#include "getsharedotucommand.h"
-//**********************************************************************************************************************
+//**********************************************************************************************************************
+vector<string> GetSharedOTUCommand::getValidParameters(){
+ try {
+ string Array[] = {"label","unique","shared","fasta","list","group","output","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSharedOTUCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetSharedOTUCommand::GetSharedOTUCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ outputTypes["sharedseqs"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSharedOTUCommand", "GetSharedOTUCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetSharedOTUCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"list","group"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSharedOTUCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> GetSharedOTUCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetSharedOTUCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
GetSharedOTUCommand::GetSharedOTUCommand(string option) {
try {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["accnos"] = tempOutNames;
+ outputTypes["sharedseqs"] = 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 = ""; }
m->openInputFile(fastafile, inFasta);
while(!inFasta.eof()) {
- if (m->control_pressed) { inFasta.close(); delete groupMap; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); inFasta.close(); delete groupMap; return 0; }
Sequence seq(inFasta); m->gobble(inFasta);
if (seq.getName() != "") { seqs.push_back(seq); }
if (m->control_pressed) {
if (lastlist != NULL) { delete lastlist; }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
delete groupMap; return 0;
}
if (lastlist != NULL) { delete lastlist; }
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete groupMap; return 0; }
+ if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } delete groupMap; return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
}else {
m->mothurOut("\t" + toString(num)); m->mothurOutEndLine();
outputNames.push_back(outputFileNames);
+ if (output != "accnos") { outputTypes["sharedseqs"].push_back(outputFileNames); }
+ else { outputTypes["accnos"].push_back(outputFileNames); }
}
//if fasta file provided output new fasta file
string outputFileFasta = outputDir + m->getRootName(m->getSimpleName(fastafile)) + shared->getLabel() + userGroups + ".shared.fasta";
ofstream outFasta;
m->openOutputFile(outputFileFasta, outFasta);
- outputNames.push_back(outputFileFasta);
+ outputNames.push_back(outputFileFasta); outputTypes["fasta"].push_back(outputFileFasta);
for (int k = 0; k < seqs.size(); k++) {
if (m->control_pressed) { outFasta.close(); return 0; }