Last change
on this file was
5825,
checked in by westram, 16 years ago
|
- replaced GB_entry/GB_create/GB_search+GB_read_XXX by GBT_read_XXX
- improved error handling in many functions
|
-
Property svn:eol-style set to
native
-
Property svn:keywords set to
Author Date Id Revision
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File size:
1.2 KB
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Line | |
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1 | #define AWAR_PVP_SAI "tmp/pos_var_pars/sai" |
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2 | #define AWAR_PVP_TREE "tmp/pos_var_pars/tree" |
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3 | |
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4 | AW_window *AP_open_pos_var_pars_window( AW_root *root ); |
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5 | |
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6 | class AP_pos_var { |
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7 | GBDATA *gb_main; |
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8 | long timer; // for the status box |
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9 | long treesize; // max value for slider |
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10 | GB_UINT4 *frequencies[256]; // count every occurrence |
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11 | GB_UINT4 *transitions; // minumum transitions |
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12 | GB_UINT4 *transversions; // minimum transversions (dna only) |
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13 | unsigned char char_2_freq[256]; // mapper (~ toupper) |
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14 | long char_2_transition[256]; // a->1 c->2 g->4 ... |
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15 | long char_2_transversion[256]; // y->1 r->2 |
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16 | |
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17 | long getsize(GBT_TREE *tree); // size of tree |
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18 | long ali_len; // max len of alignment |
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19 | long is_dna; |
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20 | char *ali_name; |
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21 | char *tree_name; |
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22 | |
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23 | const char *parsimony(GBT_TREE *tree, GB_UINT4 *bases = 0, GB_UINT4 *ltbases = 0); |
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24 | |
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25 | public: |
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26 | |
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27 | AP_pos_var(GBDATA *gb_main,char *ali_name, long ali_len, int isdna, char *tree_name); |
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28 | ~AP_pos_var(); |
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29 | |
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30 | GB_ERROR retrieve(GBT_TREE *tree); |
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31 | GB_ERROR delete_old_sai(const char *sai_name); |
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32 | GB_ERROR save_sai(const char *sai_name); |
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33 | }; |
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