try {

string firstName, secondName;

float distance;

int nseqs = nameMap->size();

list = new ListVector(nameMap->getListVector());

Progress* reading = new Progress("Formatting matrix: ", nseqs * nseqs);

int lt = 1;

int refRow = 0; //we'll keep track of one cell - Cell(refRow,refCol) - and see if it's transpose

int refCol = 0; //shows up later - Cell(refCol,refRow). If it does, then its a square matrix

//need to see if this is a square or a triangular matrix...

ofstream out;

string tempOutFile = filename + ".temp";

m->openOutputFile(tempOutFile, out);

while(fileHandle && lt == 1){ //let's assume it's a triangular matrix...

if (m->control_pressed) { out.close(); m->mothurRemove(tempOutFile); fileHandle.close(); delete reading; return 0; }

fileHandle >> firstName >> secondName >> distance; // get the row and column names and distance

map<string,int>::iterator itA = nameMap->find(firstName);

map<string,int>::iterator itB = nameMap->find(secondName);

if(itA == nameMap->end()){ m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the names file, please correct\n"); exit(1); }

if(itB == nameMap->end()){ m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the names file, please correct\n"); exit(1); }

if (distance == -1) { distance = 1000000; }

if((distance < cutoff) && (itA != itB)){

if(refRow == refCol){ // in other words, if we haven't loaded refRow and refCol...

refRow = itA->second;

refCol = itB->second;

//making it square

out << itA->second << '\t' << itB->second << '\t' << distance << endl;

out << itB->second << '\t' << itA->second << '\t' << distance << endl;

}

else if(refRow == itA->second && refCol == itB->second){ lt = 0; } //you are square

else if(refRow == itB->second && refCol == itA->second){ lt = 0; } //you are square

else{ //making it square

out << itA->second << '\t' << itB->second << '\t' << distance << endl;

out << itB->second << '\t' << itA->second << '\t' << distance << endl;

}

reading->update(itA->second * nseqs / 2);

}

m->gobble(fileHandle);

}

out.close();

fileHandle.close();

string squareFile;

if(lt == 0){ // oops, it was square

squareFile = filename;

}else{ squareFile = tempOutFile; }

//sort file by first column so the distances for each row are together

string outfile = m->getRootName(squareFile) + "sorted.dist.temp";

//use the unix sort

#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)

string command = "sort -n " + squareFile + " -o " + outfile;

system(command.c_str());

#else //sort using windows sort

string command = "sort " + squareFile + " /O " + outfile;

system(command.c_str());

#endif

if (m->control_pressed) { m->mothurRemove(tempOutFile); m->mothurRemove(outfile); delete reading; return 0; }

//output to new file distance for each row and save positions in file where new row begins

ifstream in;

m->openInputFile(outfile, in);

distFile = outfile + ".rowFormatted";

m->openOutputFile(distFile, out);

rowPos.resize(nseqs, -1);

int currentRow;

int first, second;

float dist;

map<int, float> rowMap;

map<int, float>::iterator itRow;

//get first currentRow

in >> first;

currentRow = first;

string firstString = toString(first);

for(int k = 0; k < firstString.length(); k++) { in.putback(firstString[k]); }

while(!in.eof()) {

if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(distFile); m->mothurRemove(tempOutFile); m->mothurRemove(outfile); delete reading; return 0; }

in >> first >> second >> dist; m->gobble(in);

if (first != currentRow) {

//save position in file of each new row

rowPos[currentRow] = out.tellp();

out << currentRow << '\t' << rowMap.size() << '\t';

for (itRow = rowMap.begin(); itRow != rowMap.end(); itRow++) {

out << itRow->first << '\t' << itRow->second << '\t';

}

out << endl;

currentRow = first;

rowMap.clear();

//save row you just read

if (dist < cutoff) {

rowMap[second] = dist;

}

}else{

if (dist < cutoff) {

rowMap[second] = dist;

}

}

}

//print last Row

//save position in file of each new row

rowPos[currentRow] = out.tellp();

out << currentRow << '\t' << rowMap.size() << '\t';

for (itRow = rowMap.begin(); itRow != rowMap.end(); itRow++) {

out << itRow->first << '\t' << itRow->second << '\t';

}

out << endl;

in.close();

out.close();

if (m->control_pressed) { m->mothurRemove(distFile); m->mothurRemove(tempOutFile); m->mothurRemove(outfile); delete reading; return 0; }

m->mothurRemove(tempOutFile);

m->mothurRemove(outfile);

reading->finish();

delete reading;

list->setLabel("0");

if (m->control_pressed) { m->mothurRemove(distFile); return 0; }

return 1;

}

catch(exception& e) {

m->errorOut(e, "FormatColumnMatrix", "read");

exit(1);

}