AP_pos_var Class Reference

#include <AP_pos_var.h>

Inheritance diagram for AP_pos_var:

Collaboration diagram for AP_pos_var:

Public Member Functions
	AP_pos_var (GBDATA *gb_main_, const char *ali_name_, long ali_len_, bool is_nuc_, const char *tree_name_)
	~AP_pos_var ()
GB_ERROR	retrieve (TreeNode *tree)
GB_ERROR	delete_aliEntry_from_SAI (const char *sai_name)
GB_ERROR	save_aliEntry_to_SAI (const char *sai_name)

Detailed Description

Definition at line 25 of file AP_pos_var.h.

Constructor & Destructor Documentation

AP_pos_var::AP_pos_var	(	GBDATA *	gb_main_,
		const char *	ali_name_,
		long	ali_len_,
		bool	is_nuc_,
		const char *	tree_name_
	)

Definition at line 23 of file AP_pos_var.cxx.

References NULp.

AP_pos_var::~AP_pos_var

(

)

Definition at line 43 of file AP_pos_var.cxx.

Member Function Documentation

GB_ERROR AP_pos_var::retrieve

(

TreeNode *

tree

)

Definition at line 125 of file AP_pos_var.cxx.

References AP_A, ap_assert, AP_C, AP_create_dna_to_ap_bases(), AP_G, AP_T, ARB_calloc(), AWT_get_user_translator(), error(), GBT_count_leafs(), AWT_translator::index2bitset(), AWT_translator::index2spro(), leafs_2_nodes(), AWT_translator::MaxAA(), NULp, and ROOTED.

Referenced by PVP_calculate().

GB_ERROR AP_pos_var::delete_aliEntry_from_SAI

(

const char *

sai_name

)

Definition at line 202 of file AP_pos_var.cxx.

References GB_delete(), GB_FIND, GB_search(), GBT_find_SAI(), and NULp.

Referenced by PVP_calculate().

GB_ERROR AP_pos_var::save_aliEntry_to_SAI

(

const char *

sai_name

)

Definition at line 215 of file AP_pos_var.cxx.

References error(), GB_await_error(), GB_DB, GB_INTS, GB_search(), GB_write_ints(), GBS_global_string(), GBT_find_or_create_SAI(), GBT_write_string(), GBS_strstruct::get_data(), NULp, GBS_strstruct::put(), and GBS_strstruct::putfloat().

Referenced by PVP_calculate().

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

• SL/PVP/AP_pos_var.h
• SL/PVP/AP_pos_var.cxx