Solution: Use if (argc !=3) and getline(row_as_stringstream, substr, ';')
This is a continuation of my previous question: error: no matching function for call to, which allowed the code to compile without any errors
I am new to C++ and I am trying to debug this code from my supervisor.
The original code took a csv file as input, containing rows and columns of integers
and strings. Now we're reading in a txt file having the shape:
TEXT
0; INT; INT; INT; INT; ...
0; INT; INT; INT; INT; ...
18 more lines of the above numbers and semicolons
In that file I replaced in one instance the semicolons by line breaks and in another by empty spaces, because I was not sure which we needed.
Solution: Use the txt file with the semicolons, but with the semicolons at the end of the lines removed.
It seems to have an issue with if (argc < 2 || argc > 2) . It throws the "Usage: ./a.o <> <>" error message. However, both are strict inequalities. Shouldn't this if be fine with 2 arguments? In the original code it read if (argc < 2 || argc > 3) , which I changed it back to.
EDIT: As john pointed out the "program name is an argument" as well, so I want actually 3 not 2.
Both txt files (line breaks & spaces) seem to produce the same error message below
Error message: (For the int threshold I tried various values)
Registering only edges shorter than int.
terminate called after throwing an instance of 'std::out_of_range'
what(): vector::_M_range_check: __n (which is 1) >= this->size() (which is 1)
Aborted (core dumped)
Ideas:
I am aware what this error message means when we have a simple case, for example:
#include <vector>
int main()
{
std::vector<int> v;
v.push_back(123); // v has 1 element [0 to 0]
int x4 = v.at(3); // exception
}
We get an exception, because v has 1 element and element 3 does not exist.
However, in my code I am not sure what exactly to look for.
The original code read a csv with lines and columns, but in this case a matrix form with empty spaces in between is probably causing issues. Does that mean that I just want a txt file looking like a column vector? That is one file I tried, so it might be that the code is not happy with the amount of columns?
Relevant function:
int main(int argc, char** threshold_and_distanceMatrixfilename)
{
if (argc < 2 || argc > 3)
{
std::cerr << "Usage: ./distanceMatrixToSageGraph.o <threshold>
<distanceMatrix_file_calculated_fromDGEsingleCell_data>" << std::endl;
return -1;
}
string distanceMatrixfilename = threshold_and_distanceMatrixfilename[2];
int threshold = std::stoi(threshold_and_distanceMatrixfilename[1]);
std::ifstream distanceMatrixFile(distanceMatrixfilename);
if (!distanceMatrixFile)
{
std::cerr << "Error opening distanceMatrix file: " << distanceMatrixfilename << std::endl;
return -1;
}
string row;
std::getline(distanceMatrixFile, row); // discard the first row, which specifies the format of the file.
vector<vector<int>> the_entries;
while (std::getline(distanceMatrixFile, row))
{
std::stringstream row_as_stringstream(row);
int i; i = 0;
vector<string> row_as_vector;
while (row_as_stringstream.good())
{
string substr;
getline(row_as_stringstream, substr, ',');
row_as_vector.push_back( std::stoi(substr) );
};
the_entries.push_back(row_as_vector); //LINE 104
};
}
Whole code:
// Convert distanceMatrix tables of protein interactions to SAGE graph.
///////////////////////////////////////////////////////////////////////////
#include <iostream>
#include <fstream>
#include <sstream>
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include <list>
#include <vector>
#include <tuple>
#include <algorithm>
using namespace std;
void writeGraphInSageFormat(string name, std::vector<std::vector<int>> TheEdges)
{
//////////////////////////////////////////////////////////////////////////////////////
// Write out the edges in SAGE format.
///////////////////////////////////////////////////////////////////////////////////////
int edgeNumber = TheEdges.size();
ofstream d1sageFile(name, ios::out);
d1sageFile << "g = Graph([" << endl;
for (int n = 0; n < edgeNumber; n++) {
d1sageFile << "(" << TheEdges[n][0] + 1 << "," << TheEdges[n][1] + 1 << ")," << endl;
}
d1sageFile << "])" << endl;
d1sageFile << "g.show()" << endl;
d1sageFile.close();
std::cout << "SAGE graph written into the file " << name << std::endl;
}
std::vector<std::vector<int>> ConvertEntriesMatrixToEdges(vector<vector<int>> the_entries, int threshold)
{
////////////////////////////////////////////////////////////////////////////////////////////
// Construct the edge-vertex incidence matrix (d_1) from the distanceMatrix entries matrix:
////////////////////////////////////////////////////////////////////////////////////////////
std::vector<std::string> proteinNames;
std::vector<std::vector<int>> TheEdges;
std::cout << "Registering only edges shorter than " << threshold << "." << std::endl;
int thisDistance;
for (int i = 0; i < the_entries.size(); i++)
{
for (int j = i + 1; j < the_entries.size(); j++)
{
// we could use the_entries.size() instead of the_entries.at(i).size(), because this is a square matrix.
thisDistance = the_entries.at(i).at(j);
if (thisDistance < threshold)
{
std::vector<int> CurrentEdge(2);
CurrentEdge[0] = i;
CurrentEdge[1] = j;
TheEdges.push_back(CurrentEdge);
};
};
};
return TheEdges;
}
///////////////////////////////////////////
// Main Program: Extract edges from a distanceMatrix file.
///////////////////////////////////////////
int main(int argc, char** threshold_and_distanceMatrixfilename)
{
if (argc < 2 || argc > 3)
{
std::cerr << "Usage: ./distanceMatrixToSageGraph.o <threshold> <distanceMatrix_file_calculated_fromDGEsingleCell_data>" << std::endl;
return -1;
}
string distanceMatrixfilename = threshold_and_distanceMatrixfilename[2];
int threshold = std::stoi(threshold_and_distanceMatrixfilename[1]);
std::ifstream distanceMatrixFile(distanceMatrixfilename);
if (!distanceMatrixFile) {
std::cerr << "Error opening distanceMatrix file: " << distanceMatrixfilename << std::endl;
return -1;
}
string row; //LINE 88
std::getline(distanceMatrixFile, row); // discard the first row, which specifies the format of the file.
vector<vector<int>> the_entries;
while (std::getline(distanceMatrixFile, row))
{
std::stringstream row_as_stringstream(row);
int i; i = 0;
vector<string> row_as_vector;
while (row_as_stringstream.good())
{
string substr;
getline(row_as_stringstream, substr, ',');
row_as_vector.push_back( std::stoi(substr) );
};
the_entries.push_back(row_as_vector); //LINE 104
};
////////////////////////////////////////////////////////////
// Now we assemble the entries to an edges matrix, and write it into a Sage file:
////////////////////////////////////////////////////////////
std::vector<std::vector<int>> TheEdges = ConvertEntriesMatrixToEdges(the_entries, threshold);
char outputFilename[60]; strcpy(outputFilename, distanceMatrixfilename.c_str()); strcat(outputFilename, "AtThreshold"); string thrshld = std::to_string(threshold); strcat(outputFilename, thrshld.c_str()); strcat(outputFilename, ".txt");
writeGraphInSageFormat(outputFilename, TheEdges);
return 0;
}
First question. What you're missing is that the program name is an argument, so
program arg1 arg2
is three arguments and argc will equal 3 not 2. You could have found this out for yourself by either using a debugger (you really need to learn how to use one, much better than asking here) or at the very least adding cout << "argc=" << argc << '\n'; to your code.
Second question, your original code was written for comma separated values, see the comma here getline(row_as_stringstream, substr, ','); so obviously you need to change it for semi colon or space separated values.
Above all though you need to learn to use a debugger. Trying to debug programs by looking at code is not easy.