#include "getrabundcommand.h"
//**********************************************************************************************************************
+vector<string> GetRAbundCommand::setParameters(){
+ try {
+ CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
+ CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
+ CommandParameter psorted("sorted", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(psorted);
+ 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, "GetRAbundCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string GetRAbundCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The get.rabund command parameters are list, sabund, label and sorted. list or sabund parameters are required, unless you have valid current files.\n";
+ helpString += "The label parameter allows you to select what distance levels you would like included in your .rabund file, and are separated by dashes.\n";
+ helpString += "The sorted parameters allows you to print the rabund results sorted by abundance or not. The default is sorted.\n";
+ helpString += "The get.rabund command should be in the following format: get.rabund(label=yourLabels, sorted=yourSorted).\n";
+ helpString += "Example get.rabund(sorted=F).\n";
+ helpString += "The default value for label is all labels in your inputfile.\n";
+ helpString += "The get.rabund command outputs a .rabund file containing the lines you selected.\n";
+ helpString += "Note: No spaces between parameter labels (i.e. label), '=' and parameters (i.e.yourLabels).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRAbundCommand", "getHelpString");
+ exit(1);
+ }
+}
-GetRAbundCommand::GetRAbundCommand(string option){
+//**********************************************************************************************************************
+GetRAbundCommand::GetRAbundCommand(){
try {
- globaldata = GlobalData::getInstance();
- abort = false;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["rabund"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GetRAbundCommand", "GetRAbundCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+GetRAbundCommand::GetRAbundCommand(string option) {
+ try {
+ abort = false; calledHelp = false;
allLines = 1;
- lines.clear();
- labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ 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[] = {"line","label","sorted"};
- vector<string> myArray (Array, Array+(sizeof(Array)/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; }
}
- //make sure the user has already run the read.otu command
- if (globaldata->getListFile() == "") { mothurOut("You must read a listfile before you can use the get.rabund command."); mothurOutEndLine(); abort = true; }
+ //initialize outputTypes
+ vector<string> 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 = ""; }
+ 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("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; }
+ }
+ }
+
+
+ //check for required parameters
+ listfile = validParameter.validFile(parameters, "list", true);
+ if (listfile == "not open") { listfile = ""; abort = true; }
+ else if (listfile == "not found") { listfile = ""; }
+ else { format = "list"; inputfile = listfile; m->setListFile(listfile); }
+
+ sabundfile = validParameter.validFile(parameters, "sabund", true);
+ if (sabundfile == "not open") { sabundfile = ""; abort = true; }
+ else if (sabundfile == "not found") { sabundfile = ""; }
+ else { format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
+
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
-
string temp;
temp = validParameter.validFile(parameters, "sorted", false); if (temp == "not found") { temp = "T"; }
- sorted = isTrue(temp);
-
- line = validParameter.validFile(parameters, "line", false);
- if (line == "not found") { line = ""; }
- else {
- if(line != "all") { splitAtDash(line, lines); allLines = 0; }
- else { allLines = 1; }
- }
+ sorted = m->isTrue(temp);
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
- if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
- //make sure user did not use both the line and label parameters
- if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; }
- //if the user has not specified any line or labels use the ones from read.otu
- else if((line == "") && (label == "")) {
- allLines = globaldata->allLines;
- labels = globaldata->labels;
- lines = globaldata->lines;
- }
-
- if (abort == false) {
- filename = getRootName(globaldata->inputFileName) + "rabund";
- openOutputFile(filename, out);
+ if ((listfile == "") && (sabundfile == "")) {
+ //is there are current file available for any of these?
+ //give priority to shared, then list, then rabund, then sabund
+ //if there is a current shared file, use it
+ listfile = m->getListFile();
+ if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
+ else {
+ sabundfile = m->getSabundFile();
+ if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current files. You must provide a list or sabund file."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
}
+
+
+ //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(inputfile); }
+
}
+
}
catch(exception& e) {
- errorOut(e, "GetRAbundCommand", "GetRAbundCommand");
+ m->errorOut(e, "GetRAbundCommand", "GetRAbundCommand");
exit(1);
}
}
//**********************************************************************************************************************
-void GetRAbundCommand::help(){
- try {
- mothurOut("The get.rabund command can only be executed after a successful read.otu of a listfile.\n");
- mothurOut("The get.rabund command parameters are line, label and sorted. No parameters are required, and you may not use line and label at the same time.\n");
- mothurOut("The line and label allow you to select what distance levels you would like included in your .rabund file, and are separated by dashes.\n");
- mothurOut("The sorted parameters allows you to print the rabund results sorted by abundance or not. The default is sorted.\n");
- mothurOut("The get.rabund command should be in the following format: get.rabund(line=yourLines, label=yourLabels, sorted=yourSorted).\n");
- mothurOut("Example get.rabund(line=1-3-5, sorted=F).\n");
- mothurOut("The default value for line and label are all lines in your inputfile.\n");
- mothurOut("The get.rabund command outputs a .rabund file containing the lines you selected.\n");
- mothurOut("Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines).\n\n");
- }
- catch(exception& e) {
- errorOut(e, "GetRAbundCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-GetRAbundCommand::~GetRAbundCommand(){
- if (abort == false) { globaldata->gListVector = NULL; }
-}
-
-//**********************************************************************************************************************
-
int GetRAbundCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
- int count = 1;
+ filename = outputDir + m->getRootName(m->getSimpleName(inputfile)) + "rabund";
+ m->openOutputFile(filename, out);
- //read first line
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
- input = globaldata->ginput;
- list = globaldata->gListVector;
- string lastLabel = list->getLabel();
+ input = new InputData(inputfile, format);
+ rabund = input->getRAbundVector();
+ string lastLabel = rabund->getLabel();
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
set<string> userLabels = labels;
- set<int> userLines = lines;
-
- while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+ if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete rabund; delete input; return 0; }
+
+ while((rabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if(allLines == 1 || lines.count(count) == 1 || labels.count(list->getLabel()) == 1){
- mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine();
- rabund = new RAbundVector();
- *rabund = (list->getRAbundVector());
+ if(allLines == 1 || labels.count(rabund->getLabel()) == 1){
+ m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
+
+ if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete input; delete rabund; return 0; }
if(sorted) { rabund->print(out); }
else { rabund->nonSortedPrint(out); }
-
- delete rabund;
- processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
- userLines.erase(count);
+ processedLabels.insert(rabund->getLabel());
+ userLabels.erase(rabund->getLabel());
}
- if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- delete list;
- list = input->getListVector(lastLabel);
+ if ((m->anyLabelsToProcess(rabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = rabund->getLabel();
- mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine();
- rabund = new RAbundVector();
- *rabund = (list->getRAbundVector());
+ delete rabund;
+ rabund = input->getRAbundVector(lastLabel);
+
+ m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
+
+ if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete input; delete rabund; return 0; }
if(sorted) { rabund->print(out); }
else { rabund->nonSortedPrint(out); }
- delete rabund;
-
- processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
+ processedLabels.insert(rabund->getLabel());
+ userLabels.erase(rabund->getLabel());
+
+ //restore real lastlabel to save below
+ rabund->setLabel(saveLabel);
}
- lastLabel = list->getLabel();
+ lastLabel = rabund->getLabel();
- delete list;
- list = input->getListVector();
- count++;
+ delete rabund;
+ rabund = input->getRAbundVector();
}
//output error messages about any remaining user labels
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
- mothurOut("Your file does not include the label " + *it);
+ m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
- mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
- mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
- //run last line if you need to
+ //run last label if you need to
if (needToRun == true) {
- delete list;
- list = input->getListVector(lastLabel);
+ if (rabund != NULL) { delete rabund; }
+ rabund = input->getRAbundVector(lastLabel);
- mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine();
- rabund = new RAbundVector();
- *rabund = (list->getRAbundVector());
+ m->mothurOut(rabund->getLabel()); m->mothurOutEndLine();
+
+ if (m->control_pressed) { outputTypes.clear(); out.close(); remove(filename.c_str()); delete input; delete rabund; return 0; }
if(sorted) { rabund->print(out); }
else { rabund->nonSortedPrint(out); }
delete rabund;
- delete list;
}
-
+
+ m->mothurOutEndLine();
+ m->mothurOut("Output File Name: "); m->mothurOutEndLine();
+ m->mothurOut(filename); m->mothurOutEndLine(); outputNames.push_back(filename); outputTypes["rabund"].push_back(filename);
+ m->mothurOutEndLine();
+
out.close();
+
+ //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); }
+ }
+
return 0;
}
catch(exception& e) {
- errorOut(e, "GetRAbundCommand", "execute");
+ m->errorOut(e, "GetRAbundCommand", "execute");
exit(1);
}
}
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