/*  Sequence.cpp
 * Copyright (C) 2010, Francisco Claude, all rights reserved.
 *
 * Francisco Claude <fclaude@cs.uwaterloo.ca>
 *
 * 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/>.
 *
 */

#include <Sequence.h>

#include <BitmapsSequence.h>
#include <WaveletTree.h>
#include <WaveletTreeNoptrs.h>
#include <WaveletMatrix.h>
#include <SequenceGMR.h>
#include <SequenceGMRChunk.h>
#include <SequenceAlphPart.h>

namespace cds_static
{

	Sequence::Sequence(size_t _length) {
		length = _length;
	}

	size_t Sequence::rank(uint c, size_t i) const
	{
		size_t count = 0;
		for(size_t k=0;k<=i;k++)
			if(access(k)==c) count++;
		return count;
	}

	size_t Sequence::select(uint c, size_t j) const
	{
		size_t count = 0;
		for(size_t k=0;k<length;k++) {
			if(access(k)==c) {
				count++;
				if(count==j) return k;
			}
		}
		return length;
	}

	size_t Sequence::selectNext(uint c, size_t j) const
	{
		uint pos = rank(c,j);
		return select(c,pos+1);
	}

	uint Sequence::access(size_t i) const
	{
		#define prev(k) ((i>0)?rank(k,i-1):0)
		for(uint k=0;k<sigma;k++) {
			if(rank(k,i)>prev(k)) return k;
		}
		// throw exception
		return (uint)-1;
	}

	uint Sequence::access(size_t i, size_t & _rank) const
	{
		uint s = access(i);
		_rank = rank(s,i);
		return s;
	}

	Sequence * Sequence::load(istream & fp) {
		uint type = loadValue<uint>(fp);
		size_t pos = fp.tellg();
		fp.seekg(pos-sizeof(uint),ios::beg);
		switch(type) {
			case GMR_CHUNK_HDR: return SequenceGMRChunk::load(fp);
			case GMR_HDR: return SequenceGMR::load(fp);
			case BS_HDR: return BitmapsSequence::load(fp);
			case WVTREE_HDR: return WaveletTree::load(fp);
			case WVTREE_NOPTRS_HDR: return WaveletTreeNoptrs::load(fp);
			case ALPHPART_HDR: return SequenceAlphPart::load(fp);
			case WVMATRIX_HDR: return WaveletMatrix::load(fp);
		}
		return NULL;
	}

};