m->openInputFile(fastafile, inFASTA);
alignDB = SequenceDB(inFASTA);
inFASTA.close();
+ m->setFastaFile(fastafile);
}
oldfastafile = validParameter.validFile(parameters, "oldfasta", true);
column = validParameter.validFile(parameters, "column", true);
if (column == "not found") { column = ""; }
else if (column == "not open") { abort = true; }
+ else { m->setColumnFile(column); }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
if (output == "lt") { //does the user want lower triangle phylip formatted file
outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "phylip.dist";
- remove(outputFile.c_str()); outputTypes["phylip"].push_back(outputFile);
+ m->mothurRemove(outputFile); outputTypes["phylip"].push_back(outputFile);
//output numSeqs to phylip formatted dist file
}else if (output == "column") { //user wants column format
rename(column.c_str(), tempcolumn.c_str());
}
- remove(outputFile.c_str());
+ m->mothurRemove(outputFile);
}else { //assume square
outputFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + "square.dist";
- remove(outputFile.c_str());
+ m->mothurRemove(outputFile);
outputTypes["phylip"].push_back(outputFile);
}
#endif
#endif
- if (m->control_pressed) { outputTypes.clear(); delete distCalculator; remove(outputFile.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete distCalculator; m->mothurRemove(outputFile); return 0; }
#ifdef USE_MPI
MPI_Comm_rank(MPI_COMM_WORLD, &pid);
if (outputFile == column) {
string tempcolumn = column + ".old";
m->appendFiles(tempcolumn, outputFile);
- remove(tempcolumn.c_str());
+ m->mothurRemove(tempcolumn);
}else{
m->appendFiles(outputFile, column);
- remove(outputFile.c_str());
+ m->mothurRemove(outputFile);
outputFile = column;
}
if (outputDir != "") {
string newOutputName = outputDir + m->getSimpleName(outputFile);
rename(outputFile.c_str(), newOutputName.c_str());
- remove(outputFile.c_str());
+ m->mothurRemove(outputFile);
outputFile = newOutputName;
}
}
}
#endif
- if (m->control_pressed) { outputTypes.clear(); delete distCalculator; remove(outputFile.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); delete distCalculator; m->mothurRemove(outputFile); return 0; }
delete distCalculator;
//append and remove temp files
for (int i=0;i<processIDS.size();i++) {
m->appendFiles((filename + toString(processIDS[i]) + ".temp"), filename);
- remove((filename + toString(processIDS[i]) + ".temp").c_str());
+ m->mothurRemove((filename + toString(processIDS[i]) + ".temp"));
}
#endif
}
//m->openInputFile(outfile, in);
while(!in.eof()) {
- if (m->control_pressed) { in.close(); remove(outfile.c_str()); out.close(); return 0; }
+ if (m->control_pressed) { in.close(); m->mothurRemove(outfile); out.close(); return 0; }
in >> first >> second >> dist; m->gobble(in);
in.close();
out.close();
- remove(outfile.c_str());
+ m->mothurRemove(outfile);
return 1;
//m->openInputFile(outfile, in);
while(!in.eof()) {
- if (m->control_pressed) { in.close(); remove(outfile.c_str()); out.close(); return 0; }
+ if (m->control_pressed) { in.close(); m->mothurRemove(outfile); out.close(); return 0; }
in >> first >> second >> dist; m->gobble(in);
in.close();
out.close();
- remove(outfile.c_str());
+ m->mothurRemove(outfile);
return 1;
string name1, name2;
float dist;
while (!inDist.eof()) {
- if (m->control_pressed) { inDist.close(); outDist.close(); remove(outputFile.c_str()); return good; }
+ if (m->control_pressed) { inDist.close(); outDist.close(); m->mothurRemove(outputFile); return good; }
inDist >> name1 >> name2 >> dist; m->gobble(inDist);
outDist.close();
if (good) {
- remove(column.c_str());
+ m->mothurRemove(column);
rename(outputFile.c_str(), column.c_str());
}else{
- remove(outputFile.c_str()); //temp file is bad because file mismatch above
+ m->mothurRemove(outputFile); //temp file is bad because file mismatch above
}
return good;