/*-------------------------------------------------------------

Copyright (C) 2005 Fabrizio Ferre'.
All Rights Reserved.

Permission to use, copy, modify, and distribute this
software and its documentation for NON-COMMERCIAL purposes
and without fee is hereby granted provided that this
copyright notice appears in all copies.


THE AUTHOR AND PUBLISHER MAKE NO REPRESENTATIONS OR
WARRANTIES ABOUT THE SUITABILITY OF THE SOFTWARE, EITHER
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
PARTICULAR PURPOSE, OR NON-INFRINGEMENT. THE AUTHORS
AND PUBLISHER SHALL NOT BE LIABLE FOR ANY DAMAGES SUFFERED
BY LICENSEE AS A RESULT OF USING, MODIFYING OR DISTRIBUTING
THIS SOFTWARE OR ITS DERIVATIVES.

-------------------------------------------------------------*/


/****************************************************
	Program: timeWarpingBoltzmann_2.h
	Fabrizio Ferre, 19 Jan 2005

Function prototypes for timeWarpingBoltzmann_2.cpp
****************************************************/

#include <string.h>
#include <stdio.h>
#include <stdlib.h>     // def of RAND_MAX 
#include <math.h>
#define N 100           // size of time series data
#define MIN2(x,y)     ((x)>(y) ? (y) : (x))
#define MIN3(x,y,z)   (MIN2(x,y)>(z) ? (z) : MIN2(x,y))
#define MAX2(x,y)     ((x)<(y) ? (y) : (x))
#define lenLine 1000   //max length of time series data file

/** function prototypes **/
int    parseInputFile(char fileName[], float timePoints[], float expressionArray[]); /** returns size of arrays **/
float  distance(double timePoint1, double timePoint2, float scalingFactor);   /** compute distance between time series points as absoulte value of their difference **/
float  scale(double array1[], double array2[], int size1, int size2);         /** finds the min and max values and scale according to 1/(sqrt(n*pow(max-min,2))) **/
double forwardPathMatrix(double pathMatrix[][N], char backtrackArrows[][N], double timeSeries1[], double timeSeries2[], float timeIntervals1[], float timeIntervals2[], int size1, int size2, float scalingFactor);
double backwardPathMatrix(double pathMatrix[][N], double timeSeries1[], double timeSeries2[], float timeIntervals1[], float timeIntervals2[], int size1, int size2, float scalingFactor);
int    traceback(char arrows[][N], int alignment1[], int alignment2[], int size1, int size2);
double forwardPartitionFunction(double partitionFunction[][N], double timeSeries1[], double timeSeries2[], float temperature, float BoltzmannK, float timeIntervals1[], float timeIntervals2[], int size1, int size2, float scalingFactor);
double backwardPartitionFuntion(double partitionFunction[][N], double timeSeries1[], double timeSeries2[], float temperature, float BoltzmannK, float timeIntervals1[], float timeIntervals2[], int size1, int size2, float scalingFactor);
void   computePairAlignmentProb(double forwardPartitionFunction[][N], double backwardPartitionFunction[][N], int alignment1[], int alignment2[], int sizeAlignment, double probabilities[], double timeSeries1[], double timeSeries2[], float temperature, float boltzmannK, float timeIntervals1[], float timeIntervals2[], float scalingFactor);
void   computeTimeIntervals(float timePoints[], float timeIntervals[], int lenghtOfArray, float scalingFactor);
void   normalize(float array[], int itsSize, double normalizedArray[], double mean, double stdev);

void   meanStdDev(float array[], int itsSize, double *mean, double *stdev);
void   printForwardPathMatrix(double pathMatrix[][N], int n, int m);   
void   printBackwardPathMatrix(double pathMatrix[][N], int n, int m);
void   printAlignment(int alignmentArray1[], int alignmentArray2[], int alignmentSize);
void   printFloatArray(float array[], int itsSize);
void   printIntArray(int array[], int itsSize);
void   printDoubleArray(double array[], int itsSize);
void   printTwoArrays(float array1[], float array2[], int itsSize); 
void   printThreeArrays(float array1[], float array2[], float array3[], int itsSize);
void   printPairProbabilities(int alignmentArray1[], int alignmentArray2[], double probabilities[], int alignmentSize);
void   reverseIntArray(int array[], unsigned short int itsSize);