| 1 | // =============================================================== // |
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| 2 | // // |
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| 3 | // File : AP_sequence.cxx // |
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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 | #include "AP_sequence.hxx" |
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| 12 | #include <arbdbt.h> |
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| 13 | |
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| 14 | long AP_combinableSeq::global_combineCount = 0; |
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| 15 | |
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| 16 | AP_sequence::AP_sequence(const AliView *aliview) : |
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| 17 | ali(aliview), |
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| 18 | gb_sequence(NULp), |
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| 19 | has_sequence(false), |
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| 20 | update(0), |
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| 21 | cached_wbc(-1.0) |
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| 22 | {} |
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| 23 | |
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| 24 | GB_ERROR AP_sequence::bind_to_species(GBDATA *gb_species) { |
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| 25 | GB_ERROR error = NULp; |
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| 26 | |
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| 27 | ap_assert(!gb_sequence); // already bound to species! |
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| 28 | if (!gb_sequence) { |
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| 29 | GB_transaction ta(ali->get_gb_main()); |
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| 30 | gb_sequence = GBT_find_sequence(gb_species, ali->get_aliname()); |
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| 31 | if (!gb_sequence) { |
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| 32 | error = GBS_global_string("Species '%s' has no data in alignment '%s'", |
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| 33 | GBT_get_name_or_description(gb_species), ali->get_aliname()); |
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| 34 | } |
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| 35 | unset(); |
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| 36 | } |
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| 37 | return error; |
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| 38 | } |
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| 39 | |
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| 40 | void AP_sequence::unbind_from_species() { |
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| 41 | ap_assert(gb_sequence); |
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| 42 | gb_sequence = NULp; |
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| 43 | unset(); |
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| 44 | } |
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| 45 | |
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| 46 | void AP_sequence::do_lazy_load() const { |
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| 47 | ap_assert(gb_sequence); |
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| 48 | ap_assert(!has_sequence); |
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| 49 | |
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| 50 | GB_transaction ta(gb_sequence); |
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| 51 | const char *seq = GB_read_char_pntr(gb_sequence); |
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| 52 | if (!seq) { |
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| 53 | GB_ERROR error = GB_await_error(); |
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| 54 | GBDATA *gb_species = GB_get_grandfather(gb_sequence); |
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| 55 | |
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| 56 | GB_warningf("Failed to load sequence of '%s'\n(Reason: %s)", |
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| 57 | GBT_get_name_or_description(gb_species), error); |
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| 58 | seq = ""; // fake empty sequence |
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| 59 | } |
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| 60 | |
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| 61 | // this is no modification, this is lazy initialization |
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| 62 | const_cast<AP_sequence*>(this)->set(seq); |
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| 63 | } |
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| 64 | |
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| 65 | |
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