}
//make sure the user has already run the read.otu command
- if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { cout << "You must read a list, sabund or rabund before you can use the summary.single command." << endl; abort = true; }
+ if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { mothurOut("You must read a list, sabund or rabund before you can use the summary.single command."); mothurOutEndLine(); abort = true; }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
}
//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;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function SummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "SummaryCommand", "SummaryCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the SummaryCommand class function SummaryCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
void SummaryCommand::help(){
try {
- cout << "The summary.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION." << "\n";
- cout << "The summary.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster." << "\n";
- cout << "The summary.single command parameters are label, line, calc, abund. No parameters are required, but you may not use " << "\n";
- cout << "both the line and label parameters at the same time. The summary.single command should be in the following format: " << "\n";
- cout << "summary.single(label=yourLabel, line=yourLines, calc=yourEstimators)." << "\n";
- cout << "Example summary.single(label=unique-.01-.03, line=0,5,10, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson)." << "\n";
+ mothurOut("The summary.single command can only be executed after a successful read.otu WTIH ONE EXECEPTION.\n");
+ mothurOut("The summary.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster.\n");
+ mothurOut("The summary.single command parameters are label, line, calc, abund. No parameters are required, but you may not use \n");
+ mothurOut("both the line and label parameters at the same time. The summary.single command should be in the following format: \n");
+ mothurOut("summary.single(label=yourLabel, line=yourLines, calc=yourEstimators).\n");
+ mothurOut("Example summary.single(label=unique-.01-.03, line=0,5,10, calc=sobs-chao-ace-jack-bootstrap-shannon-npshannon-simpson).\n");
validCalculator->printCalc("summary", cout);
- cout << "The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson" << "\n";
- cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
- cout << "Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines)." << "\n" << "\n";
+ mothurOut("The default value calc is sobs-chao-ace-jack-shannon-npshannon-simpson\n");
+ mothurOut("The label and line parameters are used to analyze specific lines in your input.\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 SummaryCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "SummaryCommand", "help");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the SummaryCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
read->read(&*globaldata);
sabund = globaldata->sabund;
- SAbundVector* lastSAbund = sabund;
+ string lastLabel = sabund->getLabel();
input = globaldata->ginput;
for(int i=0;i<sumCalculators.size();i++){
if(allLines == 1 || lines.count(count) == 1 || labels.count(sabund->getLabel()) == 1){
- cout << sabund->getLabel() << '\t' << count << endl;
+ mothurOut(sabund->getLabel() + "\t" + toString(count)); mothurOutEndLine();
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
userLines.erase(count);
outputFileHandle << endl;
}
- if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastSAbund->getLabel()) != 1)) {
-
- cout << lastSAbund->getLabel() << '\t' << count << endl;
- processedLabels.insert(lastSAbund->getLabel());
- userLabels.erase(lastSAbund->getLabel());
+ if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ delete sabund;
+ sabund = input->getSAbundVector(lastLabel);
+
+ mothurOut(sabund->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ processedLabels.insert(sabund->getLabel());
+ userLabels.erase(sabund->getLabel());
- outputFileHandle << lastSAbund->getLabel();
+ outputFileHandle << sabund->getLabel();
for(int i=0;i<sumCalculators.size();i++){
- vector<double> data = sumCalculators[i]->getValues(lastSAbund);
+ vector<double> data = sumCalculators[i]->getValues(sabund);
outputFileHandle << '\t';
sumCalculators[i]->print(outputFileHandle);
}
outputFileHandle << endl;
}
- if (count != 1) { delete lastSAbund; }
- lastSAbund = sabund;
-
+ lastLabel = sabund->getLabel();
+
+ delete sabund;
sabund = input->getSAbundVector();
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(lastSAbund->getLabel()) != 1) {
- cout << ". I will use " << lastSAbund->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 " << lastSAbund->getLabel() << "." << endl;
+ mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
}
}
//run last line if you need to
if (needToRun == true) {
- cout << lastSAbund->getLabel() << '\t' << count << endl;
- outputFileHandle << lastSAbund->getLabel();
+ delete sabund;
+ sabund = input->getSAbundVector(lastLabel);
+
+ mothurOut(sabund->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ outputFileHandle << sabund->getLabel();
for(int i=0;i<sumCalculators.size();i++){
- vector<double> data = sumCalculators[i]->getValues(lastSAbund);
+ vector<double> data = sumCalculators[i]->getValues(sabund);
outputFileHandle << '\t';
sumCalculators[i]->print(outputFileHandle);
}
outputFileHandle << endl;
+ delete sabund;
}
outputFileHandle.close();
- delete lastSAbund;
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the SummaryCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "SummaryCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the SummaryCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
projects / mothur.git / blobdiff