/***************************************************************************************************

* The PolyMoSim project is distributed under the following license:

*

* Copyright (c) 2006-2025, Christoph Mayer, Leibniz Institute for the Analysis of Biodiversity Change,

* Bonn, Germany

* All rights reserved.

*

* Redistribution and use in source and binary forms, with or without

* modification, are permitted provided that the following conditions are met:

* 1. Redistributions of source code (complete or in parts) must retain

* the above copyright notice, this list of conditions and the following disclaimer.

* 2. 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.

* 3. All advertising materials mentioning features or any use of this software

* e.g. in publications must display the following acknowledgement:

* This product includes software developed by Christoph Mayer, Forschungsmuseum

* Alexander Koenig, Bonn, Germany.

* 4. Neither the name of the organization nor the

* names of its contributors may be used to endorse or promote products

* derived from this software without specific prior written permission.

*

* THIS SOFTWARE IS PROVIDED BY CHRISTOPH MAYER ''AS IS'' AND ANY

* EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED

* WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE

* DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHTHOLDER OR ITS ORGANISATION BE LIABLE FOR ANY

* DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES

* (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;

* LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND

* ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT

* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS

* SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

*

* IMPORTANT (needs to be included, if code is redistributed):

* Please not that this license is not compatible with the GNU Public License (GPL)

* due to paragraph 3 in the copyright. It is not allowed under any

* circumstances to use the code of this software in projects distributed under the GPL.

* Furthermore, it is not allowed to redistribute the code in projects which are

* distributed under a license which is incompatible with one of the 4 paragraphs above.

*

* This project makes use of code coming from other projects. What follows is a complete

* list of files which make use of external code. Please refer to the copyright within

* these files.

*

* Files in tclap foler: Copyright (c) 2003 Michael E. Smoot

* See copyright in tclap/COPYRIGHT file for details.

* discrete_gamma.c: Copyright 1993-2004 by Ziheng Yang.

* See copyright in this file for details.

* CRandom.h: Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura

* See copyright in this file for details.

***************************************************************************************************/

#ifndef Tree_adminH // error checking still inconsisten xxxxxxxxxxxxxxxxxxxxxxxx

#define Tree_adminH

#include "PolyMoSim.h"

#include <vector>

#include "BasicTree.h"

struct tree_struct {

double scalingfactor;

unsigned partitionSize;

faststring default_modelName;

faststring treeString;

BasicTree *treeData;

tree_struct(double pscalingfactor = 1, unsigned ppartitionSize = 0,

faststring pdefault_modelName = "default",

faststring ptreeString = ""):

scalingfactor(pscalingfactor), partitionSize(ppartitionSize),

default_modelName(pdefault_modelName), treeString(ptreeString), treeData(NULL) //, BasicTree* treeptr = NULL)

{}

};

class tree_admin {

public:

class indexerror {

};

class readerror {

private:

int line;

faststring unknown;

public:

readerror(int l, faststring u):line(l),unknown(u) {}

int getLine() {return line; }

faststring getUnknwonKeyword() {return unknown; }

};

private:

vector<tree_struct*> treevector;

public:

void destroy(int);

void add(int, double, unsigned, const faststring&, const faststring &);

void swap(unsigned, unsigned);

void create(const char*);

void print(ostream& = cout, unsigned = 0, const char * = "");

void default_treevector(int);

void set(int, double, unsigned, const faststring &, const faststring &);

void set_BasicTree(unsigned);

void set_itsBasicTree(unsigned, BasicTree *);

BasicTree* get_itsBasicTree(unsigned);

void ini(int);

int getNumTrees() const;

unsigned getAlignmentLength() const;

unsigned getPartitionStartCoordinate(unsigned) const;

faststring get_dataTypeString() const;

double getScalingFactor(unsigned) const;

unsigned getPartitionSize(unsigned) const;

const faststring& getDefaultModelName(unsigned) const;

const faststring& getTreeString(unsigned) const;

bool equal_takon_sets() const;

};

inline int tree_admin::getNumTrees() const {

return (int) treevector.size();

}

#endif