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sim_RALRAS.h
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/*
*
* sim_RALRAS.h
* Hetero2
*
* CSIRO Open Source Software License Agreement (variation of the BSD / MIT License)
* Copyright (c) 2014, Commonwealth Scientific and Industrial Research Organisation (CSIRO) ABN 41 687 119 230.
* All rights reserved. CSIRO is willing to grant you a license to this Hetero Version 2 on the following terms,
* except where otherwise indicated for third party material.
* Redistribution and use of this software in source and binary forms, with or without modification, are permitted
* provided that the following conditions are met:
* • Redistributions of source code must retain the above copyright notice, this list of conditions and the
* following disclaimer.
* • Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the
* following disclaimer in the documentation and/or other materials provided with the distribution.
* • Neither the name of CSIRO nor the names of its contributors may be used to endorse or promote products
* derived from this software without specific prior written permission of CSIRO.
* EXCEPT AS EXPRESSLY STATED IN THIS AGREEMENT AND TO THE FULL EXTENT PERMITTED BY APPLICABLE LAW, THE SOFTWARE
* IS PROVIDED "AS-IS". CSIRO MAKES NO REPRESENTATIONS, WARRANTIES OR CONDITIONS OF ANY KIND, EXPRESS OR IMPLIED,
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* Third Party Components
* The following third party components are distributed with the Software. You agree to comply with the license terms
* for these components as part of accessing the Software. Other third party software may also be identified in
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* ___________________________________________________________________
*
* JACOBI_EIGENVALUE.C (http://people.sc.fsu.edu/~jburkardt/c_src/jacobi_eigenvalue/jacobi_eigenvalue.c)
* Copyright (C) 2003-2013 John Burkardt
* This software is licensed under GNU LGPL (http://www.gnu.org/licenses/lgpl.html)
* ___________________________________________________________________
*/
#ifndef __phylo_data_simulation__experiment__
#define __phylo_data_simulation__experiment__
#include <iostream>
#include <fstream>
#include <vector>
#include <string>
#include "tool_box.h"
#include "parameters.h"
#include "simulation.h"
#include "definitions.h"
using namespace std;
// Input: Trees file
// Output: 1. number of rows of the matrix, 2. List of leaf names,
// 3. edge length (# of items = # of edges * # of site categories)
// 4. List of node names, 5. List of category
// return: Topology matrix
int* genTopMatrix(char* treesFile, int& rowNum, vector<string>& leafList, vector<double>& edgeLens,
vector<string>& nodeList, vector<string>& siteCatNames);
// simulate the sequences according to the parameters resulting from RAL-RAS model
void simSeqFrRASParam(char* treeFile, char* siteInfoFile, char* paramFilelist, int seqLen, int outFormat, string outPrefix, int edgeRepresent);
// simulate PERFECT sequences according to the parameters resulting from RAL-RAS model
void simPerfectSeqFrRASParam(char* treeFile, char* siteInfoFile, char* paramFilelist, int seqLen, int outFormat, string outPrefix, int edgeRepresent);
#endif /* defined(__phylo_data_simulation__experiment__) */