#include "getrelabundcommand.h"
//**********************************************************************************************************************
-vector<string> GetRelAbundCommand::getValidParameters(){
+vector<string> GetRelAbundCommand::setParameters(){
try {
- string Array[] = {"groups","label","scale","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none","relabund",false,true, true); parameters.push_back(pshared);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter pscale("scale", "Multiple", "totalgroup-totalotu-averagegroup-averageotu", "totalgroup", "", "", "","",false,false); parameters.push_back(pscale);
+ CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
+
+ vector<string> myArray;
+ for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
- m->errorOut(e, "GetRelAbundCommand", "getValidParameters");
+ m->errorOut(e, "GetRelAbundCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-GetRelAbundCommand::GetRelAbundCommand(){
+string GetRelAbundCommand::getHelpString(){
try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["relabund"] = tempOutNames;
+ string helpString = "";
+ helpString += "The get.relabund command parameters are shared, groups, scale and label. shared is required, unless you have a valid current file.\n";
+ helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.\n";
+ helpString += "The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n";
+ helpString += "The scale parameter allows you to select what scale you would like to use. Choices are totalgroup, totalotu, averagegroup, averageotu, default is totalgroup.\n";
+ helpString += "The get.relabund command should be in the following format: get.relabund(groups=yourGroups, label=yourLabels).\n";
+ helpString += "Example get.relabund(groups=A-B-C, scale=averagegroup).\n";
+ helpString += "The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n";
+ helpString += "The get.relabund command outputs a .relabund file.\n";
+ helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "GetRelAbundCommand", "GetRelAbundCommand");
+ m->errorOut(e, "GetRelAbundCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> GetRelAbundCommand::getRequiredParameters(){
- try {
- vector<string> myArray;
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "GetRelAbundCommand", "getRequiredParameters");
- exit(1);
- }
+string GetRelAbundCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "relabund") { pattern = "[filename],relabund"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRelAbundCommand", "getOutputPattern");
+ exit(1);
+ }
}
//**********************************************************************************************************************
-vector<string> GetRelAbundCommand::getRequiredFiles(){
+GetRelAbundCommand::GetRelAbundCommand(){
try {
- string Array[] = {"shared"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["relabund"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "GetRelAbundCommand", "getRequiredFiles");
+ m->errorOut(e, "GetRelAbundCommand", "GetRelAbundCommand");
exit(1);
}
}
//**********************************************************************************************************************
GetRelAbundCommand::GetRelAbundCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
abort = false; calledHelp = false;
allLines = 1;
- labels.clear();
-
+
//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 AlignArray[] = {"groups","label","scale","outputdir","inputdir"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
+ map<string,string>::iterator it;
ValidParameters validParameter;
//check to make sure all parameters are valid for command
- for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ 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["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 += 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
- if ((globaldata->getSharedFile() == "")) {
- m->mothurOut("You must read a list and a group, or a shared file before you can use the get.relabund command."); m->mothurOutEndLine(); abort = true;
+ //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("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; }
+ }
}
+
+ //get shared file
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { sharedfile = ""; abort = true; }
+ else if (sharedfile == "not found") {
+ //if there is a current shared file, use it
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
+ }else { m->setSharedFile(sharedfile); }
+
+
+ //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->hasPath(sharedfile); }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
else { allLines = 1; }
}
- //if the user has not specified any labels use the ones from read.otu
- if (label == "") {
- allLines = globaldata->allLines;
- labels = globaldata->labels;
- }
-
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; pickedGroups = false; }
else {
pickedGroups = true;
m->splitAtDash(groups, Groups);
- globaldata->Groups = Groups;
+ m->setGroups(Groups);
}
scale = validParameter.validFile(parameters, "scale", false); if (scale == "not found") { scale = "totalgroup"; }
exit(1);
}
}
-
-//**********************************************************************************************************************
-
-void GetRelAbundCommand::help(){
- try {
- m->mothurOut("The get.relabund command can only be executed after a successful read.otu command of a list and group or shared file.\n");
- m->mothurOut("The get.relabund command parameters are groups, scale and label. No parameters are required.\n");
- m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included. The group names are separated by dashes.\n");
- m->mothurOut("The label parameter allows you to select what distance levels you would like, and are also separated by dashes.\n");
- m->mothurOut("The scale parameter allows you to select what scale you would like to use. Choices are totalgroup, totalotu, averagegroup, averageotu, default is totalgroup.\n");
- m->mothurOut("The get.relabund command should be in the following format: get.relabund(groups=yourGroups, label=yourLabels).\n");
- m->mothurOut("Example get.relabund(groups=A-B-C, scale=averagegroup).\n");
- m->mothurOut("The default value for groups is all the groups in your groupfile, and all labels in your inputfile will be used.\n");
- m->mothurOut("The get.relabund command outputs a .relabund file.\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
-
- }
- catch(exception& e) {
- m->errorOut(e, "GetRelAbundCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-GetRelAbundCommand::~GetRelAbundCommand(){
-}
-
//**********************************************************************************************************************
int GetRelAbundCommand::execute(){
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- string outputFileName = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "relabund";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+ string outputFileName = getOutputFileName("relabund", variables);
ofstream out;
m->openOutputFile(outputFileName, out);
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
- input = globaldata->ginput;
+ input = new InputData(sharedfile, "sharedfile");
lookup = input->getSharedRAbundVectors();
string lastLabel = lookup[0]->getLabel();
//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) { 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 (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } m->clearGroups(); delete input; out.close(); m->mothurRemove(outputFileName); return 0; }
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
getRelAbundance(lookup, out);
processedLabels.insert(lookup[0]->getLabel());
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-
+ if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
getRelAbundance(lookup, out);
processedLabels.insert(lookup[0]->getLabel());
//prevent memory leak
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; lookup[i] = NULL; }
- if (m->control_pressed) { outputTypes.clear(); globaldata->Groups.clear(); delete read; out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); m->clearGroups(); delete input; out.close(); m->mothurRemove(outputFileName); return 0; }
//get next line to process
lookup = input->getSharedRAbundVectors();
}
- if (m->control_pressed) { outputTypes.clear(); globaldata->Groups.clear(); delete read; out.close(); remove(outputFileName.c_str()); return 0; }
+ if (m->control_pressed) { outputTypes.clear(); m->clearGroups(); delete input; out.close(); m->mothurRemove(outputFileName); return 0; }
//output error messages about any remaining user labels
set<string>::iterator it;
lookup = input->getSharedRAbundVectors(lastLabel);
m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
-
+ if (!m->printedHeaders) { lookup[0]->printHeaders(out); }
getRelAbundance(lookup, out);
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
//reset groups parameter
- globaldata->Groups.clear();
- delete input; globaldata->ginput = NULL;
- delete read;
+ m->clearGroups();
+ delete input;
out.close();
- if (m->control_pressed) { outputTypes.clear(); remove(outputFileName.c_str()); return 0;}
+ if (m->control_pressed) { outputTypes.clear(); m->mothurRemove(outputFileName); return 0;}
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
m->mothurOut(outputFileName); m->mothurOutEndLine(); outputNames.push_back(outputFileName); outputTypes["relabund"].push_back(outputFileName);
m->mothurOutEndLine();
+ //set relabund file as new current relabundfile
+ string current = "";
+ itTypes = outputTypes.find("relabund");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setRelAbundFile(current); }
+ }
+
return 0;
}
catch(exception& e) {
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