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CAFE
Computational Analysis of gene Family Evolution
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CAFE
Computational Analysis of gene Family Evolution
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Singleton structure that holds all of the global data that Cafe acts on. More...
#include <family.h>
Data Fields | |
| FILE * | fout |
| FILE * | flog |
| pString | str_fdata |
| pCafeTree | pcafe |
| tree information stored when the user calls the "tree" command More... | |
| pCafeFamily | pfamily |
| family information stored when the user calls the "load" command More... | |
| int | eqbg |
| int | posterior |
| double * | ML |
| Max Likelihood - Initialized by the "load" command with the number of families in the table. More... | |
| double * | MAP |
| root size condition with max likelihood for each family - Initialized by the "load" command with the number of families in the table More... | |
| double * | prior_rfsize |
| prior is a poisson distribution on the root size based on leaves' size More... | |
| input_values | input |
| int | num_params |
| enum OPTIMIZER_INIT_TYPE | optimizer_init_type |
| double * | lambda |
| pTree | lambda_tree |
| int | num_lambdas |
| double * | mu |
| int | num_mus |
| int | parameterized_k_value |
| double * | k_weights |
| double ** | p_z_membership |
| int | fixcluster0 |
| int | checkconv |
| int * | old_branchlength |
| double | max_branch_length |
| double | sum_branch_length |
| int | num_branches |
| family_size_range | family_size |
| int * | root_dist |
| double | pvalue |
| int | num_threads |
| double ** | likelihoodRatios |
| int | quiet |
Singleton structure that holds all of the global data that Cafe acts on.
Initialized at program startup by cafe_shell_init
| int tagCafeParam::checkconv |
| int tagCafeParam::eqbg |
| family_size_range tagCafeParam::family_size |
| int tagCafeParam::fixcluster0 |
| FILE * tagCafeParam::flog |
| FILE* tagCafeParam::fout |
| input_values tagCafeParam::input |
| double* tagCafeParam::k_weights |
| double* tagCafeParam::lambda |
| pTree tagCafeParam::lambda_tree |
| double** tagCafeParam::likelihoodRatios |
| double* tagCafeParam::MAP |
root size condition with max likelihood for each family - Initialized by the "load" command with the number of families in the table
| double tagCafeParam::max_branch_length |
| double* tagCafeParam::ML |
Max Likelihood - Initialized by the "load" command with the number of families in the table.
| double* tagCafeParam::mu |
| int tagCafeParam::num_branches |
| int tagCafeParam::num_lambdas |
| int tagCafeParam::num_mus |
| int tagCafeParam::num_params |
| int tagCafeParam::num_threads |
| int* tagCafeParam::old_branchlength |
| enum OPTIMIZER_INIT_TYPE tagCafeParam::optimizer_init_type |
| double** tagCafeParam::p_z_membership |
| int tagCafeParam::parameterized_k_value |
| pCafeTree tagCafeParam::pcafe |
tree information stored when the user calls the "tree" command
| pCafeFamily tagCafeParam::pfamily |
family information stored when the user calls the "load" command
| int tagCafeParam::posterior |
| double* tagCafeParam::prior_rfsize |
prior is a poisson distribution on the root size based on leaves' size
| double tagCafeParam::pvalue |
| int tagCafeParam::quiet |
| int* tagCafeParam::root_dist |
| pString tagCafeParam::str_fdata |
| double tagCafeParam::sum_branch_length |
1.8.6