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190 lines
7.5 KiB
C++
190 lines
7.5 KiB
C++
// $Id: someUtil.h 11905 2013-12-26 10:12:03Z itaymay $
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#ifndef ___SOME_UTIL_H
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#define ___SOME_UTIL_H
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#include "logFile.h"
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#include "definitions.h"
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#include "alphabet.h"
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#include <string>
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#include <iostream>
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using namespace std;
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//to be used for orderVec
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template <class T>
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class vecElem
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{
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public:
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vecElem();
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virtual ~vecElem() {};
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void setValue(const T val) {m_value = val;}
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T getValue() {return m_value;}
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void setPlace(const int place) {m_place = place;}
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int getPlace() {return m_place;}
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inline bool operator< (const vecElem& elemIn) const;
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private:
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int m_place;
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T m_value;
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};
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template <class T>
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vecElem< T >::vecElem()
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{
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m_value = -1;
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m_place = -1;
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}
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//template <class T>
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//vecElement< T >::~vecElement()
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//{
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//}
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template <class T>
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bool vecElem< T >::operator<(const vecElem& elemIn) const
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{
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if (m_value == elemIn.m_value)
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return (m_place < elemIn.m_place);
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else
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return (m_value < elemIn.m_value);
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}
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// STATISTICAL UTILITIES:
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MDOUBLE computeAverage(const vector<int>& vec);
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MDOUBLE computeAverage(const vector<MDOUBLE>& vec, const Vdouble* weightsV = NULL);
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MDOUBLE computeAverageOfAbs(const vector<MDOUBLE>& vec, const Vdouble* weightsV = NULL);
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MDOUBLE computeMedian(const vector<MDOUBLE>& vec);
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MDOUBLE computeQuantile(const vector<MDOUBLE>& vec, MDOUBLE quantile);
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MDOUBLE computeQuantileFrac(const vector<MDOUBLE>& vec, MDOUBLE quantile);
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MDOUBLE computeStd(const vector<MDOUBLE>& vec);// page 60, Sokal and Rohlf
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MDOUBLE computeStd(const vector<int>& vec);// page 60, Sokal and Rohlf
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MDOUBLE copmutePoissonProbability(const int& k, const long double& lamda);
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// re-computes a vector of frequencies after one value is changed:
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// all other values are set according to their relative value
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void computeRelativeFreqsFollowingOneChanged(MDOUBLE newValFreq, int indexNewFreq,Vdouble &freqs);//freqs is the old vector into which we write the new values
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// SIMULATIONS:
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int giveRandomState(const int alphabetSize, const int beginningState, const VVdouble &changeProbabilities);
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int giveRandomState(const int alphabetSize, const Vdouble &frequencies);
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// TIME UTILITIES
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void printTime(ostream& out);
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// TEXT UTILITIES
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string int2string(const int i);
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string double2string(const double x, int const howManyDigitsAfterTheDot=5, bool round = false);
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MDOUBLE string2double(const string& inString);
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bool allowCharSet(const string& allowableChars, const string& string2check);
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bool isCharInString(const string& stringToCheck, const char charToCheck);
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void putFileIntoVectorStringArray(istream &infile,vector<string> &inseqFile);
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bool fromStringIterToInt(string::const_iterator & it,
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const string::const_iterator endOfString,
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int& res);
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string takeCharOutOfString(const string& charsToTakeOut, const string& fromString);
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void toLower(string& str);
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void toUpper(string& str);
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string toUpper2(const string& str);
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//splits the string to substr according to the given delimiter (parallel to split in perl)
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void splitString(const string& str,vector<string>& subStrs,const string& delimiter);
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//input: a list of INTs seperated by commas ("1,3,5") returns the int in the vector
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Vint getVintFromStr(const string& str);
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//return a list of INTs seperated by commas ("1,3,5")
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string getStrFromVint(const Vint& inVec);
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// FILE UTILITIES
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bool checkThatFileExist(const string& fileName);
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string* searchStringInFile(const string& string2find,
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const int index,
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const string& inFileName);
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string* searchStringInFile(const string& string2find,
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const string& inFileName);
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bool doesWordExistInFile(const string& string2find,const string& inFileName);
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void createDir(const string& curDir,const string& dirName);
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//BIT UTILITIES
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//void nextBit(bitset<64> &cur);
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//ARITHMETIC UTILITIES
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//DEQUAL: == UP TO EPSILON
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//DBIG_EQUAL: >= UP TO EPSILON
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//DSMALL_EQUAL: <= UP TO EPSILON
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bool DEQUAL(const MDOUBLE x1, const MDOUBLE x2, const MDOUBLE epsilon = 1.192092896e-07F); // epsilon taken from WINDOW'S FILE FLOAT.H
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bool DBIG_EQUAL(const MDOUBLE x1, const MDOUBLE x2, const MDOUBLE epsilon = 1.192092896e-07F);
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bool DSMALL_EQUAL(const MDOUBLE x1, const MDOUBLE x2, const MDOUBLE epsilon = 1.192092896e-07F); // {return ((x1 < x2) || DEQUAL(x1, x2));}
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//swap between the 4 variables such that the first becomes the second, second becomes the third and third becomes the fourth.
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//used in functoin mnbrack below.
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void shift3(MDOUBLE &a, MDOUBLE &b, MDOUBLE &c, const MDOUBLE d);
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// print vector and VVdoulbe util
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ostream &operator<<(ostream &out, const Vdouble &v);
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ostream &operator<<(ostream &out, const VVdouble &m);
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void mult(Vdouble& vec, const MDOUBLE factor);
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void mult(VVdouble& vec, const MDOUBLE factor);
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//scale vecToScale so that its new average is AvgIn. return the scaling factor.
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MDOUBLE scaleVec(Vdouble& vecToScale, const MDOUBLE avgIn);
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//determine the relative order of vecIn. The order vector is returned
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//ex: vecIn = [0.1 0.4 0.01 0.9 1.8] orderVecOut = [1 2 0 3 4]
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MDOUBLE orderVec(const vector<MDOUBLE>& vecIn, vector<MDOUBLE>& orderVecOut);
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void orderRankNoTies(const vector<MDOUBLE>& vecIn, vector<MDOUBLE>& orderVecOut);
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//in this version orderVecOut does not preserv the same order as vecIn.
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//orderVecOut[0] cotains the lowest score and it is stored in orderVecOut[0].getValue()
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//The place in the original vector is stored in orderVecOut[0].getPlace()
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void orderVec(const Vdouble& vecIn, vector< vecElem<MDOUBLE> >& orderVecOut);
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//calculates the spearman rank correlation value
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MDOUBLE calcRankCorrelation(const Vdouble& oneRatesVec, const Vdouble& otherRatesVec);
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//calculates the spearman rank correlation value, Ofir implementation
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MDOUBLE calcRankCorrelation2(const Vdouble& oneRatesVec, const Vdouble& otherRatesVec);
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MDOUBLE calcCoVariance(const Vdouble& oneRatesVec, const Vdouble& otherRatesVec);
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MDOUBLE calcPearsonCorrelation(const Vdouble& oneRatesVec, const Vdouble& otherRatesVec, const int numberOfSignificantDigits=5);
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MDOUBLE computeFDRthreshold(Vdouble& sortedPVals, MDOUBLE levelOfFDRcontroled, bool isPValsSorted=false);
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MDOUBLE calcRelativeMSEDistBetweenVectors(const Vdouble& trueValues, const Vdouble& inferredValues, const MDOUBLE threshhold = 0.0);
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MDOUBLE calcMSEDistBetweenVectors(const Vdouble& trueValues, const Vdouble& inferredValues);
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//MAD = mean absolute deviations distance
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MDOUBLE calcMADDistBetweenVectors(const Vdouble& oneRatesVec, const Vdouble& otherRatesVec);
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MDOUBLE calcRelativeMADDistBetweenVectors(const Vdouble& trueValues, const Vdouble& inferredValues, const MDOUBLE threshhold = 0.0);
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MDOUBLE sumVdouble(const Vdouble & vec);
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/* Will split a string into 2 by the given seperator
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Example for usage:
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string a, b, c;
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a.assign("Hello world!");
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splitString2(a, " ", b, c);
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cout << "b = " << b << endl << "c = " << c << endl;
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//b == Hello
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//c == world!
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*/
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void splitString2(string str, string seperater, string &first, string &second);
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// used for gainLoss project
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int fromIndex2gainIndex(const int i, const int gainCategories, const int lossCategories);
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int fromIndex2lossIndex(const int i, const int gainCategories, const int lossCategories);
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int sign(MDOUBLE r);
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MDOUBLE factorial(int x);
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MDOUBLE BinomialCoeff(int a, int b);
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int round2int(MDOUBLE num);
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//This function does: ln(e**(valuesVec[0])+e**(valuesVec[1])+..e**(valuesVec[n]))
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//Which is: ln(e**(valuesVec[x]))*(1+sum_over_i_leave_x(e**(valuesVec[i]-valuesVec[x])))
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//Which is: valuesVec[x]+ln(1+sum_over_i_leave_x(e**(valuesVec[i]-valuesVec[x])))
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//Where: x is the index of the largest element in valuesVec and every valuesVec[i] which is really small should be neglected in order to avoid underflow
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MDOUBLE exponentResolver(Vdouble& valuesVec);
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#endif
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