ARB
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#include <di_matr.hxx>
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 |
Definition at line 136 of file di_matr.hxx.
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explicit |
Definition at line 320 of file DI_matr.cxx.
DI_MATRIX::~DI_MATRIX | ( | ) |
Definition at line 343 of file DI_matr.cxx.
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inline |
Definition at line 159 of file di_matr.hxx.
References AliView::get_aliname().
Referenced by DI_ENTRY::DI_ENTRY(), and load().
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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 | ||
) |
Definition at line 415 of file DI_matr.cxx.
References MatrixOrder::applyTo(), arb_assert, ARB_calloc(), ARB_realloc(), MatrixOrder::defined(), DI_LOAD_ALL, DI_LOAD_LIST, DI_LOAD_MARKED, entries, error(), gb_main, GBS_global_string(), GBT_first_marked_species_rel_species_data(), GBT_first_species_rel_species_data(), GBT_get_alignment_len(), GBT_get_species_data(), GBT_is_alignment_protein(), GBT_message(), GBT_next_marked_species(), GBT_next_species(), get_aliname(), get_load_count(), arb_progress::inc_and_check_user_abort(), is_AA, nentries, NULp, DI_ENTRY::sequence, and ta.
Referenced by di_autodetect_callback(), di_calculate_matrix(), and di_mark_by_distance().
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().
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().
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().
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().