ARB: DI_MATRIX Class Reference

ARB

#include <di_matr.hxx>

Inheritance diagram for DI_MATRIX:

Inheritance graph

Collaboration diagram for DI_MATRIX:

Collaboration graph

Public Member Functions
	DI_MATRIX (const AliView &aliview)

	~DI_MATRIX ()

const char *	get_aliname () const

const AliView *	get_aliview () const

GB_ERROR	load (LoadWhat what, const MatrixOrder &order, bool show_warnings, GBDATA **species_list) __ATTR__USERESULT

char *	unload ()

const char *	save (const char *filename, enum DI_SAVE_TYPE type)

GB_ERROR	calculate (const char cancel, DI_TRANSFORMATION transformation, bool aborted_flag, AP_matrix *userdef_matrix)

GB_ERROR	calculate_pro (DI_TRANSFORMATION transformation, bool *aborted_flag)

GB_ERROR	extract_from_tree (const char treename, bool aborted_flag)

DI_TRANSFORMATION	detect_transformation (std::string &msg)

char *	compress (TreeNode *tree)

Public Attributes
bool	is_AA

DI_ENTRY **	entries

size_t	nentries

AP_smatrix *	matrix

DI_MATRIX_TYPE	matrix_type

Detailed Description

Definition at line 136 of file di_matr.hxx.

Constructor & Destructor Documentation

DI_MATRIX::DI_MATRIX ( const AliView & aliview )

explicit

Definition at line 320 of file DI_matr.cxx.

DI_MATRIX::~DI_MATRIX ( )

Definition at line 343 of file DI_matr.cxx.

References matrix, and unload().

Member Function Documentation

const char* DI_MATRIX::get_aliname ( ) const

inline

Definition at line 159 of file di_matr.hxx.

References AliView::get_aliname().

Referenced by DI_ENTRY::DI_ENTRY(), and load().

const AliView* DI_MATRIX::get_aliview ( ) const

inline

Definition at line 160 of file di_matr.hxx.

Referenced by DI_ENTRY::DI_ENTRY().

GB_ERROR DI_MATRIX::load	(	LoadWhat	what,
		const MatrixOrder &	order,
		bool	show_warnings,
		GBDATA **	species_list
	)

char * DI_MATRIX::unload ( )

Definition at line 334 of file DI_matr.cxx.

References entries, nentries, and NULp.

Referenced by ~DI_MATRIX().

GB_ERROR DI_MATRIX::save	(	const char *	filename,
		enum DI_SAVE_TYPE	type
	)

Definition at line 14 of file DI_save_matr.cxx.

References ARB_strdup(), DI_SAVE_PHYLIP_COMP, DI_SAVE_READABLE, DI_SAVE_TABBED, dot(), entries, error(), fputc(), fputs(), GB_export_error(), gb_main, GBT_find_species_rel_species_data(), symmetric_matrix< T >::get(), matrix, max, min, DI_ENTRY::name, NDS_OUTPUT_LEAFTEXT_UNLIMITED, nentries, NULp, and ta.

Referenced by di_save_matrix_cb().

GB_ERROR DI_MATRIX::calculate	(	const char *	cancel,
		DI_TRANSFORMATION	transformation,
		bool *	aborted_flag,
		AP_matrix *	userdef_matrix
	)

Definition at line 548 of file DI_matr.cxx.

References arb_progress::aborted(), AP_A, AP_C, AP_G, AP_MAX, AP_T, aw_message(), di_assert, DI_TRANSFORMATION_FELSENSTEIN, DI_TRANSFORMATION_FROM_TREE, DI_TRANSFORMATION_JUKES_CANTOR, DI_TRANSFORMATION_KIMURA, DI_TRANSFORMATION_NONE, DI_TRANSFORMATION_OLSEN, DI_TRANSFORMATION_SIMILARITY, entries, error(), AP_matrix::get(), AliView::get_length(), DI_ENTRY::get_nucl_seq(), arb_progress::inc_and_check_user_abort(), is_AA, M, matrix, matrix_halfsize(), N, NULp, P, safeCharIndex(), symmetric_matrix< T >::set(), UNCOVERED, and y.

Referenced by di_calculate_matrix(), and di_mark_by_distance().

GB_ERROR DI_MATRIX::calculate_pro	(	DI_TRANSFORMATION	transformation,
		bool *	aborted_flag
	)

Definition at line 753 of file DI_matr.cxx.

References CHEMICAL, di_assert, DI_TRANSFORMATION_CATEGORIES_BARKER, DI_TRANSFORMATION_CATEGORIES_CHEMICAL, DI_TRANSFORMATION_CATEGORIES_HALL, DI_TRANSFORMATION_KIMURA, DI_TRANSFORMATION_NONE, DI_TRANSFORMATION_PAM, DI_TRANSFORMATION_SIMILARITY, entries, GEORGE, AliView::get_length(), HALL, is_AA, KIMURA, di_protdist::makedists(), matrix, NONE, PAM, SIMILARITY, and UNIVERSAL.

Referenced by di_calculate_matrix(), and di_mark_by_distance().

GB_ERROR DI_MATRIX::extract_from_tree	(	const char *	treename,
		bool *	aborted_flag
	)

Definition at line 841 of file DI_matr.cxx.

References arb_progress::aborted(), destroy(), arb_progress::done(), entries, error(), GB_await_error(), GBT_read_tree(), arb_progress::inc_and_check_user_abort(), init(), TreeNode::intree_distance_to(), matrix, matrix_halfsize(), node::name, DI_ENTRY::name, NULp, symmetric_matrix< T >::set(), ta, tree, and UNCOVERED.

Referenced by di_calculate_matrix().

DI_TRANSFORMATION DI_MATRIX::detect_transformation ( std::string & msg )

Definition at line 17 of file distanalyse.cxx.

References AP_A, AP_C, AP_G, AP_T, di_assert, DI_TRANSFORMATION_FELSENSTEIN, DI_TRANSFORMATION_JUKES_CANTOR, DI_TRANSFORMATION_KIMURA, DI_TRANSFORMATION_NONE, DI_TRANSFORMATION_NONE_DETECTED, DI_TRANSFORMATION_OLSEN, DI_TRANSFORMATION_PAM, entries, GBS_global_string(), AliView::get_length(), DI_ENTRY::get_nucl_seq(), is_AA, max, min, nentries, and result.

Referenced by di_autodetect_callback().

char * DI_MATRIX::compress ( TreeNode * tree )

Definition at line 49 of file DI_compress_matrix.cxx.

References DI_MATRIX_COMPRESSED, entries, error(), GB_IGNORE_CASE, GBS_create_hash(), GBS_free_hash(), GBS_write_hash(), symmetric_matrix< T >::get(), DI_ENTRY::group_nr, matrix, matrix_type, nentries, NULp, symmetric_matrix< T >::set(), and y.

Referenced by di_calculate_compressed_matrix_cb().

Member Data Documentation

bool DI_MATRIX::is_AA

Definition at line 150 of file di_matr.hxx.

Referenced by calculate(), calculate_pro(), detect_transformation(), di_calculate_matrix(), DI_ENTRY::DI_ENTRY(), di_mark_by_distance(), and load().

DI_ENTRY** DI_MATRIX::entries

Definition at line 151 of file di_matr.hxx.

Referenced by calculate(), calculate_pro(), compress(), detect_transformation(), di_calculate_tree_cb(), extract_from_tree(), load(), save(), and unload().

size_t DI_MATRIX::nentries

Definition at line 152 of file di_matr.hxx.

Referenced by compress(), detect_transformation(), di_calculate_tree_cb(), di_mark_by_distance(), load(), save(), and unload().

AP_smatrix* DI_MATRIX::matrix

Definition at line 153 of file di_matr.hxx.

Referenced by calculate(), calculate_pro(), compress(), di_calculate_tree_cb(), di_mark_by_distance(), extract_from_tree(), save(), and ~DI_MATRIX().

DI_MATRIX_TYPE DI_MATRIX::matrix_type

Definition at line 154 of file di_matr.hxx.

Referenced by compress(), di_calculate_matrix(), di_mark_by_distance(), DI_GLOBAL_MATRIX::forget_if_not_has_type(), and DI_GLOBAL_MATRIX::has_type().

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