#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;
- lines.clear();
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[] = {"line","label"};
+ string Array[] = {"label","outputdir","inputdir"};
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; }
}
+ //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() == "")) { cout << "You must read a list or rabund before you can use the get.sabund command." << endl; 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...
- 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; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
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;
}
- delete validParameter;
-
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) {
- cout << "Standard Error: " << e.what() << " has occurred in the GetSAbundCommand class Function GetSAbundCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->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";
+ 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) {
- cout << "Standard Error: " << e.what() << " has occurred in the GetSAbundCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->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);
- }
}
//**********************************************************************************************************************
int GetSAbundCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
- int count = 1;
-
//using order vector so you don't have to distinguish between the list and rabund files
read = new ReadOTUFile(globaldata->inputFileName);
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.
set<string> processedLabels;
set<string> userLabels = labels;
- set<int> userLines = lines;
+
+ 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) || (userLines.size() != 0))) {
+ while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if(allLines == 1 || lines.count(count) == 1 || labels.count(order->getLabel()) == 1){
- cout << order->getLabel() << '\t' << count << endl;
+ if(allLines == 1 || labels.count(order->getLabel()) == 1){
+ 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());
- userLines.erase(count);
}
- if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastOrder->getLabel()) != 1)) {
- cout << lastOrder->getLabel() << '\t' << count << endl;
+ if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = order->getLabel();
+
+ delete order;
+ order = (input->getOrderVector(lastLabel));
+
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
sabund = new SAbundVector();
- *sabund = (lastOrder->getSAbundVector());
+ *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(lastOrder->getLabel());
- userLabels.erase(lastOrder->getLabel());
+ processedLabels.insert(order->getLabel());
+ userLabels.erase(order->getLabel());
+
+ //restore real lastlabel to save below
+ order->setLabel(saveLabel);
}
- if (count != 1) { delete lastOrder; }
- lastOrder = order;
-
+
+ lastLabel = order->getLabel();
+
+ delete order;
order = (input->getOrderVector());
- 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;
- if (processedLabels.count(lastOrder->getLabel()) != 1) {
- cout << ". I will use " << lastOrder->getLabel() << "." << endl;
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
- cout << ". Please refer to " << lastOrder->getLabel() << "." << endl;
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
- //run last line if you need to
+ //run last label if you need to
if (needToRun == true) {
- cout << lastOrder->getLabel() << '\t' << count << endl;
+ if (order != NULL) { delete order; }
+ order = (input->getOrderVector(lastLabel));
+
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
sabund = new SAbundVector();
- *sabund = (lastOrder->getSAbundVector());
+ *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;
}
- delete lastOrder;
+ 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) {
- cout << "Standard Error: " << e.what() << " has occurred in the GetSAbundCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->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