source: cpp/frams/_demos/simil_test.cpp @ 920

// This file is a part of Framsticks SDK.  http://www.framsticks.com/
// Copyright (C) 1999-2016  Maciej Komosinski and Szymon Ulatowski.
// See LICENSE.txt for details.


#include <vector>
#include "common/loggers/loggertostdout.h"
#include "frams/_demos/genotypeloader.h"
#include "frams/genetics/preconfigured.h"
#include "common/virtfile/stdiofile.h"
#include "frams/model/similarity/simil_model.h"



using namespace std;

/** Computes a matrix of distances between all genotypes in the specified
        .gen file, using the matching and measure weights as specified in the
        command line. */
int main(int argc, char *argv[])
{
        LoggerToStdout messages_to_stdout(LoggerBase::Enable);
        typedef double *pDouble;
        int iCurrParam = 0; // index of the currently processed parameter
        char *szCurrParam = NULL;
        ModelSimil M; // similarity computing object
        bool bPrintNames = false; // specifies if names of genotypes are to be printed
        int nResult = 0; // a temporary result

        if (argc < 8)
        {
                printf("Too few parameters!\n");
                printf("Command line: [-names] <genotypesFile> <measure> <w_dP> <w_dDEG> <w_dNEU> <w_dGEO> <fixZaxis?>\n\n");

                printf("Parameters:\n");
                printf("  <genotypesFile> name of a file with genotypes\n");
                printf("  <measure> similarity measure\n");
                printf("  <w_dP> weight of the difference in the number of parts\n");
                printf("  <w_dDEG> weight of the difference in degrees of matched parts\n");
                printf("  <w_dNEU> weight of the difference in neurons of matched parts\n");
                printf("  <w_dGEO> weight of the distance of matched parts\n");
                printf("  <fixZaxis?> should the 'z' (vertical) coordinate be fixed during the alignment? (0 or 1)\n\n");

                printf("Switches:\n");
                printf("  -names specifies that the number and names of genotypes are to be printed to output\n");
                printf("  before the distance matrix; by default the number and names are not printed\n\n");

                printf("Outputs a symmetric distance matrix in the format:\n");
                printf("  <row_1> (columns in a row are separated by TABs)\n");
                printf("  ...\n");
                printf("  <row_n>\n");

                return -1;
        }

        // prepare output parameters from .gen file
        vector<Geno *> pvGenos;
        vector<char *> pvNames;

        // check if there is a switch
        iCurrParam = 1;
        szCurrParam = argv[iCurrParam];
        if (strcmp(szCurrParam, "-names") == 0)
        {
                // switch "-names" was given; print names also
                bPrintNames = true;
                // pass to the next parameter
                iCurrParam++;
        }

        // check the parameters
        // get <genotypesFile> name from command line
        char *szFileName = argv[iCurrParam];

        // initially set measure components' weights to invalid values (negative)
        for (int i = 0; i < M.GetNOFactors(); i++)
        {
                M.m_adFactors[i] = -1.0;
        }
        
        iCurrParam++;
        szCurrParam = argv[iCurrParam];
        int measure_type = -1; 
        nResult = sscanf(szCurrParam, "%d", &measure_type);
        if (nResult != 1)
        {
                printf("Measure type should be a number!\n");
                return -1;
        }
        
        if (measure_type != 0 && measure_type != 1)
        {
                printf("Measure type should be 0 (flexible criteria order and optimal matching) or 1 (vertex degree order and greedy matching)!\n");
                return -1;              
        }
        
        M.matching_method = measure_type;

        const char *params[] = { "<w_dP>", "<w_dDEG>", "<w_dNEU>", "<w_dGEO>" };
        for (int i = 0; i < M.GetNOFactors(); i++)
        {
                iCurrParam++;
                szCurrParam = argv[iCurrParam];
                nResult = sscanf(szCurrParam, "%lf", &M.m_adFactors[i]);
                if (nResult != 1)
                {
                        // <w_dX> is not a number -- error
                        printf("%s", params[i]);
                        printf(" should be a number\n");
                        return -1;
                }
                else
                {
                        // <w_dX> is a number; check if nonnegative
                        if (M.m_adFactors[i] < 0.0)
                        {
                                printf("%s", params[i]);
                                printf(" should be a nonnegative number\n");
                                return -1;
                        }
                }
        }

        iCurrParam++;
        szCurrParam = argv[iCurrParam];
        nResult = sscanf(szCurrParam, "%d", &M.fixedZaxis);
        if (nResult != 1)
        {
                // <isZFixed> is not a number -- error
                printf("<isZFixed> should be a number\n");
                return -1;
        }
        else if (M.fixedZaxis != 0 && M.fixedZaxis != 1)
        {
                printf("<isZFixed>=%d. <isZFixed> should be equal to 0 or 1\n", M.fixedZaxis);
                return -1;
        }

        // read the input file
        // prepare loading of genotypes from a .gen file
        // create some basic genotype converters
        PreconfiguredGenetics genetics;
        StdioFileSystem_autoselect stdiofilesys;

        long count = 0, totalsize = 0;
        GenotypeMiniLoader loader(szFileName);
        GenotypeMini *loaded;
        while (loaded = loader.loadNextGenotype())
        {
                // while a valid genotype was loaded
                count++;
                totalsize += loaded->genotype.len();
                // create a Geno object based on the MiniGenotype
                Geno *pNextGenotype = new Geno(loaded->genotype);
                if ((pNextGenotype != NULL) && (pNextGenotype->isValid()))
                {
                        pvGenos.push_back(pNextGenotype);
                        char *szNewName = new char[loaded->name.len() + 1];
                        strcpy(szNewName, loaded->name.c_str());
                        pvNames.push_back(szNewName);
                }
                else
                {
                        printf("Genotype %2li is not valid\n", count);
                        if (pNextGenotype != NULL) delete pNextGenotype;
                }
        }
        if (loader.getStatus() == GenotypeMiniLoader::OnError)
        {
                printf("Error: %s", loader.getError().c_str());
        }

        double dSimilarity = 0.0;
        double **aaSimil = NULL; // array of similarities

        // create the empty array of similarities
        aaSimil = new pDouble[pvGenos.size()];
        for (unsigned int k = 0; k < pvGenos.size(); k++)
        {
                aaSimil[k] = new double[pvGenos.size()];
                for (unsigned int l = 0; l < pvGenos.size(); l++)
                        aaSimil[k][l] = 0.0;
        }

        // compute and remember similarities
        for (unsigned int i = 0; i < pvGenos.size(); i++)
        {
                for (unsigned int j = 0; j < pvGenos.size(); j++)
                {
                        dSimilarity = M.EvaluateDistance(pvGenos.operator[](i), pvGenos.operator[](j));
                        aaSimil[i][j] = dSimilarity;
                }
        }

        if (bPrintNames)
        {
                // if "-names" switch was given, print the number of genotypes and their names
                printf("%li\n", pvGenos.size());
                for (unsigned int iGen = 0; iGen < pvNames.size(); iGen++)
                {
                        printf("%s\n", pvNames.at(iGen));
                }
        }

        // print out the matrix of similarities
        for (unsigned int i = 0; i < pvGenos.size(); i++)
        {
                for (unsigned int j = 0; j < pvGenos.size(); j++)
                {
                        printf("%.2lf\t", aaSimil[i][j]);
                }
                printf("\n");
        }

        // delete vectors and arrays
        for (unsigned int i = 0; i < pvGenos.size(); i++)
        {
                delete pvGenos.operator[](i);
                delete[] pvNames.operator[](i);
                delete[] aaSimil[i];
        }

        delete[] aaSimil;

        return 0;
}