| 1 | // ==================================================================== // |
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| 2 | // // |
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| 3 | // File : SQ_functions.h // |
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| 4 | // Purpose : Functions used for calculation of alignment quality // |
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| 5 | // // |
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| 6 | // // |
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| 7 | // Coded by Juergen Huber in July 2003 - February 2004 // |
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| 8 | // Coded by Kai Bader (baderk@in.tum.de) in 2007 - 2008 // |
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| 9 | // Copyright Department of Microbiology (Technical University Munich) // |
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| 10 | // // |
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| 11 | // Visit our web site at: http://www.arb-home.de/ // |
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| 12 | // // |
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| 13 | // ==================================================================== // |
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| 14 | |
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| 15 | |
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| 16 | #ifndef SQ_FUNCTIONS_H |
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| 17 | #define SQ_FUNCTIONS_H |
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| 18 | |
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| 19 | #ifndef SQ_GROUPDATA_H |
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| 20 | # include "SQ_GroupData.h" |
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| 21 | #endif |
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| 22 | |
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| 23 | #ifndef __MAP__ |
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| 24 | # include <map> |
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| 25 | #endif |
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| 26 | #ifndef __STRING__ |
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| 27 | # include <string> |
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| 28 | #endif |
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| 29 | |
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| 30 | #ifndef SMARTPTR_H |
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| 31 | #include <smartptr.h> |
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| 32 | #endif |
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| 33 | |
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| 34 | #ifndef ARBDB_BASE_H |
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| 35 | #include <arbdb_base.h> |
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| 36 | #endif |
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| 37 | |
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| 38 | class AP_filter; |
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| 39 | class arb_progress; |
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| 40 | |
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| 41 | typedef SmartPtr < SQ_GroupData> SQ_GroupDataPtr; |
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| 42 | typedef std::map < std::string, SQ_GroupDataPtr> SQ_GroupDataDictionary; |
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| 43 | |
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| 44 | GB_ERROR SQ_remove_quality_entries(GBDATA *gb_main); |
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| 45 | |
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| 46 | GB_ERROR SQ_pass1_no_tree(SQ_GroupData * globalData, GBDATA * gb_main, AP_filter * filter, arb_progress& progress); |
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| 47 | GB_ERROR SQ_pass2_no_tree(const SQ_GroupData * globalData, GBDATA * gb_main, AP_filter * filter, arb_progress& progress); |
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| 48 | |
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| 49 | int SQ_count_nodes(TreeNode *node); |
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| 50 | |
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| 51 | void SQ_calc_and_apply_group_data(TreeNode * node, GBDATA * gb_main, SQ_GroupData * data, AP_filter * filter, arb_progress& progress); |
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| 52 | void SQ_calc_and_apply_group_data2(TreeNode * node, GBDATA * gb_main, const SQ_GroupData * data, AP_filter * filter, arb_progress& progress); |
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| 53 | |
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| 54 | /* |
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| 55 | "option" is variable which is passed to function "SQ_get_value()". |
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| 56 | SQ_get_value() returns the values that are stored in the specific containers used for alignment quality evaluation. |
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| 57 | */ |
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| 58 | |
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| 59 | struct SQ_weights { |
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| 60 | int bases; |
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| 61 | int diff_from_average; |
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| 62 | int helix; |
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| 63 | int consensus; |
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| 64 | int iupac; |
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| 65 | int gc; |
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| 66 | }; |
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| 67 | |
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| 68 | GB_ERROR SQ_evaluate(GBDATA * gb_main, const SQ_weights & weights, bool marked_only); |
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| 69 | /* |
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| 70 | The "weight_..." -values are passed to the function "SQ_evaluate()". |
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| 71 | SQ_evaluate() generates the final estimation for the quality of an alignment. |
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| 72 | It takes the values from the different containers, which are generated by the other functions, weights them |
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| 73 | and calculates a final value. The final value is stored in "value_of_evaluation" (see options). |
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| 74 | So, with the "weight_..." -values one can customize how important a value stored in a container becomes |
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| 75 | for the final result. |
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| 76 | */ |
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| 77 | |
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| 78 | GB_ERROR SQ_mark_species(GBDATA * gb_main, int condition, bool marked_only); |
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| 79 | |
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| 80 | void SQ_clear_group_dictionary(); |
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| 81 | |
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| 82 | enum SQ_TREE_ERROR { |
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| 83 | NONE = 0, ZOMBIE = 1, MISSING_NODE = 2 |
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| 84 | }; |
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| 85 | |
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| 86 | SQ_TREE_ERROR SQ_check_tree_structure(TreeNode * node); |
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| 87 | |
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| 88 | #else |
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| 89 | #error SQ_functions.h included twice |
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| 90 | #endif |
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