proteinortho  6.0.14
Global Variables

Variables

bool param_verbose = false
 By default no verbose is printed. More...
 
floattype param_con_threshold = 0.1
 as a reference: a chain a-b-c-d has 0.25 More...
 
unsigned int debug_level = 0
 Debug stderr level. More...
 
floattype param_sep_purity = 1e-7
 as a reference: a-b-c will give +/-0.707107 and 2.34857e-08 More...
 
unsigned int param_max_nodes = 16777216
 = 2^24. The absolute maximal number of nodes for a connected component. If exceeded then it is skipped entirely. More...
 
floattype param_min_species = 1
 Minimum number of species per connected component. More...
 
string param_rmgraph = "remove.graph"
 Name of the remove graph, containing all edges that are removed by this clustering algorithm. More...
 
bool param_useWeights = true
 If true, then weights are used for the calculation of the algebraic connectivity. More...
 
unsigned int param_minOpenmp = 256
 the minimum size of a for-loop for openmp to activate (openmp has some initialization costs) More...
 
bool param_useKmereHeuristic = true
 If true then kmere-heuristic is used. For ambigous splits (e.g. all but one entrie of the fiedler vector are below 0) then the fiedler vector is clustered in k groups instead. This will lead to k new groups instead of 2. See the variables kmereHeuristic_* for more informations when the kmere-heuristic will be activated. More...
 
unsigned int param_maxRam_inKB = 16777216
 = 16 GB of memory as default. Decreasing this may lead to more power iterations and thus to a increase in runtime as a trade-off More...
 
bool param_useLapack = true
 If true, then lapack is used accordingly to param_lapack_power_threshold_d. More...
 
unsigned int critical_min_nodes = 16777216
 Depricated. More...
 
const unsigned int min_iter = 16
 Minimal number of iterations for power iteration. More...
 
unsigned int param_max_iter = 8192
 Maximal number of iterations for power iteration. More...
 
floattype param_epsilon = 1e-8
 Epsilon for lapack functions dsyevr/ssyevr as well as the power iteration. Set analog to http://people.sc.fsu.edu/~jburkardt/c_src/power_method/power_method_prb.c. More...
 
const unsigned int kmereHeuristic_minNodes = 1048576
 = 2^20. The minimum number of nodes of the connected component for the kmere-heuristic. More...
 
const unsigned int kmereHeuristic_protPerSpecies = 1
 The mimum number of proteins per species for the kmere-heuristic. More...
 
const unsigned int kmereHeuristic_minNumberOfGroups = 3
 The minimum number of species for the kmere-heuristic. More...
 
const unsigned int maxUseWeightsNumNodes = 1048576
 = 2^20. The maximum number of nodes for a connected component such that weights are still used for calculations. If the connected component is too large, the unweighted version is used instead to save time. More...
 
floattype param_lapack_power_threshold_d = -1
 The minimum graph density for the power iteration method, lapacks (d|s)syevr is used otherwise. If -1 then the linear function is used instead : If d<10^(-5.2)*n, then lapack otherwise power. More...
 
unsigned int species_counter = 0
 Number of species (in the input graph) More...
 
unsigned int protein_counter = 0
 Number of proteins total (in the input graph) More...
 
vector< string > species
 Species ID (number) -> Species name. More...
 
vector< proteingraph
 Graph containing all protein data (see the class protein for more informations) More...
 
floattype last_stat = 0
 For buffering progress stats. More...
 
unsigned int edges = 0
 Total number of edges. More...
 
vector< shared_ptr< ofstream > > graph_clean
 File handler to store graph data. More...
 
vector< int > reorder_table
 Tells how proteins/species must be sorted. More...
 
unsigned long graph_ram_total_inKB =0
 The internal size of the input graph in KB (this will be set in parse_file() ) More...
 
unsigned int num_cpus =1
 By default only one core is used (change this with -cpus) More...
 

Detailed Description

Variable Documentation

◆ critical_min_nodes

unsigned int critical_min_nodes = 16777216

Depricated.

◆ debug_level

unsigned int debug_level = 0

Debug stderr level.

◆ edges

unsigned int edges = 0

Total number of edges.

◆ graph

vector<protein> graph

Graph containing all protein data (see the class protein for more informations)

◆ graph_clean

vector<shared_ptr<ofstream> > graph_clean

File handler to store graph data.

◆ graph_ram_total_inKB

unsigned long graph_ram_total_inKB =0

The internal size of the input graph in KB (this will be set in parse_file() )

◆ kmereHeuristic_minNodes

const unsigned int kmereHeuristic_minNodes = 1048576

= 2^20. The minimum number of nodes of the connected component for the kmere-heuristic.

◆ kmereHeuristic_minNumberOfGroups

const unsigned int kmereHeuristic_minNumberOfGroups = 3

The minimum number of species for the kmere-heuristic.

◆ kmereHeuristic_protPerSpecies

const unsigned int kmereHeuristic_protPerSpecies = 1

The mimum number of proteins per species for the kmere-heuristic.

◆ last_stat

floattype last_stat = 0

For buffering progress stats.

◆ maxUseWeightsNumNodes

const unsigned int maxUseWeightsNumNodes = 1048576

= 2^20. The maximum number of nodes for a connected component such that weights are still used for calculations. If the connected component is too large, the unweighted version is used instead to save time.

◆ min_iter

const unsigned int min_iter = 16

Minimal number of iterations for power iteration.

◆ num_cpus

unsigned int num_cpus =1

By default only one core is used (change this with -cpus)

◆ param_con_threshold

floattype param_con_threshold = 0.1

as a reference: a chain a-b-c-d has 0.25

◆ param_epsilon

floattype param_epsilon = 1e-8

Epsilon for lapack functions dsyevr/ssyevr as well as the power iteration. Set analog to http://people.sc.fsu.edu/~jburkardt/c_src/power_method/power_method_prb.c.

◆ param_lapack_power_threshold_d

floattype param_lapack_power_threshold_d = -1

The minimum graph density for the power iteration method, lapacks (d|s)syevr is used otherwise. If -1 then the linear function is used instead : If d<10^(-5.2)*n, then lapack otherwise power.

◆ param_max_iter

unsigned int param_max_iter = 8192

Maximal number of iterations for power iteration.

◆ param_max_nodes

unsigned int param_max_nodes = 16777216

= 2^24. The absolute maximal number of nodes for a connected component. If exceeded then it is skipped entirely.

◆ param_maxRam_inKB

unsigned int param_maxRam_inKB = 16777216

= 16 GB of memory as default. Decreasing this may lead to more power iterations and thus to a increase in runtime as a trade-off

◆ param_min_species

floattype param_min_species = 1

Minimum number of species per connected component.

◆ param_minOpenmp

unsigned int param_minOpenmp = 256

the minimum size of a for-loop for openmp to activate (openmp has some initialization costs)

◆ param_rmgraph

string param_rmgraph = "remove.graph"

Name of the remove graph, containing all edges that are removed by this clustering algorithm.

◆ param_sep_purity

floattype param_sep_purity = 1e-7

as a reference: a-b-c will give +/-0.707107 and 2.34857e-08

◆ param_useKmereHeuristic

bool param_useKmereHeuristic = true

If true then kmere-heuristic is used. For ambigous splits (e.g. all but one entrie of the fiedler vector are below 0) then the fiedler vector is clustered in k groups instead. This will lead to k new groups instead of 2. See the variables kmereHeuristic_* for more informations when the kmere-heuristic will be activated.

◆ param_useLapack

bool param_useLapack = true

If true, then lapack is used accordingly to param_lapack_power_threshold_d.

◆ param_useWeights

bool param_useWeights = true

If true, then weights are used for the calculation of the algebraic connectivity.

◆ param_verbose

bool param_verbose = false

By default no verbose is printed.

◆ protein_counter

unsigned int protein_counter = 0

Number of proteins total (in the input graph)

◆ reorder_table

vector<int> reorder_table

Tells how proteins/species must be sorted.

◆ species

vector<string> species

Species ID (number) -> Species name.

◆ species_counter

unsigned int species_counter = 0

Number of species (in the input graph)