}
}
//**********************************************************************************************************************
+string ChimeraCcodeCommand::getOutputFileNameTag(string type, string inputName=""){
+ try {
+ string outputFileName = "";
+ map<string, vector<string> >::iterator it;
+
+ //is this a type this command creates
+ it = outputTypes.find(type);
+ if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+ else {
+ if (type == "chimera") { outputFileName = "ccode.chimeras"; }
+ else if (type == "mapinfo") { outputFileName = "mapinfo"; }
+ else if (type == "accnos") { outputFileName = "ccode.accnos"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
+ }
+ return outputFileName;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ChimeraCcodeCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
ChimeraCcodeCommand::ChimeraCcodeCommand(){
try {
abort = true; calledHelp = true;
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
temp = validParameter.validFile(parameters, "window", false); if (temp == "not found") { temp = "0"; }
- convert(temp, window);
+ m->mothurConvert(temp, window);
temp = validParameter.validFile(parameters, "numwanted", false); if (temp == "not found") { temp = "20"; }
- convert(temp, numwanted);
+ m->mothurConvert(temp, numwanted);
temp = validParameter.validFile(parameters, "save", false); if (temp == "not found"){ temp = "f"; }
save = m->isTrue(temp);
if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it
string outputFileName, accnosFileName;
if (maskfile != "") {
- outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + ".ccode.chimeras";
- accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + ".ccode.accnos";
+ outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + getOutputFileNameTag("chimera");
+ accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + maskfile + getOutputFileNameTag("accnos");
}else {
- outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "ccode.chimeras";
- accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "ccode.accnos";
+ outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("chimera");
+ accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("accnos");
+
}
- string mapInfo = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "mapinfo";
+ string mapInfo = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("mapinfo");
+
if (m->control_pressed) { delete chimera; for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } outputTypes.clear(); return 0; }
//break up file
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
vector<unsigned long long> positions = m->divideFile(fastaFileNames[s], processors);
for (int i = 0; i < (positions.size()-1); i++) {
}
delete candidateSeq;
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
unsigned long long pos = inFASTA.tellg();
if ((pos == -1) || (pos >= filePos->end)) { break; }
#else
int ChimeraCcodeCommand::createProcesses(string outputFileName, string filename, string accnos) {
try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
int process = 0;
int num = 0;