/*
 * 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.
 *
 * Written (W) 2009 Soeren Sonnenburg
 * Copyright (C) 2009 Berlin Institute of Technology
 */

#include <shogun/lib/common.h>
#include <shogun/io/SGIO.h>
#include <shogun/kernel/string/SNPStringKernel.h>
#include <shogun/kernel/normalizer/SqrtDiagKernelNormalizer.h>
#include <shogun/features/Features.h>
#include <shogun/features/StringFeatures.h>

using namespace shogun;

CSNPStringKernel::CSNPStringKernel()
: CStringKernel<char>(0),
  m_degree(0), m_win_len(0), m_inhomogene(false)
{
	init();
	set_normalizer(new CSqrtDiagKernelNormalizer());
	register_params();
}

CSNPStringKernel::CSNPStringKernel(int32_t size,
		int32_t degree, int32_t win_len, bool inhomogene)
: CStringKernel<char>(size),
	m_degree(degree), m_win_len(2*win_len), m_inhomogene(inhomogene)
{
	init();
	set_normalizer(new CSqrtDiagKernelNormalizer());
	register_params();
}

CSNPStringKernel::CSNPStringKernel(
	CStringFeatures<char>* l, CStringFeatures<char>* r,
	int32_t degree, int32_t win_len, bool inhomogene)
: CStringKernel<char>(10), m_degree(degree), m_win_len(2*win_len),
	m_inhomogene(inhomogene)
{
	init();
	set_normalizer(new CSqrtDiagKernelNormalizer());
	if (l==r)
		obtain_base_strings();
	init(l, r);
	register_params();
}

CSNPStringKernel::~CSNPStringKernel()
{
	cleanup();
}

bool CSNPStringKernel::init(CFeatures* l, CFeatures* r)
{
	CStringKernel<char>::init(l, r);
	return init_normalizer();
}

void CSNPStringKernel::cleanup()
{
	CKernel::cleanup();
	SG_FREE(m_str_min);
	SG_FREE(m_str_maj);
}

void CSNPStringKernel::obtain_base_strings()
{
	//should only be called on training data
	ASSERT(lhs==rhs)

	m_str_len=0;

	for (int32_t i=0; i<num_lhs; i++)
	{
		int32_t len;
		bool free_vec;
		char* vec = ((CStringFeatures<char>*) lhs)->get_feature_vector(i, len, free_vec);

		if (m_str_len==0)
		{
			m_str_len=len;
			m_str_min=SG_CALLOC(char, len+1);
			m_str_maj=SG_CALLOC(char, len+1);
		}
		else
		{
			ASSERT(m_str_len==len)
		}

		for (int32_t j=0; j<len; j++)
		{
			// skip sequencing errors
			if (vec[j]=='0')
				continue;

			if (m_str_min[j]==0)
				m_str_min[j]=vec[j];
            else if (m_str_maj[j]==0 && vec[j]!=m_str_min[j])
				m_str_maj[j]=vec[j];
		}

		((CStringFeatures<char>*) lhs)->free_feature_vector(vec, i, free_vec);
	}

	for (int32_t j=0; j<m_str_len; j++)
	{
        // if only one one symbol occurs use 0
		if (m_str_min[j]==0)
            m_str_min[j]='0';
		if (m_str_maj[j]==0)
            m_str_maj[j]='0';

		if (m_str_min[j]>m_str_maj[j])
			CMath::swap(m_str_min[j], m_str_maj[j]);
	}
}

float64_t CSNPStringKernel::compute(int32_t idx_a, int32_t idx_b)
{
	int32_t alen, blen;
	bool free_avec, free_bvec;

	char* avec = ((CStringFeatures<char>*) lhs)->get_feature_vector(idx_a, alen, free_avec);
	char* bvec = ((CStringFeatures<char>*) rhs)->get_feature_vector(idx_b, blen, free_bvec);

	ASSERT(alen==blen)
	if (alen!=m_str_len)
		SG_ERROR("alen (%d) !=m_str_len (%d)\n", alen, m_str_len)
	ASSERT(m_str_min)
	ASSERT(m_str_maj)

	float64_t total=0;
	int32_t inhomogene= (m_inhomogene) ? 1 : 0;

	for (int32_t i = 0; i<alen-1; i+=2)
	{
		int32_t sumaa=0;
		int32_t sumbb=0;
		int32_t sumab=0;

		for (int32_t l=0; l<m_win_len && i+l<alen-1; l+=2)
		{
			char a1=avec[i+l];
			char a2=avec[i+l+1];
			char b1=bvec[i+l];
			char b2=bvec[i+l+1];

			if ((a1!=a2 || a1=='0' || a1=='0') && (b1!=b2 || b1=='0' || b2=='0'))
				sumab++;
			else if (a1==a2 && b1==b2)
			{
				if (a1!=b1)
					continue;

				if (a1==m_str_min[i+l])
					sumaa++;
				else if (a1==m_str_maj[i+l])
					sumbb++;
				else
				{
					SG_ERROR("The impossible happened i=%d l=%d a1=%c "
							"a2=%c b1=%c b2=%c min=%c maj=%c\n", i, l, a1,a2, b1,b2, m_str_min[i+l], m_str_maj[i+l]);
				}
			}

		}
		total+=CMath::pow(float64_t(sumaa+sumbb+sumab+inhomogene),
				(int32_t) m_degree);
	}

	((CStringFeatures<char>*) lhs)->free_feature_vector(avec, idx_a, free_avec);
	((CStringFeatures<char>*) rhs)->free_feature_vector(bvec, idx_b, free_bvec);
	return total;
}

void CSNPStringKernel::register_params()
{
	SG_ADD(&m_degree, "m_degree", "the order of the kernel", MS_AVAILABLE);
	SG_ADD(&m_win_len, "m_win_len", "the window length", MS_AVAILABLE);
	SG_ADD(&m_inhomogene, "m_inhomogene",
	  "the mark of whether it's an inhomogeneous poly kernel", MS_NOT_AVAILABLE);
	m_parameters->add_vector(&m_str_min, &m_str_len, "m_str_min", "allele A");
	m_parameters->add_vector(&m_str_maj, &m_str_len, "m_str_maj", "allele B");
}

void CSNPStringKernel::init()
{
	m_str_min=NULL;
	m_str_maj=NULL;
}
