#include "readotucommand.h"
+
//**********************************************************************************************************************
-ReadOtuCommand::ReadOtuCommand(){
+ReadOtuCommand::ReadOtuCommand(){
try {
- globaldata = GlobalData::getInstance();
- filename = globaldata->inputFileName;
- read = new ReadPhilFile(filename);
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+ outputTypes["shared"] = tempOutNames;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function ReadOtuCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ReadOtuCommand class function ReadOtuCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ReadOtuCommand", "ReadOtuCommand");
exit(1);
}
}
-
//**********************************************************************************************************************
+ReadOtuCommand::ReadOtuCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
+ allLines = 1;
+
+ //allow user to run help
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
+
+ else {
+ /*
+ //valid paramters for this command
+ string Array[] = {"list","order","shared","relabund","label","group","sabund", "rabund","groups","ordergroup","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+
+ OptionParser parser(option);
+ map<string, string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+ map<string, string>::iterator it;
+
+ //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; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+ outputTypes["shared"] = tempOutNames;
+
+ globaldata->newRead();
+
+ //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 = ""; }
+ else {
+ string path;
+ it = parameters.find("list");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["list"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("order");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["order"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("shared");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["shared"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("group");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["group"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("sabund");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["sabund"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("rabund");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["rabund"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("ordergroup");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["ordergroup"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("relabund");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["relabund"] = inputDir + it->second; }
+ }
+ }
-ReadOtuCommand::~ReadOtuCommand(){
- delete read;
-}
+
+ //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 = ""; }
-//**********************************************************************************************************************
+ //check for required parameters
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not open") { abort = true; }
+ else if (listfile == "not found") { listfile = ""; }
+ else { globaldata->setListFile(listfile); globaldata->setFormat("list"); }
+
+ sabundfile = validParameter.validFile(parameters, "sabund", true);
+ if (sabundfile == "not open") { abort = true; }
+ else if (sabundfile == "not found") { sabundfile = ""; }
+ else { globaldata->setSabundFile(sabundfile); globaldata->setFormat("sabund"); }
+
+ rabundfile = validParameter.validFile(parameters, "rabund", true);
+ if (rabundfile == "not open") { abort = true; }
+ else if (rabundfile == "not found") { rabundfile = ""; }
+ else { globaldata->setRabundFile(rabundfile); globaldata->setFormat("rabund");}
+
+ ordergroupfile = validParameter.validFile(parameters, "ordergroup", true);
+ if (ordergroupfile == "not open") { abort = true; }
+ else if (ordergroupfile == "not found") { ordergroupfile = ""; }
+ else { globaldata->setOrderGroupFile(ordergroupfile); }
+
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { abort = true; }
+ else if (sharedfile == "not found") { sharedfile = ""; }
+ else { globaldata->setSharedFile(sharedfile); globaldata->setFormat("sharedfile"); }
+
+ relAbundfile = validParameter.validFile(parameters, "relabund", true);
+ if (relAbundfile == "not open") { abort = true; }
+ else if (relAbundfile == "not found") { relAbundfile = ""; }
+ else { globaldata->setRelAbundFile(relAbundfile); globaldata->setFormat("relabund"); }
+
+
+ groupfile = validParameter.validFile(parameters, "group", true);
+ if (groupfile == "not open") { abort = true; }
+ else if (groupfile == "not found") { groupfile = ""; }
+ else {
+ globaldata->setGroupFile(groupfile);
+ groupMap = new GroupMap(groupfile);
+
+ int error = groupMap->readMap();
+ if (error == 1) { abort = true; }
+
+ globaldata->gGroupmap = groupMap;
+ }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ m->splitAtDash(groups, Groups);
+ globaldata->Groups = Groups;
+ }
+
+ //you are doing a list and group shared
+ if ((listfile != "") && (groupfile != "")) { globaldata->setFormat("shared"); }
+
+ //you have not given a file
+ if ((listfile == "") && (sharedfile == "") && (rabundfile == "") && (sabundfile == "") && (relAbundfile == "")) {
+ m->mothurOut("You must enter either a listfile, rabundfile, sabundfile, relabund or a sharedfile with the read.otu command. "); m->mothurOutEndLine(); abort = true;
+ }
+
+ //check for optional parameter and set defaults
+ // ...at some point should added some additional type checking...
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; }
+ else {
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
+ else { allLines = 1; }
+ globaldata->labels = labels;
+ }
+
+ globaldata->allLines = allLines;
+
+ orderfile = validParameter.validFile(parameters, "order", true);
+ if (orderfile == "not open") { abort = true; }
+ else if (orderfile == "not found") { orderfile = ""; }
+ else { globaldata->setOrderFile(orderfile); }
+
+
+ if (abort == false) {
+ //gets whichever one of the above is set
+ filename = globaldata->inputFileName;
+ }
+ */
+ }
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ReadOtuCommand", "ReadOtuCommand");
+ exit(1);
+ }
+}
+///**********************************************************************************************************************
int ReadOtuCommand::execute(){
try {
- read->read(&*globaldata);
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+ m->mothurOut(getHelpString()); m->mothurOutEndLine();
+
+ /*
+ if (globaldata->getFormat() == "shared") {
+
+ shared = new SharedCommand(outputDir);
+ int okay = shared->execute();
+
+ //problem with shared
+ if (okay == 1) {
+ globaldata->setListFile("");
+ globaldata->setGroupFile("");
+ globaldata->setSharedFile("");
+ }else { //shared command outputs the filenames
+ //m->mothurOutEndLine();
+ //m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ //m->mothurOut(globaldata->getSharedFile()); m->mothurOutEndLine();
+ //m->mothurOutEndLine();
+ }
+
+ outputTypes = shared->getOutputFiles();
+
+ //set rabund file as new current rabundfile
+ string current = "";
+ itTypes = outputTypes.find("rabund");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRabundFile(current); }
+ }
+
+ itTypes = outputTypes.find("shared");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
+ }
+
+ delete shared;
+ }
+ */
+
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the ReadOtuCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the ReadOtuCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "ReadOtuCommand", "execute");
exit(1);
}
}
-//**********************************************************************************************************************
\ No newline at end of file
+//**********************************************************************************************************************
projects / mothur.git / blobdiff