//make sure the user has already run the read.otu command
if (globaldata->getSharedFile() == "") {
- if (globaldata->getListFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared command." << endl; abort = true; }
- else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared command." << endl; abort = true; }
+ if (globaldata->getListFile() == "") { mothurOut("You must read a list and a group, or a shared before you can use the collect.shared command."); mothurOutEndLine(); abort = true; }
+ else if (globaldata->getGroupFile() == "") { mothurOut("You must read a list and a group, or a shared before you can use the collect.shared command."); mothurOutEndLine(); abort = true; }
}
}
//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;
if (abort == false) {
string fileNameRoot = getRootName(globaldata->inputFileName);
-// format = globaldata->getFormat();
+ format = globaldata->getFormat();
int i;
validCalculator = new ValidCalculators();
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function CollectSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "CollectSharedCommand", "CollectSharedCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the CollectSharedCommand class function CollectSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
-
}
//**********************************************************************************************************************
void CollectSharedCommand::help(){
try {
- cout << "The collect.shared command can only be executed after a successful read.otu command." << "\n";
- cout << "The collect.shared command parameters are label, line, freq, calc and groups. No parameters are required, but you may not use " << "\n";
- cout << "both the line and label parameters at the same time. The collect.shared command should be in the following format: " << "\n";
- cout << "collect.shared(label=yourLabel, line=yourLines, freq=yourFreq, calc=yourEstimators, groups=yourGroups)." << "\n";
- cout << "Example collect.shared(label=unique-.01-.03, line=0-5-10, freq=10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan)." << "\n";
- cout << "The default values for freq is 100 and calc are sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan." << "\n";
- cout << "The default value for groups is all the groups in your groupfile." << "\n";
+ mothurOut("The collect.shared command can only be executed after a successful read.otu command.\n");
+ mothurOut("The collect.shared command parameters are label, line, freq, calc and groups. No parameters are required, but you may not use \n");
+ mothurOut("both the line and label parameters at the same time. The collect.shared command should be in the following format: \n");
+ mothurOut("collect.shared(label=yourLabel, line=yourLines, freq=yourFreq, calc=yourEstimators, groups=yourGroups).\n");
+ mothurOut("Example collect.shared(label=unique-.01-.03, line=0-5-10, freq=10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n");
+ mothurOut("The default values for freq is 100 and calc are sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan.\n");
+ mothurOut("The default value for groups is all the groups in your groupfile.\n");
validCalculator->printCalc("shared", cout);
- cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
- cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups." << "\n";
- cout << "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile)." << "\n" << "\n";
+ mothurOut("The label and line parameters are used to analyze specific lines in your input.\n");
+ mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups.\n");
+ mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "CollectSharedCommand", "help");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the CollectSharedCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
CollectSharedCommand::~CollectSharedCommand(){
- delete order;
- delete input;
- delete cCurve;
- delete read;
- delete util;
- delete validCalculator;
+ if (abort == false) {
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ delete util;
+ delete validCalculator;
+ globaldata->gorder = NULL;
+ }
}
//**********************************************************************************************************************
input = globaldata->ginput;
order = input->getSharedOrderVector();
- SharedOrderVector* lastOrder = order;
+ string lastLabel = order->getLabel();
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
cCurve->getSharedCurve(freq);
delete cCurve;
- cout << order->getLabel() << '\t' << count << endl;
+ mothurOut(order->getLabel()); mothurOutEndLine();
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
userLines.erase(count);
-
- //you have a label the user want that is smaller than this line and the last line has not already been processed
}
- if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) {
+ //you have a label the user want that is smaller than this line and the last line has not already been processed
+ if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ delete order;
+ order = input->getSharedOrderVector(lastLabel);
+
//create collectors curve
- cCurve = new Collect(lastOrder, cDisplays);
+ cCurve = new Collect(order, cDisplays);
cCurve->getSharedCurve(freq);
delete cCurve;
- cout << lastOrder->getLabel() << '\t' << count << endl;
- processedLabels.insert(lastOrder->getLabel());
- userLabels.erase(lastOrder->getLabel());
+ mothurOut(order->getLabel()); mothurOutEndLine();
+ processedLabels.insert(order->getLabel());
+ userLabels.erase(order->getLabel());
}
- if (count != 1) { delete lastOrder; }
- lastOrder = order;
+
+ lastLabel = order->getLabel();
//get next line to process
+ delete order;
order = input->getSharedOrderVector();
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) {
- cCurve = new Collect(lastOrder, cDisplays);
+ delete order;
+ order = input->getSharedOrderVector(lastLabel);
+
+ cCurve = new Collect(order, cDisplays);
cCurve->getCurve(freq);
delete cCurve;
- cout << lastOrder->getLabel() << '\t' << count << endl;
+ mothurOut(order->getLabel()); mothurOutEndLine();
+ delete order;
}
- delete lastOrder;
for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
//reset groups parameter
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the CollectSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "CollectSharedCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the CollectSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/***********************************************************/
-
projects / mothur.git / blobdiff