trie
p_use_compact_terminal_nodesif compact terminal nodes shall be used

Definition at line 1157 of file Trie.h.

CSGObject * deep_copy ( ) const
virtualinherited

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

Definition at line 200 of file SGObject.cpp.

void delete_trees ( bool  p_use_compact_terminal_nodes = true)

delete trees

Parameters
p_use_compact_terminal_nodesif compact terminal nodes shall be used

Definition at line 1172 of file Trie.h.

void destroy ( )

destroy

Definition at line 1136 of file Trie.h.

void display_node ( int32_t  node) const

display node

Parameters
nodenode to display

Definition at line 1065 of file Trie.h.

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.

void fill_backtracking_table ( int32_t  pos,
DynArray< ConsensusEntry > *  prev,
DynArray< ConsensusEntry > *  cur,
bool  cumulative,
float64_t weights 
)

fill backtracking table

Parameters
posposition
prevprevious concencus entry
curcurrent concensus entry
cumulativeif is cumulative
weightsweights

Definition at line 2088 of file Trie.h.

void fill_backtracking_table_recursion ( Trie *  tree,
int32_t  depth,
uint64_t  seq,
float64_t  value,
DynArray< ConsensusEntry > *  table,
float64_t weights 
)

fill backtracking table recursion

Parameters
treetree
depthdepth
seqsequence
valuevalue
tabletable of concensus entries
weightsweights

Definition at line 2014 of file Trie.h.

int32_t find_deepest_node ( int32_t  start_node,
int32_t &  deepest_node 
) const

find deepest node

Parameters
start_nodestart node
deepest_nodedeepest node will be stored in here
Returns
depth of deepest node

Definition at line 758 of file Trie.h.

bool find_node ( int32_t  node,
int32_t *  trace,
int32_t &  trace_len 
) const

find node

Parameters
nodenode to find
tracetrace
trace_lenlength of trace

Definition at line 1024 of file Trie.h.

float64_t get_cumulative_score ( int32_t  pos,
uint64_t  seq,
int32_t  deg,
float64_t weights 
)

get cumulative score

Parameters
posposition
seqsequence
degdegree
weightsweights
Returns
cumulative score

Definition at line 2056 of file Trie.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.

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.

virtual const char* get_name ( ) const
virtual
Returns
object name

Implements CSGObject.

Definition at line 630 of file Trie.h.

int32_t get_node ( bool  last_node = false)

get node

Returns
node

Definition at line 495 of file Trie.h.

int32_t get_num_used_nodes ( )

get number of used nodes

Returns
number of used nodes

Definition at line 477 of file Trie.h.

bool get_use_compact_terminal_nodes ( )

get use compact terminal nodes

Returns
if compact terminal nodes are used

Definition at line 457 of file Trie.h.

bool get_weights_in_tree ( )

get weights in tree

Returns
if weights are in tree

Definition at line 543 of file Trie.h.

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 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.

const CTrie< Trie > & operator= ( const CTrie< Trie > &  to_copy)

overload operator =

Definition at line 724 of file Trie.h.

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

Definition at line 263 of file SGObject.cpp.

void POIMs_add_SLR ( float64_t *const *const  poims,
const int32_t  K,
const int32_t  debug 
)

Definition at line 411 of file Trie.cpp.

void POIMs_add_SLR ( float64_t *const *const  poims,
const int32_t  K,
const int32_t  debug 
)

POIMs add SLR

Parameters
poimsPOIMs
KK
debugdebug level
void POIMs_add_SLR_helper1 ( const int32_t  nodeIdx,
const int32_t  depth,
const int32_t  i,
const int32_t  y0,
float64_t *const *const  poims,
const int32_t  K,
const int32_t  debug 
)

Definition at line 354 of file Trie.cpp.

void POIMs_add_SLR_helper1 ( const int32_t  nodeIdx,
const int32_t  depth,
const int32_t  i,
const int32_t  y0,
float64_t *const *const  poims,
const int32_t  K,
const int32_t  debug 
)

POIMs add SLR helper 1

Parameters
nodeIdxnode index
depthdepth
ii
y0y0
poimsPOIMs
KK
debugdebug level
void POIMs_add_SLR_helper2 ( float64_t *const *const  poims,
const int32_t  K,
const int32_t  k,
const int32_t  i,
const int32_t  y,
const float64_t  valW,
const float64_t  valS,
const float64_t  valL,
const float64_t  valR,
const int32_t  debug 
)

Definition at line 293 of file Trie.cpp.

void POIMs_add_SLR_helper2 ( float64_t *const *const  poims,
const int32_t  K,
const int32_t  k,
const int32_t  i,
const int32_t  y,
const float64_t  valW,
const float64_t  valS,
const float64_t  valL,
const float64_t  valR,
const int32_t  debug 
)

POIMs add SLR helper 2

Parameters
poimsPOIMs
KK
kk
ii
yy
valWvalue W
valSvalue S
valLvalue L
valRvalue R
debugdebug level
void POIMs_calc_SLR_helper1 ( const float64_t *const  distrib,
const int32_t  i,
const int32_t  nodeIdx,
int32_t  left_tries_idx[4],
const int32_t  depth,
int32_t const  lastSym,
float64_t S,
float64_t L,
float64_t R 
)

Definition at line 73 of file Trie.cpp.

void POIMs_calc_SLR_helper1 ( const float64_t *const  distrib,
const int32_t  i,
const int32_t  nodeIdx,
int32_t  left_tries_idx[4],
const int32_t  depth,
int32_t const  lastSym,
float64_t S,
float64_t L,
float64_t R 
)

POIMs calc SLR helper

Parameters
distribdistribution
ii
nodeIdxnode index
left_tries_idxleft tries index
depthdepth
lastSymlast symbol
SS
LL
RR
void POIMs_calc_SLR_helper2 ( const float64_t *const  distrib,
const int32_t  i,
const int32_t  nodeIdx,
int32_t  left_tries_idx[4],
const int32_t  depth,
float64_t S,
float64_t L,
float64_t R 
)

Definition at line 133 of file Trie.cpp.

void POIMs_calc_SLR_helper2 ( const float64_t *const  distrib,
const int32_t  i,
const int32_t  nodeIdx,
int32_t  left_tries_idx[4],
const int32_t  depth,
float64_t S,
float64_t L,
float64_t R 
)

POIMs calc SLR helper 2

Parameters
distribdistribution
ii
nodeIdxnode index
left_tries_idxleft tries index
depthdepth
SS
LL
RR
void POIMs_extract_W ( float64_t *const *const  W,
const int32_t  K 
)

Definition at line 59 of file Trie.cpp.

void POIMs_extract_W ( float64_t *const *const  W,
const int32_t  K 
)

POIMs extract W

Parameters
WW
KK
void POIMs_extract_W_helper ( const int32_t  nodeIdx,
const int32_t  depth,
const int32_t  offset,
const int32_t  y0,
float64_t *const *const  W,
const int32_t  K 
)

Definition at line 18 of file Trie.cpp.

void POIMs_extract_W_helper ( const int32_t  nodeIdx,
const int32_t  depth,
const int32_t  offset,
const int32_t  y0,
float64_t *const *const  W,
const int32_t  K 
)

POIMs extract W helper

Parameters
nodeIdxnode index
depthdepth
offsetoffset
y0y0
WW
KK
void POIMs_get_SLR ( const int32_t  parentIdx,
const int32_t  sym,
const int32_t  depth,
float64_t S,
float64_t L,
float64_t R 
)

Definition at line 271 of file Trie.cpp.

void POIMs_get_SLR ( const int32_t  parentIdx,
const int32_t  sym,
const int32_t  depth,
float64_t S,
float64_t L,
float64_t R 
)

POIMs get SLR

Parameters
parentIdxparent index
symsymbol
depthdepth
Swill point to S
Lwill point to L
Rwill point to R
void POIMs_precalc_SLR ( const float64_t *const  distrib)

Definition at line 244 of file Trie.cpp.

void POIMs_precalc_SLR ( const float64_t *const  distrib)

POIMs precalc SLR

Parameters
distribdistribution
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.

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_degree ( int32_t  d)

set degree

Parameters
dnew degree

Definition at line 1151 of file Trie.h.

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_position_weights ( float64_t p_position_weights)

set position weights

Parameters
p_position_weightsnew position weights

Definition at line 486 of file Trie.h.

void set_use_compact_terminal_nodes ( bool  p_use_compact_terminal_nodes)

set use compact terminal nodes

Parameters
p_use_compact_terminal_nodesif compact terminal nodes shall be used

Definition at line 467 of file Trie.h.

void set_weights_in_tree ( bool  weights_in_tree_)

set weights in tree

Parameters
weights_in_tree_if weights shall be in tree

Definition at line 534 of file Trie.h.

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 traverse ( int32_t  tree,
const int32_t  p,
struct TreeParseInfo  info,
const int32_t  depth,
int32_t *const  x,
const int32_t  k 
)

traverse

Parameters
treetree
pp
infotree parse info
depthdepth
xx
kk

Definition at line 1393 of file Trie.h.

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 degree
protected

degree

Definition at line 643 of file Trie.h.

SGIO* io
inherited

io

Definition at line 496 of file SGObject.h.

int32_t length
protected

length

Definition at line 638 of file Trie.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.

Parameter* m_model_selection_parameters
inherited

model selection parameters

Definition at line 508 of file SGObject.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.

int32_t* nofsKmers
protected

nofsKmers

Definition at line 660 of file Trie.h.

int32_t NUM_SYMS

number of symbols

Definition at line 634 of file Trie.h.

Parallel* parallel
inherited

parallel

Definition at line 499 of file SGObject.h.

float64_t* position_weights
protected

position weights

Definition at line 645 of file Trie.h.

Trie* TreeMem
protected

tree memory

Definition at line 648 of file Trie.h.

int32_t TreeMemPtr
protected

tree memory pointer

Definition at line 650 of file Trie.h.

int32_t TreeMemPtrMax
protected

tree memory pointer maximum

Definition at line 652 of file Trie.h.

int32_t* trees
protected

trees

Definition at line 640 of file Trie.h.

bool use_compact_terminal_nodes
protected

if compact terminal nodes are used

Definition at line 654 of file Trie.h.

Version* version
inherited

version

Definition at line 502 of file SGObject.h.

bool weights_in_tree
protected

if weights are in tree

Definition at line 657 of file Trie.h.


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

SHOGUN Machine Learning Toolbox - Documentation