| 1 | // =============================================================== // |
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| 2 | // // |
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| 3 | // File : ali_pt.hxx // |
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| 4 | // Purpose : // |
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| 5 | // // |
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| 6 | // Institute of Microbiology (Technical University Munich) // |
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| 7 | // http://www.arb-home.de/ // |
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| 8 | // // |
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| 9 | // =============================================================== // |
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| 10 | |
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| 11 | #ifndef ALI_PT_HXX |
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| 12 | #define ALI_PT_HXX |
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| 13 | |
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| 14 | #ifndef ALI_OTHER_STUFF_HXX |
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| 15 | #include "ali_other_stuff.hxx" |
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| 16 | #endif |
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| 17 | #ifndef ALI_TLIST_HXX |
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| 18 | #include "ali_tlist.hxx" |
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| 19 | #endif |
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| 20 | #ifndef ALI_SEQUENCE_HXX |
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| 21 | #include "ali_sequence.hxx" |
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| 22 | #endif |
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| 23 | #ifndef CLIENT_H |
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| 24 | #include <client.h> |
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| 25 | #endif |
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| 26 | |
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| 27 | enum ALI_PT_MODE { ServerMode, SpecifiedMode }; |
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| 28 | |
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| 29 | struct ALI_PT_CONTEXT { |
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| 30 | char *servername; |
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| 31 | GBDATA *gb_main; |
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| 32 | |
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| 33 | int matches_min; |
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| 34 | float percent_min; |
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| 35 | unsigned long fam_list_max; |
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| 36 | unsigned long ext_list_max; |
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| 37 | |
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| 38 | char *use_specified_family; |
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| 39 | }; |
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| 40 | |
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| 41 | // class of family members |
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| 42 | struct ali_pt_member : virtual Noncopyable { |
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| 43 | char *name; |
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| 44 | int matches; |
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| 45 | |
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| 46 | ali_pt_member(char *speciesname, int number_of_matches) { |
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| 47 | name = speciesname; |
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| 48 | matches = number_of_matches; |
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| 49 | } |
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| 50 | ~ali_pt_member() { |
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| 51 | if (name) |
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| 52 | free((char *) name); |
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| 53 | } |
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| 54 | }; |
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| 55 | |
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| 56 | |
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| 57 | // Class for accessing the PT server |
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| 58 | class ALI_PT : virtual Noncopyable { |
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| 59 | private: |
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| 60 | ALI_PT_MODE mode; |
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| 61 | |
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| 62 | char *specified_family; |
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| 63 | unsigned long fam_list_max; |
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| 64 | unsigned long ext_list_max; |
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| 65 | float percent_min; |
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| 66 | int matches_min; |
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| 67 | |
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| 68 | aisc_com *link; |
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| 69 | T_PT_LOCS locs; |
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| 70 | T_PT_MAIN com; |
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| 71 | |
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| 72 | ALI_TLIST<ali_pt_member *> *family_list; |
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| 73 | ALI_TLIST<ali_pt_member *> *extension_list; |
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| 74 | |
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| 75 | |
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| 76 | int init_communication(); |
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| 77 | char *get_family_member(char *specified_family, unsigned long number); |
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| 78 | char *get_extension_member(char *specified_family, unsigned long number); |
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| 79 | int open(char *servername); |
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| 80 | void close(); |
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| 81 | |
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| 82 | public: |
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| 83 | ALI_PT(ALI_PT_CONTEXT *context); |
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| 84 | ~ALI_PT(); |
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| 85 | |
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| 86 | int find_family(ALI_SEQUENCE *sequence, int find_type = 1); |
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| 87 | |
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| 88 | ALI_TLIST<ali_pt_member *> *get_family_list(); |
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| 89 | ALI_TLIST<ali_pt_member *> *get_extension_list(); |
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| 90 | |
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| 91 | int first_family_(char **seq_name, int *matches); |
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| 92 | int next_family_(char **seq_name, int *matches); |
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| 93 | }; |
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| 94 | |
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| 95 | #else |
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| 96 | #error ali_pt.hxx included twice |
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| 97 | #endif // ALI_PT_HXX |
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