GUI_aliview.cxx

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// ================================================================ //
//                                                                  //
//   File      : GUI_aliview.cxx                                    //
//   Purpose   :                                                    //
//                                                                  //
//   Coded by Ralf Westram (coder@reallysoft.de) in November 2009   //
//   Institute of Microbiology (Technical University Munich)        //
//   http://www.arb-home.de/                                        //
//                                                                  //
// ================================================================ //

#include "gui_aliview.hxx"
#include "awt_filter.hxx"
#include "ColumnStat.hxx"
#include "ga_local.h"

#include <AliView.hxx>
#include <AP_filter.hxx>
#include <arb_msg.h>

WeightedFilter::WeightedFilter(GBDATA *gb_main, AW_root *aw_root, const char *awar_filter_name, const char *awar_columnStat_name, AW_awar *awar_default_alignment) {
    // @@@ let awt_create_select_filter create filter awars and automatically map it to awar_default_alignment
    // (see [6476] for changes done for ColumnStat)

    adfilter    = awt_create_select_filter(aw_root, gb_main, awar_filter_name);
    column_stat = awar_columnStat_name ? new ColumnStat(gb_main, aw_root, awar_columnStat_name, awar_default_alignment) : NULp;
}

WeightedFilter::~WeightedFilter() {
    delete column_stat;
    // @@@ leak: adfilter (no destruction implemented)
}

AP_filter *WeightedFilter::create_filter() const {
    return awt_get_filter(adfilter);
}

AP_weights *WeightedFilter::create_weights(const AP_filter *filter, GB_ERROR& error) const {
    ga_assert(!error);

    AP_weights *weights   = NULp;
    bool        haveRates = false;

    if (column_stat) {
        error            = column_stat->calculate(NULp);
        if (error) error = GBS_global_string("Failed to calculate weights (Reason: %s)", error);

        haveRates = column_stat->has_rates();
    }

    if (!error) {
        if (haveRates) {
            column_stat->weight_by_inverseRates();
            weights = new AP_weights(column_stat->get_weights(), column_stat->get_length(), filter);
        }
        else {
            weights = new AP_weights(filter);
        }
    }
    if (column_stat) column_stat->forget();

    ga_assert(contradicted(error, weights));
    return weights;
}

AliView *WeightedFilter::create_aliview(const char *aliname, GB_ERROR& error) const {
    ga_assert(!error);
    ga_assert(!GB_have_error());

    AliView *aliview = NULp;
    {
        AP_filter *filter = create_filter();
        error             = filter->is_invalid();

        if (!error) {
            AP_weights *weights = create_weights(filter, error);
            aliview = error ? NULp : new AliView(adfilter->gb_main, *filter, *weights, aliname);
            delete weights;
        }
        delete filter;
    }
    ga_assert(contradicted(error, aliview));
    ga_assert(!GB_have_error()); // @@@ should be returned via 'error'
    return aliview;
}

GBDATA *WeightedFilter::get_gb_main() const {
    return adfilter->gb_main;
}

AW_root *WeightedFilter::get_aw_root() const {
    return adfilter->awr;
}