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/*****************************************************************************
* GATB : Genome Assembly Tool Box
* Copyright (C) 2014 INRIA
* Authors: R.Chikhi, G.Rizk, E.Drezen
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero 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 Affero General Public License for more details.
*
* You should have received a copy of the GNU Affero General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*****************************************************************************/
/** \file IHistogram.hpp
* \date 01/03/2013
* \author edrezen
* \brief Interface for histogram (something counting abundances).
*/
#ifndef _GATB_CORE_TOOLS_MISC_IHISTOGRAM_HPP_
#define _GATB_CORE_TOOLS_MISC_IHISTOGRAM_HPP_
#include <gatb/system/api/ISmartPointer.hpp>
#include <hdf5.h>
/********************************************************************************/
namespace gatb {
namespace core {
namespace tools {
namespace misc {
/********************************************************************************/
/** Here is a command line for showing the histogram with gnuplot from the hdf5 file 'graph.h5'
h5dump -y -d dsk/histogram graph.h5 | grep [0-9] | grep -v [A-Z].* | paste - - | gnuplot -p -e 'plot [][0:100] "-" with lines'
For the sum of the distribution, you can use;
h5dump -y -d dsk/histogram graph.h5 | grep [0-9] | grep -v [A-Z].* | paste - - | gawk 'BEGIN{s=0; i=0} { s=s+$2; i=i+1; print i," ", s}' | gnuplot -p -e 'plot [0:10][0:] "-" with lines'
*/
/** \brief TBD */
class IHistogram : virtual public system::ISmartPointer
{
public:
/********************************************************************************/
struct Entry
{
u_int16_t index;
u_int64_t abundance;
inline static hid_t hdf5 (bool& compound)
{
hid_t result = H5Tcreate (H5T_COMPOUND, sizeof(Entry));
H5Tinsert (result, "index", HOFFSET(Entry, index), H5T_NATIVE_UINT16);
H5Tinsert (result, "abundance", HOFFSET(Entry, abundance), H5T_NATIVE_UINT64);
compound = true;
return result;
}
/** Comparison operator
* \param[in] other : object to be compared to
* \return true if the provided kmer value is greater than the current one. */
bool operator< (const Entry& other) const { return this->index < other.index; }
/** Equal operator
* \param[in] other : object to be compared to
* \return true if the provided kmer value is greater than the current one. */
bool operator== (const Entry& other) const { return (this->index == other.index && this->abundance == other.abundance); }
};
/** */
virtual ~IHistogram() {}
/** */
virtual size_t getLength() = 0;
/** */
virtual void inc (u_int16_t index) = 0;
/** */
virtual void save () = 0;
/** */
virtual void compute_threshold () = 0;
//compute_threshold needs to be called first
virtual u_int16_t get_solid_cutoff () = 0;
virtual u_int64_t get_nbsolids_auto () = 0;
/** */
virtual u_int64_t& get (u_int16_t idx) = 0;
};
/********************************************************************************/
} } } } /* end of namespaces. */
/********************************************************************************/
#endif /* _GATB_CORE_TOOLS_MISC_IHISTOGRAM_HPP_ */
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