BioUpgma.h

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#ifndef BIOUPGMA_H
#define BIOUPGMA_H

#include <fstream>
#include <string>
#include <iostream>
#include <cmath>
#include <cstring>
#include "BioUtilities.h"
#include "BioLenPos.h"
#include "BioFasta.h"
#include "BioMultipleGenBank.h"
#include "BioMultipleSwissProt.h"
#include "BioMultipleEmbl.h"
#include "BioOutputStream.h"
#include "BioProteinSequenceGlobalAlignment.h"
#include "BioDnaSequenceGlobalAlignment.h"

#define MAXOTU 200

class BioUpgma
{
float  *dist;               /* list of the genetic distances to be analyzed */
vector < node > nodetable;                             /* list of nodes in the tree */
vector < branch > tree;                                       /* text diagram of tree */
FILE   *fpt;                              /* pointer for output (tree) file */
int     notu   ;                     /* total number of OTUs in data set */
int     cotu   ;                     /* current number of OTUs remaining */
int     ndist  ;                /* total number of distances in data set */
int     cdist  ;                /* total number of distances in data set */
int     nnodes ;                                 /* number of nodes made */
string  otulist[MAXOTU];                 /* list of the OTUs to be compared */

public: 
BioUpgma();
//Added on 5.12.2012
BioUpgma(BioMultipleFasta,string,string); //1st arg is multiple sequence format file, of is output tree file.
BioUpgma(BioMultipleGenBank, string);
BioUpgma(BioMultipleEmbl, string);
BioUpgma(BioMultipleSwissProt, string);
~BioUpgma();

private:
/****************** EXTRACT DATA FROM DISTANCE MATRIX FILE ******************/
void getotus(string infl);                     /* gets otus from input file */
void getdist(ifstream &fs);                  /* gets distances from input file */
/******************* FLIP MATRIX TO UPPER-RIGHT TRIANGLE ********************/
void flipmatrix();                /* flips matrix from 'D' type to 'U' type */
/***************************** NEIGHBOR-JOINING *****************************/
void cluster(char outfl[]);   /* operates clustering algorithm */
void reducematrix(coord xy);             /* reduces matrix after each cycle */
void reduceotulist(int nodenumber,int x,int y);          /* reduces otulist */
/******************************** DRAW TREE *********************************/
void drawtree();                             /* draws a diagram of the tree */
int  orderotus(int nlines, int otulen);     /* order otus and nodes in tree */
void printtree(int nlines, int otulen);     /* prints tree to screen & file */
void fliptree(int nlines);          /* turns tree around for easier reading */
void printscale(int otulen);          /* prints a distance scale under tree */
public:
void showRootedTree(string infile, string outfile, string mat_orient);

};

#endif