| 1 | // =============================================================== // |
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| 2 | // // |
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| 3 | // File : AliView.cxx // |
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| 4 | // Purpose : Defines a filtered view onto an alignment // |
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| 5 | // // |
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| 6 | // Coded by Ralf Westram (coder@reallysoft.de) in October 2009 // |
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| 7 | // Institute of Microbiology (Technical University Munich) // |
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| 8 | // http://www.arb-home.de/ // |
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| 9 | // // |
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| 10 | // =============================================================== // |
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| 11 | |
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| 12 | #include "AliView.hxx" |
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| 13 | |
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| 14 | #include <AP_filter.hxx> |
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| 15 | |
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| 16 | #define av_assert(cond) arb_assert(cond) |
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| 17 | |
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| 18 | using namespace std; |
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| 19 | |
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| 20 | void AliView::create_real_view(const AP_filter *filter_, const AP_weights *weights_, const char *aliname_) { |
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| 21 | av_assert(!filter && !weights && !aliname); |
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| 22 | av_assert(filter_ && weights_ && aliname_); |
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| 23 | |
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| 24 | filter = new AP_filter(*filter_); |
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| 25 | weights = new AP_weights(*weights_); |
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| 26 | aliname = strdup(aliname_); |
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| 27 | |
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| 28 | av_assert(filter->get_filtered_length() == weights->length()); |
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| 29 | av_assert(filter->was_checked_for_validity()); |
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| 30 | } |
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| 31 | |
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| 32 | |
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| 33 | AliView::AliView(GBDATA *gb_main_) |
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| 34 | : gb_main(gb_main_) |
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| 35 | , filter(NULL), weights(NULL), aliname(NULL) |
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| 36 | { |
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| 37 | // this creates a fake-AliView (used for AP_tree w/o sequence) |
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| 38 | } |
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| 39 | |
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| 40 | AliView::AliView(GBDATA *gb_main_, const AP_filter& filter_, const AP_weights& weights_, const char *aliname_) |
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| 41 | : gb_main(gb_main_) |
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| 42 | , filter(NULL), weights(NULL), aliname(NULL) |
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| 43 | { |
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| 44 | create_real_view(&filter_, &weights_, aliname_); |
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| 45 | } |
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| 46 | |
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| 47 | AliView::AliView(const AliView& other) |
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| 48 | : gb_main(other.gb_main) |
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| 49 | , filter(NULL), weights(NULL), aliname(NULL) |
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| 50 | { |
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| 51 | create_real_view(other.filter, other.weights, other.aliname); |
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| 52 | } |
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| 53 | |
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| 54 | AliView::~AliView() { |
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| 55 | delete filter; |
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| 56 | delete weights; |
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| 57 | free(aliname); |
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| 58 | } |
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| 59 | |
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| 60 | size_t AliView::get_length() const { |
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| 61 | return filter->get_filtered_length(); |
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| 62 | } |
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| 63 | |
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