#include "getrelabundcommand.h"
//**********************************************************************************************************************
-
+vector<string> GetRelAbundCommand::getValidParameters(){
+ try {
+ string Array[] = {"groups","label","scale","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRelAbundCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetRelAbundCommand::GetRelAbundCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["relabund"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRelAbundCommand", "GetRelAbundCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetRelAbundCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRelAbundCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetRelAbundCommand::getRequiredFiles(){
+ try {
+ string Array[] = {"shared"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRelAbundCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
GetRelAbundCommand::GetRelAbundCommand(string option) {
try {
globaldata = GlobalData::getInstance();
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["relabund"] = tempOutNames;
+
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
outputDir = "";
- outputDir += hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
+ 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
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 (groups == "not found") { groups = ""; pickedGroups = false; }
else {
pickedGroups = true;
- splitAtDash(groups, Groups);
+ m->splitAtDash(groups, Groups);
globaldata->Groups = Groups;
}
if (abort == true) { return 0; }
- string outputFileName = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + "relabund";
+ string outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "relabund";
ofstream out;
- openOutputFile(outputFileName, out);
+ m->openOutputFile(outputFileName, out);
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
read = new ReadOTUFile(globaldata->inputFileName);
//as long as you are not at the end of the file or done wih the lines you want
while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } globaldata->Groups.clear(); delete read; out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } globaldata->Groups.clear(); delete read; out.close(); remove(outputFileName.c_str()); return 0; }
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
userLabels.erase(lookup[0]->getLabel());
}
- if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = lookup[0]->getLabel();
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
//prevent memory leak
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
- if (m->control_pressed) { globaldata->Groups.clear(); delete read; out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); globaldata->Groups.clear(); delete read; out.close(); remove(outputFileName.c_str()); return 0; }
//get next line to process
lookup = input->getSharedRAbundVectors();
}
- if (m->control_pressed) { globaldata->Groups.clear(); delete read; out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); globaldata->Groups.clear(); delete read; out.close(); remove(outputFileName.c_str()); return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
delete read;
out.close();
- if (m->control_pressed) { remove(outputFileName.c_str()); return 0;}
+ if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0;}
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- m->mothurOut(outputFileName); m->mothurOutEndLine();
+ m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["relabund"].push_back(outputFileName);
m->mothurOutEndLine();
return 0;