exit(1);
}
}
-
+//**********************************************************************************************************************
+string ClearcutCommand::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 == "tree") { outputFileName = "tre"; }
+ else if (type == "matrixout") { outputFileName = ""; }
+ 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, "ClearcutCommand", "getOutputFileNameTag");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
ClearcutCommand::ClearcutCommand(){
try {
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not open") { fastafile = ""; abort = true; }
else if (fastafile == "not found") { fastafile = ""; }
- else { inputFile = fastafile; }
+ else { inputFile = fastafile; m->setFastaFile(fastafile); }
phylipfile = validParameter.validFile(parameters, "phylip", true);
if (phylipfile == "not open") { phylipfile = ""; abort = true; }
else if (phylipfile == "not found") { phylipfile = ""; }
- else { inputFile = phylipfile; }
+ else { inputFile = phylipfile; m->setPhylipFile(phylipfile); }
if ((phylipfile == "") && (fastafile == "")) {
//is there are current file available for either of these?
//give priority to phylip, then fasta
phylipfile = m->getPhylipFile();
- if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
+ if (phylipfile != "") { inputFile = phylipfile; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
else {
fastafile = m->getFastaFile();
- if (fastafile != "") { m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
+ if (fastafile != "") { inputFile = fastafile; m->mothurOut("Using " + fastafile + " as input file for the fasta parameter."); m->mothurOutEndLine(); }
else {
m->mothurOut("No valid current files. You must provide a phylip or fasta file before you can use the clearcut command."); m->mothurOutEndLine();
abort = true;
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//prepare filename
- string outputName = outputDir + m->getRootName(m->getSimpleName(inputFile)) + "tre";
+ string outputName = outputDir + m->getRootName(m->getSimpleName(inputFile)) + getOutputFileNameTag("tree");
outputNames.push_back(outputName); outputTypes["tree"].push_back(outputName);
vector<char*> cPara;
- char* tempClearcut = new char[8];
- strcpy(tempClearcut, "clearcut");
+ char* tempClearcut = new char[9];
+ *tempClearcut = '\0'; strncat(tempClearcut, "clearcut", 8);
cPara.push_back(tempClearcut);
//you gave us a distance matrix
- if (phylipfile != "") { char* temp = new char[10]; strcpy(temp, "--distance"); cPara.push_back(temp); }
+ if (phylipfile != "") { char* temp = new char[11]; *temp = '\0'; strncat(temp, "--distance", 10); cPara.push_back(temp); }
//you gave us a fastafile
- if (fastafile != "") { char* temp = new char[11]; strcpy(temp, "--alignment"); cPara.push_back(temp); }
+ if (fastafile != "") { char* temp = new char[12]; *temp = '\0'; strncat(temp, "--alignment", 11); cPara.push_back(temp); }
- if (version) { char* temp = new char[9]; strcpy(temp, "--version"); cPara.push_back(temp); }
- if (verbose) { char* temp = new char[9]; strcpy(temp, "--verbose"); cPara.push_back(temp); }
- if (quiet) { char* temp = new char[7]; strcpy(temp, "--quiet"); cPara.push_back(temp); }
+ if (version) { char* temp = new char[10]; *temp = '\0'; strncat(temp, "--version", 9); cPara.push_back(temp); }
+ if (verbose) { char* temp = new char[10]; *temp = '\0'; strncat(temp, "--verbose", 9); cPara.push_back(temp); }
+ if (quiet) { char* temp = new char[8]; *temp = '\0'; strncat(temp, "--quiet", 7); cPara.push_back(temp); }
if (seed != "*") {
string tempSeed = "--seed=" + seed;
- char* temp = new char[tempSeed.length()];
- strcpy(temp, tempSeed.c_str());
+ char* temp = new char[tempSeed.length()+1];
+ *temp = '\0'; strncat(temp, tempSeed.c_str(), tempSeed.length());
cPara.push_back(temp);
}
- if (norandom) { char* temp = new char[10]; strcpy(temp, "--norandom"); cPara.push_back(temp); }
- if (shuffle) { char* temp = new char[9]; strcpy(temp, "--shuffle"); cPara.push_back(temp); }
- if (neighbor) { char* temp = new char[10]; strcpy(temp, "--neighbor"); cPara.push_back(temp); }
+ if (norandom) { char* temp = new char[11]; *temp = '\0'; strncat(temp, "--norandom", 10); cPara.push_back(temp); }
+ if (shuffle) { char* temp = new char[10]; *temp = '\0'; strncat(temp, "--shuffle", 9); cPara.push_back(temp); }
+ if (neighbor) { char* temp = new char[11]; *temp = '\0'; strncat(temp, "--neighbor", 10); cPara.push_back(temp); }
string tempIn = "--in=" + inputFile;
- char* tempI = new char[tempIn.length()];
- strcpy(tempI, tempIn.c_str());
+ char* tempI = new char[tempIn.length()+1];
+ *tempI = '\0'; strncat(tempI, tempIn.c_str(), tempIn.length());
cPara.push_back(tempI);
- if (stdoutWanted) { char* temp = new char[8]; strcpy(temp, "--stdout"); cPara.push_back(temp); }
+ if (stdoutWanted) { char* temp = new char[9]; *temp = '\0'; strncat(temp, "--stdout", 8); cPara.push_back(temp); }
else{
string tempOut = "--out=" + outputName;
-
- char* temp = new char[tempOut.length()];
- strcpy(temp, tempOut.c_str());
+ char* temp = new char[tempOut.length()+1];
+ *temp = '\0'; strncat(temp, tempOut.c_str(), tempOut.length());
cPara.push_back(temp);
}
- if (DNA) { char* temp = new char[5]; strcpy(temp, "--DNA"); cPara.push_back(temp); }
- if (protein) { char* temp = new char[9]; strcpy(temp, "--protein"); cPara.push_back(temp); }
- if (jukes) { char* temp = new char[7]; strcpy(temp, "--jukes"); cPara.push_back(temp); }
- if (kimura) { char* temp = new char[8]; strcpy(temp, "--kimura"); cPara.push_back(temp); }
+ if (DNA) { char* temp = new char[6]; *temp = '\0'; strncat(temp, "--DNA", 5); cPara.push_back(temp); }
+ if (protein) { char* temp = new char[10]; *temp = '\0'; strncat(temp, "--protein", 9); cPara.push_back(temp); }
+ if (jukes) { char* temp = new char[8]; *temp = '\0'; strncat(temp, "--jukes", 7); cPara.push_back(temp); }
+ if (kimura) { char* temp = new char[9]; *temp = '\0'; strncat(temp, "--kimura", 8); cPara.push_back(temp); }
if (matrixout != "") {
string tempMatrix = "--matrixout=" + outputDir + matrixout;
- char* temp = new char[tempMatrix.length()];
- strcpy(temp, tempMatrix.c_str());
+ char* temp = new char[tempMatrix.length()+1];
+ *temp = '\0'; strncat(temp, tempMatrix.c_str(), tempMatrix.length());
cPara.push_back(temp);
outputNames.push_back((outputDir + matrixout));
outputTypes["matrixout"].push_back((outputDir + matrixout));
if (ntrees != "1") {
string tempNtrees = "--ntrees=" + ntrees;
- char* temp = new char[tempNtrees.length()];
- strcpy(temp, tempNtrees.c_str());
+ char* temp = new char[tempNtrees.length()+1];
+ *temp = '\0'; strncat(temp, tempNtrees.c_str(), tempNtrees.length());
cPara.push_back(temp);
}
- if (expblen) { char* temp = new char[9]; strcpy(temp, "--expblen"); cPara.push_back(temp); }
- if (expdist) { char* temp = new char[9]; strcpy(temp, "--expdist"); cPara.push_back(temp); }
+ if (expblen) { char* temp = new char[10]; *temp = '\0'; strncat(temp, "--expblen", 9); cPara.push_back(temp); }
+ if (expdist) { char* temp = new char[10]; *temp = '\0'; strncat(temp, "--expdist", 9); cPara.push_back(temp); }
char** clearcutParameters;
clearcutParameters = new char*[cPara.size()];
projects / mothur.git / blobdiff