globaldata = GlobalData::getInstance();
abort = false;
allLines = 1;
- lines.clear();
labels.clear();
Estimators.clear();
else {
//valid paramters for this command
- string Array[] = {"line","label","calc","abund","size"};
+ string Array[] = {"label","calc","abund","size"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
}
//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...
- 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);
if (label == "not found") { label = ""; }
else {
else { allLines = 1; }
}
- //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 the user has not specified any line or labels use the ones from read.otu
- else if((line == "") && (label == "")) {
+ //if the user has not specified any labels use the ones from read.otu
+ if(label == "") {
allLines = globaldata->allLines;
labels = globaldata->labels;
- lines = globaldata->lines;
}
calc = validParameter.validFile(parameters, "calc", false);
}
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, calc, abund. No parameters are required.\n");
+ mothurOut("The summary.single command should be in the following format: \n");
+ mothurOut("summary.single(label=yourLabel, calc=yourEstimators).\n");
+ mothurOut("Example summary.single(label=unique-.01-.03, 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 parameter is used to analyze specific labels in your input.\n");
+ mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\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);
- }
}
//**********************************************************************************************************************
if (abort == true) { return 0; }
- int count = 1;
-
//if the users entered no valid calculators don't execute command
if (sumCalculators.size() == 0) { return 0; }
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
set<string> userLabels = labels;
- set<int> userLines = lines;
-
- while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
- if(allLines == 1 || lines.count(count) == 1 || labels.count(sabund->getLabel()) == 1){
+ while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
+
+ if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
- cout << sabund->getLabel() << '\t' << count << endl;
+ mothurOut(sabund->getLabel()); mothurOutEndLine();
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
- userLines.erase(count);
-
-
+
outputFileHandle << sabund->getLabel();
for(int i=0;i<sumCalculators.size();i++){
vector<double> data = sumCalculators[i]->getValues(sabund);
delete sabund;
sabund = input->getSAbundVector(lastLabel);
- cout << sabund->getLabel() << '\t' << count << endl;
+ mothurOut(sabund->getLabel()); mothurOutEndLine();
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
delete sabund;
sabund = input->getSAbundVector();
- count++;
}
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
- cout << "Your file does not include the label "<< *it;
+ mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
- cout << ". I will use " << lastLabel << "." << endl;
+ mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
needToRun = true;
}else {
- cout << ". Please refer to " << lastLabel << "." << endl;
+ mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
}
}
- //run last line if you need to
+ //run last label if you need to
if (needToRun == true) {
- delete sabund;
+ if (sabund != NULL) { delete sabund; }
sabund = input->getSAbundVector(lastLabel);
- cout << sabund->getLabel() << '\t' << count << endl;
+ mothurOut(sabund->getLabel()); mothurOutEndLine();
outputFileHandle << sabund->getLabel();
for(int i=0;i<sumCalculators.size();i++){
vector<double> data = sumCalculators[i]->getValues(sabund);
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