49 #include "morphydefs.h" 202 (
const char* symbols,
244 (
const char* rawmatrix,
264 int mpl_set_gap_symbol
270 int mpl_set_missing_symbol
306 int mpl_set_charac_weight
333 const MPLchtype chtype,
357 (
const gap_t gaptype,
593 (
const int l_root_id,
597 int mpl_get_insertcost
607 int mpl_get_packed_states
615 char* mpl_get_stateset
int mpl_second_down_recon(const int node_id, const int left_id, const int right_id, Morphy m)
Performs the second nodal reconstructions for characters with inapplicability.
Definition: mpl.c:398
int mpl_update_tip(const int tip_id, const int anc_id, Morphy m)
Initial update of tip values following uppass reconstruction.
Definition: mpl.c:453
int mpl_set_num_internal_nodes(const int nnodes, Morphy m)
Sets the number of internal nodes in the dataset.
Definition: mpl.c:112
int mpl_delete_rawdata(Morphy m)
Deletes the caller-input data.
Definition: mpl.c:222
int mpl_finalize_tip(const int tip_id, const int anc_id, Morphy m)
Finalizes ambiguous or missing values in the tips.
Definition: mpl.c:477
int mpl_get_num_charac(Morphy m)
Retrieve the number of taxa (rows) in the dataset.
Definition: mpl.c:102
int mpl_set_parsim_t(const int charID, const MPLchtype chtype, Morphy m)
Sets a character's parsimony function type.
Definition: mpl.c:283
char * mpl_get_symbols(const Morphy m)
Retrieves the current list of symbols.
Definition: mpl.c:183
int mpl_attach_rawdata(const char *rawmatrix, Morphy m)
Attach raw character state data (i.e. tip data).
Definition: mpl.c:192
int mpl_first_up_recon(const int node_id, const int left_id, const int right_id, const int anc_id, Morphy m)
Reconstructs the second (uppass) nodal reconstructions.
Definition: mpl.c:370
int mpl_update_lower_root(const int l_root_id, const int root_id, Morphy m)
Updates the nodal sets for a lower ('dummy') root node.
Definition: mpl.c:500
int mpl_query_gaphandl(Morphy m)
Returns the type of gap handling method currently in effect.
Definition: mpl.c:333
int mpl_get_numtaxa(Morphy m)
Retrieve the number of taxa (rows) in the dataset.
Definition: mpl.c:92
int mpl_first_down_recon(const int node_id, const int left_id, const int right_id, Morphy m)
Reconstructs the first (downpass) nodal reconstructions.
Definition: mpl.c:344
Error codes and descriptions for MorphyLib.
int mpl_init_Morphy(const int ntax, const int nchar, Morphy m)
Sets up the dimensions of the dataset.
Definition: mpl.c:44
int mpl_set_gaphandl(const gap_t gaptype, Morphy m)
Tells MorphyLib how to treat the gap symbol.
Definition: mpl.c:321
int mpl_apply_tipdata(Morphy m)
Commits parameters prior to nodal set calculations.
Definition: mpl.c:240
int mpl_delete_Morphy(Morphy m)
Destroys an instance of a Morphy object.
Definition: mpl.c:24
int mpl_get_num_internal_nodes(Morphy m)
Gets the number of internal nodal reconstruction sets being used by MorphyLib.
Definition: mpl.c:129
int mpl_second_up_recon(const int node_id, const int left_id, const int right_id, const int anc_id, Morphy m)
Finalises the ancestral state reconstructions for characters with inapplicable values.
Definition: mpl.c:427
int mpl_attach_symbols(const char *symbols, Morphy m)
Attach a caller-specified list of symbols.
Definition: mpl.c:139
Morphy mpl_new_Morphy(void)
Creates a new instance of a Morphy object.
Definition: mpl.c:16