nested.cpp

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/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2018 Lucas Czech and HITS gGmbH
 
    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.
 
    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.
 
    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
    Contact:
    Lucas Czech <lucas.czech@h-its.org>
    Exelixis Lab, Heidelberg Institute for Theoretical Studies
    Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany
*/
 
#include "genesis/taxonomy/printers/nested.hpp"
 
#include "genesis/taxonomy/taxonomy.hpp"
#include "genesis/taxonomy/taxon.hpp"
 
#include <sstream>
 
namespace genesis {
namespace taxonomy {
 
// =================================================================================================
//     Print
// =================================================================================================
 
void PrinterNested::print(
    std::ostream&   out,
    Taxonomy const& tax
) const {
    size_t lines = 0;
    print_to_ostream( out, tax, 0, lines );
}
 
std::string PrinterNested::print(
    Taxonomy const& tax
) const {
    std::ostringstream res;
    print( res, tax );
    return res.str();
}
 
std::string PrinterNested::operator() (
    Taxonomy const& tax
) const {
    return print( tax );
}
 
bool PrinterNested::print_to_ostream(
    std::ostream&   out,
    Taxonomy const& tax,
    size_t          depth,
    size_t&         lines
) const {
    // Check depth limit. The cast is always legel, because we first check.
    if( depth_limit_ > -1 && depth > static_cast< size_t >( depth_limit_ )) {
        return true;
    }
 
    // Indent string.
    auto in = std::string( depth, '\t' );
 
    bool finished = true;
    for( auto const& t : tax ) {
        if( line_limit_ > -1 && lines >= static_cast< size_t >( line_limit_ ) ) {
            return false;
        }
 
        // Print and count.
        out << in << t.name();
        if(( print_ranks_ && t.rank() != "" ) || ( print_ids_ && t.id() != "" )) {
            out << " (";
        }
        if( print_ranks_ && t.rank() != "" ) {
            out << t.rank();
        }
        if( print_ids_ && t.id() != "" ) {
            if( print_ranks_ && t.rank() != "" ) {
                out << ", ";
            }
            out << t.id();
        }
        if(( print_ranks_ && t.rank() != "" ) || ( print_ids_ && t.id() != "" )) {
            out << ")";
        }
        out << "\n";
        ++lines;
 
        // Recurse.
        finished &= print_to_ostream( out, t, depth + 1, lines );
    }
 
    if( depth == 0 && ! finished ) {
        out << "...\n";
    }
    return finished;
}
 
// =================================================================================================
//     Properties
// =================================================================================================
 
PrinterNested& PrinterNested::line_limit( int value )
{
    line_limit_ = value;
    return *this;
}
 
int PrinterNested::line_limit() const
{
    return line_limit_;
}
 
PrinterNested& PrinterNested::depth_limit( int value )
{
    depth_limit_ = value;
    return *this;
}
 
int PrinterNested::depth_limit() const
{
    return depth_limit_;
}
 
PrinterNested& PrinterNested::print_ranks( bool value )
{
    print_ranks_ = value;
    return *this;
}
 
bool PrinterNested::print_ranks() const
{
    return print_ranks_;
}
 
PrinterNested& PrinterNested::print_ids( bool value )
{
    print_ids_ = value;
    return *this;
}
 
bool PrinterNested::print_ids() const
{
    return print_ids_;
}
 
} // namespace taxonomy
} // namespace genesis