#include "rabundvector.hpp"
#include "sabundvector.hpp"
+//**********************************************************************************************************************
+vector<string> PhylotypeCommand::getValidParameters(){
+ try {
+ string Array[] = {"taxonomy","cutoff","label","name","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhylotypeCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+PhylotypeCommand::PhylotypeCommand(){
+ try {
+ abort = true; calledHelp = true;
+ vector<string> tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ outputTypes["sabund"] = tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhylotypeCommand", "PhylotypeCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> PhylotypeCommand::getRequiredParameters(){
+ try {
+ string Array[] = {"taxonomy"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhylotypeCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> PhylotypeCommand::getRequiredFiles(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhylotypeCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
/**********************************************************************************************************************/
PhylotypeCommand::PhylotypeCommand(string option) {
try {
- abort = false;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["list"] = tempOutNames;
+ outputTypes["sabund"] = tempOutNames;
+ outputTypes["rabund"] = 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("taxonomy");
//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["taxonomy"] = 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(taxonomyFileName); //if user entered a file with a path then preserve it
+ outputDir += m->hasPath(taxonomyFileName); //if user entered a file with a path then preserve it
}
string temp = validParameter.validFile(parameters, "cutoff", false);
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; allLines = 1; }
else {
- if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
int PhylotypeCommand::execute(){
try {
- if (abort == true) { return 0; }
-
- vector<string> outputNames;
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
//reads in taxonomy file and makes all the taxonomies the same length
//by appending the last taxon to a given taxonomy as many times as needed to
if (m->control_pressed) { delete tree; return 0; }
- string fileroot = outputDir + getRootName(getSimpleName(taxonomyFileName));
+ string fileroot = outputDir + m->getRootName(m->getSimpleName(taxonomyFileName));
ofstream outList;
string outputListFile = fileroot + "tx.list";
- openOutputFile(outputListFile, outList);
+ m->openOutputFile(outputListFile, outList);
ofstream outSabund;
string outputSabundFile = fileroot + "tx.sabund";
- openOutputFile(outputSabundFile, outSabund);
+ m->openOutputFile(outputSabundFile, outSabund);
ofstream outRabund;
string outputRabundFile = fileroot + "tx.rabund";
- openOutputFile(outputRabundFile, outRabund);
+ m->openOutputFile(outputRabundFile, outRabund);
- outputNames.push_back(outputListFile);
- outputNames.push_back(outputSabundFile);
- outputNames.push_back(outputRabundFile);
+ outputNames.push_back(outputListFile); outputTypes["list"].push_back(outputListFile);
+ outputNames.push_back(outputSabundFile); outputTypes["sabund"].push_back(outputSabundFile);
+ outputNames.push_back(outputRabundFile); outputTypes["rabund"].push_back(outputRabundFile);
int count = 1;
//start at leaves of tree and work towards root, processing the labels the user wants
try {
ifstream in;
- openInputFile(namefile, in);
+ m->openInputFile(namefile, in);
string first, second;
map<string, string>::iterator itNames;
while(!in.eof()) {
- in >> first >> second; gobble(in);
+ in >> first >> second; m->gobble(in);
itNames = namemap.find(first);
if (itNames == namemap.end()) {