string Array[] = {"line","label"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- parser = new OptionParser();
- parser->parse(option, parameters); delete parser;
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
- ValidParameters* validParameter = new ValidParameters();
-
//check to make sure all parameters are valid for command
- for (it = parameters.begin(); it != parameters.end(); it++) {
- if (validParameter->isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
//make sure the user has already run the read.otu command
- if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "")) { cout << "You must read a list or rabund before you can use the get.sabund command." << endl; abort = true; }
+ if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "")) { mothurOut("You must read a list or rabund before you can use the get.sabund command."); mothurOutEndLine(); abort = true; }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
- line = validParameter->validFile(parameters, "line", false);
+ line = validParameter.validFile(parameters, "line", false);
if (line == "not found") { line = ""; }
else {
if(line != "all") { splitAtDash(line, lines); allLines = 0; }
else { allLines = 1; }
}
- label = validParameter->validFile(parameters, "label", false);
+ label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
if(label != "all") { splitAtDash(label, labels); allLines = 0; }
}
//make sure user did not use both the line and label parameters
- if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; }
+ if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; }
//if the user has not specified any line or labels use the ones from read.otu
else if((line == "") && (label == "")) {
allLines = globaldata->allLines;
lines = globaldata->lines;
}
- delete validParameter;
-
if (abort == false) {
filename = getRootName(globaldata->inputFileName) + "sabund";
openOutputFile(filename, out);
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GetSAbundCommand class Function GetSAbundCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "GetSAbundCommand", "GetSAbundCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the GetSAbundCommand class function GetSAbundCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
//**********************************************************************************************************************
void GetSAbundCommand::help(){
try {
- cout << "The get.sabund command can only be executed after a successful read.otu of a listfile." << "\n";
- cout << "The get.sabund command parameters are line and label. No parameters are required, and you may not use line and label at the same time." << "\n";
- cout << "The line and label allow you to select what distance levels you would like included in your .sabund file, and are separated by dashes." << "\n";
- cout << "The get.sabund command should be in the following format: get.sabund(line=yourLines, label=yourLabels)." << "\n";
- cout << "Example get.sabund(line=1-3-5)." << "\n";
- cout << "The default value for line and label are all lines in your inputfile." << "\n";
- cout << "The get.sabund command outputs a .sabund file containing the lines you selected." << "\n";
- cout << "Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines)." << "\n" << "\n";
+ mothurOut("The get.sabund command can only be executed after a successful read.otu of a listfile or rabundfile.\n");
+ mothurOut("The get.sabund command parameters are line and label. No parameters are required, and you may not use line and label at the same time.\n");
+ mothurOut("The line and label allow you to select what distance levels you would like included in your .sabund file, and are separated by dashes.\n");
+ mothurOut("The get.sabund command should be in the following format: get.sabund(line=yourLines, label=yourLabels).\n");
+ mothurOut("Example get.sabund(line=1-3-5).\n");
+ mothurOut("The default value for line and label are all lines in your inputfile.\n");
+ mothurOut("The get.sabund command outputs a .sabund file containing the lines you selected.\n");
+ mothurOut("Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines).\n\n");
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GetSAbundCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "GetSAbundCommand", "help");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the GetSAbundCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
read->read(&*globaldata);
order = globaldata->gorder;
- lastOrder = order;
+ string lastLabel = order->getLabel();
input = globaldata->ginput;
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
if(allLines == 1 || lines.count(count) == 1 || labels.count(order->getLabel()) == 1){
- cout << order->getLabel() << '\t' << count << endl;
+ mothurOut(order->getLabel()); mothurOutEndLine();
sabund = new SAbundVector();
*sabund = (order->getSAbundVector());
sabund->print(out);
userLines.erase(count);
}
- if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) {
- cout << lastOrder->getLabel() << '\t' << count << endl;
+ if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ delete order;
+ order = (input->getOrderVector(lastLabel));
+
+ mothurOut(order->getLabel()); mothurOutEndLine();
sabund = new SAbundVector();
- *sabund = (lastOrder->getSAbundVector());
+ *sabund = (order->getSAbundVector());
sabund->print(out);
delete sabund;
- processedLabels.insert(lastOrder->getLabel());
- userLabels.erase(lastOrder->getLabel());
+ processedLabels.insert(order->getLabel());
+ userLabels.erase(order->getLabel());
}
- if (count != 1) { delete lastOrder; }
- lastOrder = order;
-
+
+ lastLabel = order->getLabel();
+
+ delete order;
order = (input->getOrderVector());
count++;
}
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
- cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastOrder->getLabel()) != 1) {
- cout << ". I will use " << lastOrder->getLabel() << "." << endl;
+ mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
needToRun = true;
}else {
- cout << ". Please refer to " << lastOrder->getLabel() << "." << endl;
+ mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
}
}
//run last line if you need to
if (needToRun == true) {
- cout << lastOrder->getLabel() << '\t' << count << endl;
+ if (order != NULL) { delete order; }
+ order = (input->getOrderVector(lastLabel));
+
+ mothurOut(order->getLabel()); mothurOutEndLine();
sabund = new SAbundVector();
- *sabund = (lastOrder->getSAbundVector());
+ *sabund = (order->getSAbundVector());
sabund->print(out);
delete sabund;
+ delete order;
}
- delete lastOrder;
+ globaldata->gorder = NULL;
out.close();
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GetSAbundCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "GetSAbundCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the GetSAbundCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
projects / mothur.git / blobdiff