#include "getsabundcommand.h"
//**********************************************************************************************************************
-
-GetSAbundCommand::GetSAbundCommand(string option){
+vector<string> GetSAbundCommand::getValidParameters(){
+ try {
+ string Array[] = {"label","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSAbundCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetSAbundCommand::GetSAbundCommand(){
+ try {
+ abort = true; calledHelp = true;
+ vector<string> tempOutNames;
+ outputTypes["sabund"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSAbundCommand", "GetSAbundCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetSAbundCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSAbundCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetSAbundCommand::getRequiredFiles(){
+ try {
+ string Array[] = {"list","rabund"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSAbundCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetSAbundCommand::GetSAbundCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
//valid paramters for this command
- string Array[] = {"label"};
+ string Array[] = {"label","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["sabund"] = tempOutNames;
+
+ //if the user changes the output directory command factory will send this info to us in the output parameter
+ string outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
+ outputDir = "";
+ outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
+ }
+
//make sure the user has already run the read.otu command
- if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "")) { mothurOut("You must read a list or rabund before you can use the get.sabund command."); mothurOutEndLine(); abort = true; }
+ if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "")) { m->mothurOut("You must read a list or rabund before you can use the get.sabund command."); m->mothurOutEndLine(); abort = true; }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
- if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
}
if (abort == false) {
- filename = getRootName(globaldata->inputFileName) + "sabund";
- openOutputFile(filename, out);
+ filename = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "sabund";
+ m->openOutputFile(filename, out);
}
}
}
catch(exception& e) {
- errorOut(e, "GetSAbundCommand", "GetSAbundCommand");
+ m->errorOut(e, "GetSAbundCommand", "GetSAbundCommand");
exit(1);
}
}
void GetSAbundCommand::help(){
try {
- 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 is label. No parameters are required.\n");
- mothurOut("The label parameter allows 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(label=yourLabels).\n");
- mothurOut("Example get.sabund().\n");
- mothurOut("The default value for label is all labels in your inputfile.\n");
- mothurOut("The get.sabund command outputs a .sabund file containing the labels you selected.\n");
- mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n");
+ m->mothurOut("The get.sabund command can only be executed after a successful read.otu of a listfile or rabundfile.\n");
+ m->mothurOut("The get.sabund command parameters is label. No parameters are required.\n");
+ m->mothurOut("The label parameter allows you to select what distance levels you would like included in your .sabund file, and are separated by dashes.\n");
+ m->mothurOut("The get.sabund command should be in the following format: get.sabund(label=yourLabels).\n");
+ m->mothurOut("Example get.sabund().\n");
+ m->mothurOut("The default value for label is all labels in your inputfile.\n");
+ m->mothurOut("The get.sabund command outputs a .sabund file containing the labels you selected.\n");
+ m->mothurOut("Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabel).\n\n");
}
catch(exception& e) {
- errorOut(e, "GetSAbundCommand", "help");
+ m->errorOut(e, "GetSAbundCommand", "help");
exit(1);
}
}
int GetSAbundCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//using order vector so you don't have to distinguish between the list and rabund files
read = new ReadOTUFile(globaldata->inputFileName);
set<string> processedLabels;
set<string> userLabels = labels;
+ if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; }
+
+
while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if(allLines == 1 || labels.count(order->getLabel()) == 1){
- mothurOut(order->getLabel()); mothurOutEndLine();
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
sabund = new SAbundVector();
*sabund = (order->getSAbundVector());
sabund->print(out);
delete sabund;
+
+ if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; }
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
}
- if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = order->getLabel();
+
delete order;
order = (input->getOrderVector(lastLabel));
- mothurOut(order->getLabel()); mothurOutEndLine();
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
sabund = new SAbundVector();
*sabund = (order->getSAbundVector());
sabund->print(out);
delete sabund;
+
+ if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; }
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
+
+ //restore real lastlabel to save below
+ order->setLabel(saveLabel);
}
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
- mothurOut("Your file does not include the label " + *it);
+ m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
- mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
- mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
if (order != NULL) { delete order; }
order = (input->getOrderVector(lastLabel));
- mothurOut(order->getLabel()); mothurOutEndLine();
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
sabund = new SAbundVector();
*sabund = (order->getSAbundVector());
sabund->print(out);
delete sabund;
+
+ if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete order; globaldata->gorder = NULL; return 0; }
+
delete order;
}
globaldata->gorder = NULL;
out.close();
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut(filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["sabund"].push_back(filename);
+ m->mothurOutEndLine();
+
return 0;
}
catch(exception& e) {
- errorOut(e, "GetSAbundCommand", "execute");
+ m->errorOut(e, "GetSAbundCommand", "execute");
exit(1);
}
}
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