#include "deconvolutecommand.h"
+//**********************************************************************************************************************
+vector<string> DeconvoluteCommand::getValidParameters(){
+ try {
+ string Array[] = {"fasta", "name","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeconvoluteCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+DeconvoluteCommand::DeconvoluteCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeconvoluteCommand", "DeconvoluteCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> DeconvoluteCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"fasta"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeconvoluteCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> DeconvoluteCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "DeconvoluteCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
/**************************************************************************************/
DeconvoluteCommand::DeconvoluteCommand(string option) {
try {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["fasta"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
+
//if the user changes the input directory command factory will send this info to us in the output parameter
string inputDir = validParameter.validFile(parameters, "inputdir", false);
if (inputDir == "not found"){ inputDir = ""; }
it = parameters.find("fasta");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["fasta"] = inputDir + it->second; }
}
it = parameters.find("name");
//user has given a template file
if(it != parameters.end()){
- path = hasPath(it->second);
+ path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["name"] = inputDir + it->second; }
}
//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(inFastaName); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(inFastaName); //if user entered a file with a path then preserve it
}
oldNameMapFName = validParameter.validFile(parameters, "name", true);
if (abort == true) { return 0; }
//prepare filenames and open files
- string outNameFile = outputDir + getRootName(getSimpleName(inFastaName)) + "names";
- string outFastaFile = outputDir + getRootName(getSimpleName(inFastaName)) + "unique" + getExtension(inFastaName);
+ string outNameFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "names";
+ string outFastaFile = outputDir + m->getRootName(m->getSimpleName(inFastaName)) + "unique" + m->getExtension(inFastaName);
FastaMap fastamap;
if(oldNameMapFName == "") { fastamap.readFastaFile(inFastaName); }
else { fastamap.readFastaFile(inFastaName, oldNameMapFName); }
+ if (m->control_pressed) { return 0; }
+
fastamap.printCondensedFasta(outFastaFile);
fastamap.printNamesFile(outNameFile);
+ if (m->control_pressed) { outputTypes.clear(); remove(outFastaFile.c_str()); remove(outNameFile.c_str()); return 0; }
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(outFastaFile); m->mothurOutEndLine();
m->mothurOut(outNameFile); m->mothurOutEndLine();
+ outputNames.push_back(outFastaFile); outputNames.push_back(outNameFile); outputTypes["fasta"].push_back(outFastaFile); outputTypes["name"].push_back(outNameFile);
m->mothurOutEndLine();