#include "seq_quality.h"#include "SQ_functions.h"#include <awt_filter.hxx>#include <awt_sel_boxes.hxx>#include <aw_awars.hxx>#include <aw_msg.hxx>#include <aw_root.hxx>#include <arb_progress.h>#include <TreeNode.h>#include <arb_global_defs.h>#include <awt_config_manager.hxx>
Go to the source code of this file.
Macros | |
| #define | AWAR_SQ_PERM "seq_quality/" |
| #define | AWAR_SQ_TEMP "tmp/seq_quality/" |
| #define | AWAR_SQ_WEIGHT_BASES AWAR_SQ_PERM "weight_bases" |
| #define | AWAR_SQ_WEIGHT_DEVIATION AWAR_SQ_PERM "weight_deviation" |
| #define | AWAR_SQ_WEIGHT_HELIX AWAR_SQ_PERM "weight_helix" |
| #define | AWAR_SQ_WEIGHT_CONSENSUS AWAR_SQ_PERM "weight_consensus" |
| #define | AWAR_SQ_WEIGHT_IUPAC AWAR_SQ_PERM "weight_iupac" |
| #define | AWAR_SQ_WEIGHT_GC AWAR_SQ_PERM "weight_gc" |
| #define | AWAR_SQ_MARK_ONLY_FLAG AWAR_SQ_PERM "mark_only_flag" |
| #define | AWAR_SQ_MARK_FLAG AWAR_SQ_PERM "mark_flag" |
| #define | AWAR_SQ_MARK_BELOW AWAR_SQ_PERM "mark_below" |
| #define | AWAR_SQ_REEVALUATE AWAR_SQ_PERM "reevaluate" |
| #define | AWAR_SQ_FILTER_NAME AWAR_SQ_TEMP "filter/name" |
Functions | |
| void | SQ_create_awars (AW_root *aw_root, AW_default aw_def) |
| size_t | count_nodes (TreeNode *node) |
| static void | sq_calc_seq_quality_cb (AW_window *aww, adfiltercbstruct *acbs, GBDATA *gb_main) |
| static void | sq_remove_quality_entries_cb (AW_window *, GBDATA *gb_main) |
| AW_window * | SQ_create_seq_quality_window (AW_root *aw_root, GBDATA *gb_main) |
Variables | |
| static AWT_config_mapping_def | seq_quality_config_mapping [] |
Macro Definition Documentation
| #define AWAR_SQ_PERM "seq_quality/" |
Definition at line 32 of file SQ_main.cxx.
| #define AWAR_SQ_TEMP "tmp/seq_quality/" |
Definition at line 33 of file SQ_main.cxx.
| #define AWAR_SQ_WEIGHT_BASES AWAR_SQ_PERM "weight_bases" |
Definition at line 35 of file SQ_main.cxx.
Referenced by sq_calc_seq_quality_cb(), SQ_create_awars(), and SQ_create_seq_quality_window().
| #define AWAR_SQ_WEIGHT_DEVIATION AWAR_SQ_PERM "weight_deviation" |
Definition at line 36 of file SQ_main.cxx.
Referenced by sq_calc_seq_quality_cb(), SQ_create_awars(), and SQ_create_seq_quality_window().
| #define AWAR_SQ_WEIGHT_HELIX AWAR_SQ_PERM "weight_helix" |
Definition at line 37 of file SQ_main.cxx.
Referenced by sq_calc_seq_quality_cb(), SQ_create_awars(), and SQ_create_seq_quality_window().
| #define AWAR_SQ_WEIGHT_CONSENSUS AWAR_SQ_PERM "weight_consensus" |
Definition at line 38 of file SQ_main.cxx.
Referenced by sq_calc_seq_quality_cb(), SQ_create_awars(), and SQ_create_seq_quality_window().
| #define AWAR_SQ_WEIGHT_IUPAC AWAR_SQ_PERM "weight_iupac" |
Definition at line 39 of file SQ_main.cxx.
Referenced by sq_calc_seq_quality_cb(), SQ_create_awars(), and SQ_create_seq_quality_window().
| #define AWAR_SQ_WEIGHT_GC AWAR_SQ_PERM "weight_gc" |
Definition at line 40 of file SQ_main.cxx.
Referenced by sq_calc_seq_quality_cb(), SQ_create_awars(), and SQ_create_seq_quality_window().
| #define AWAR_SQ_MARK_ONLY_FLAG AWAR_SQ_PERM "mark_only_flag" |
Definition at line 42 of file SQ_main.cxx.
Referenced by sq_calc_seq_quality_cb(), SQ_create_awars(), and SQ_create_seq_quality_window().
| #define AWAR_SQ_MARK_FLAG AWAR_SQ_PERM "mark_flag" |
Definition at line 43 of file SQ_main.cxx.
Referenced by sq_calc_seq_quality_cb(), SQ_create_awars(), and SQ_create_seq_quality_window().
| #define AWAR_SQ_MARK_BELOW AWAR_SQ_PERM "mark_below" |
Definition at line 44 of file SQ_main.cxx.
Referenced by sq_calc_seq_quality_cb(), SQ_create_awars(), and SQ_create_seq_quality_window().
| #define AWAR_SQ_REEVALUATE AWAR_SQ_PERM "reevaluate" |
Definition at line 45 of file SQ_main.cxx.
Referenced by sq_calc_seq_quality_cb(), SQ_create_awars(), and SQ_create_seq_quality_window().
| #define AWAR_SQ_FILTER_NAME AWAR_SQ_TEMP "filter/name" |
Definition at line 46 of file SQ_main.cxx.
Referenced by SQ_create_awars(), and SQ_create_seq_quality_window().
Function Documentation
| void SQ_create_awars | ( | AW_root * | aw_root, |
| AW_default | aw_def | ||
| ) |
Definition at line 48 of file SQ_main.cxx.
References AWAR_DEFAULT_ALIGNMENT, AW_root::awar_int(), AWAR_SQ_FILTER_NAME, AWAR_SQ_MARK_BELOW, AWAR_SQ_MARK_FLAG, AWAR_SQ_MARK_ONLY_FLAG, AWAR_SQ_REEVALUATE, AWAR_SQ_WEIGHT_BASES, AWAR_SQ_WEIGHT_CONSENSUS, AWAR_SQ_WEIGHT_DEVIATION, AWAR_SQ_WEIGHT_GC, AWAR_SQ_WEIGHT_HELIX, AWAR_SQ_WEIGHT_IUPAC, and awt_create_filter_awars().
Referenced by nt_create_all_awars().
Definition at line 66 of file SQ_main.cxx.
References GBT_count_leafs().
Referenced by sq_calc_seq_quality_cb().
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Definition at line 71 of file SQ_main.cxx.
References aw_message(), AW_root::awar(), AWAR_SQ_MARK_BELOW, AWAR_SQ_MARK_FLAG, AWAR_SQ_MARK_ONLY_FLAG, AWAR_SQ_REEVALUATE, AWAR_SQ_WEIGHT_BASES, AWAR_SQ_WEIGHT_CONSENSUS, AWAR_SQ_WEIGHT_DEVIATION, AWAR_SQ_WEIGHT_GC, AWAR_SQ_WEIGHT_HELIX, AWAR_SQ_WEIGHT_IUPAC, AWAR_TREE, awt_destroy_filter(), awt_get_filter(), awt_invalid_filter(), SQ_weights::bases, GB_transaction::close(), SQ_weights::consensus, count_nodes(), destroy(), SQ_weights::diff_from_average, arb_progress::done(), error(), GB_AT_DNA, GB_AT_RNA, GB_AT_UNKNOWN, GB_await_error(), GBS_global_string(), GBT_get_alignment_type(), GBT_get_default_alignment(), GBT_get_species_count(), GBT_KEEP_MARKED, GBT_link_tree(), GBT_read_tree(), GBT_remove_leafs(), GBT_REMOVE_ZOMBIES, SQ_weights::gc, AW_window::get_root(), SQ_weights::helix, TreeNode::is_leaf(), SQ_weights::iupac, MISSING_NODE, NO_TREE_SELECTED, NONE, NULp, AW_awar::read_int(), AW_awar::read_string(), SQ_check_tree_structure(), SQ_clear_group_dictionary(), SQ_evaluate(), SQ_mark_species(), SQ_pass1_no_tree(), SQ_pass1_on_tree(), SQ_pass2_no_tree(), SQ_pass2_on_tree(), arb_progress::subtitle(), ta, type, UNCOVERED, and ZOMBIE.
Referenced by SQ_create_seq_quality_window().
Definition at line 229 of file SQ_main.cxx.
References aw_message_if(), error(), and SQ_remove_quality_entries().
Referenced by SQ_create_seq_quality_window().
Definition at line 249 of file SQ_main.cxx.
References AW_POPDOWN(), AW_ROOT_DEFAULT, AWAR_SQ_FILTER_NAME, AWAR_SQ_MARK_BELOW, AWAR_SQ_MARK_FLAG, AWAR_SQ_MARK_ONLY_FLAG, AWAR_SQ_REEVALUATE, AWAR_SQ_WEIGHT_BASES, AWAR_SQ_WEIGHT_CONSENSUS, AWAR_SQ_WEIGHT_DEVIATION, AWAR_SQ_WEIGHT_GC, AWAR_SQ_WEIGHT_HELIX, AWAR_SQ_WEIGHT_IUPAC, AWAR_TREE, awt_create_select_filter(), awt_create_select_filter_win(), awt_create_TREE_selection_list(), AWT_insert_config_manager(), gb_main, AW_window::load_xfig(), makeHelpCallback(), sq_calc_seq_quality_cb(), and sq_remove_quality_entries_cb().
Referenced by popup_new_main_window().
Variable Documentation
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Definition at line 234 of file SQ_main.cxx.
