#include "sharednseqs.h"
//**********************************************************************************************************************
-vector<string> RareFactSharedCommand::getValidParameters(){
+vector<string> RareFactSharedCommand::setParameters(){
try {
- string Array[] = {"iters","freq","label","calc","groups", "jumble","outputdir","inputdir"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
+ CommandParameter pcalc("calc", "Multiple", "sharednseqs-sharedobserved", "sharedobserved", "", "", "",true,false); parameters.push_back(pcalc);
+ CommandParameter pjumble("jumble", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pjumble);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ 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, "RareFactSharedCommand", "getValidParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-RareFactSharedCommand::RareFactSharedCommand(){
- try {
- abort = true; calledHelp = true;
- vector<string> tempOutNames;
- outputTypes["sharedrarefaction"] = tempOutNames;
- outputTypes["sharedr_nseqs"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand");
+ m->errorOut(e, "RareFactSharedCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
-vector<string> RareFactSharedCommand::getRequiredParameters(){
+string RareFactSharedCommand::getHelpString(){
try {
- vector<string> myArray;
- return myArray;
+ string helpString = "";
+ ValidCalculators validCalculator;
+ helpString += "The collect.shared command parameters are shared, label, freq, calc and groups. shared is required if there is no current sharedfile. \n";
+ helpString += "The rarefaction.shared command parameters are shared, label, iters, groups, jumble and calc. shared is required if there is no current sharedfile. \n";
+ helpString += "The rarefaction command should be in the following format: \n";
+ helpString += "rarefaction.shared(label=yourLabel, iters=yourIters, calc=yourEstimators, jumble=yourJumble, groups=yourGroups).\n";
+ helpString += "The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n";
+ helpString += "Example rarefaction.shared(label=unique-0.01-0.03, iters=10000, groups=B-C, jumble=T, calc=sharedobserved).\n";
+ helpString += "The default values for iters is 1000, freq is 100, and calc is sharedobserved which calculates the shared rarefaction curve for the observed richness.\n";
+ helpString += "The default value for groups is all the groups in your groupfile, and jumble is true.\n";
+ helpString += validCalculator.printCalc("sharedrarefaction");
+ helpString += "The label parameter is used to analyze specific labels in your input.\n";
+ helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups.\n";
+ helpString += "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n";
+ return helpString;
}
catch(exception& e) {
- m->errorOut(e, "RareFactSharedCommand", "getRequiredParameters");
+ m->errorOut(e, "RareFactSharedCommand", "getHelpString");
exit(1);
}
}
+
//**********************************************************************************************************************
-vector<string> RareFactSharedCommand::getRequiredFiles(){
+RareFactSharedCommand::RareFactSharedCommand(){
try {
- string Array[] = {"shared"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- return myArray;
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["sharedrarefaction"] = tempOutNames;
+ outputTypes["sharedr_nseqs"] = tempOutNames;
}
catch(exception& e) {
- m->errorOut(e, "RareFactSharedCommand", "getRequiredFiles");
+ m->errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand");
exit(1);
}
}
RareFactSharedCommand::RareFactSharedCommand(string option) {
try {
- globaldata = GlobalData::getInstance();
-
abort = false; calledHelp = false;
allLines = 1;
- labels.clear();
- Estimators.clear();
- Groups.clear();
//allow user to run help
- if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; calledHelp = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
else {
- //valid paramters for this command
- string Array[] = {"iters","freq","label","calc","groups", "jumble","outputdir","inputdir"};
- 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; }
}
outputTypes["sharedrarefaction"] = tempOutNames;
outputTypes["sharedr_nseqs"] = tempOutNames;
- //make sure the user has already run the read.otu command
- if (globaldata->getSharedFile() == "") {
- if (globaldata->getListFile() == "") { m->mothurOut("You must read a list and a group, or a shared before you can use the collect.shared command."); m->mothurOutEndLine(); abort = true; }
- else if (globaldata->getGroupFile() == "") { m->mothurOut("You must read a list and a group, or a shared before you can use the collect.shared 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; }
+ }
}
- //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
+ //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; }
}
-
+
+
+ //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;
- }
calc = validParameter.validFile(parameters, "calc", false);
if (calc == "not found") { calc = "sharedobserved"; }
else {
m->splitAtDash(groups, Groups);
}
- globaldata->Groups = Groups;
+ m->Groups = Groups;
string temp;
temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
temp = validParameter.validFile(parameters, "jumble", false); if (temp == "not found") { temp = "T"; }
if (m->isTrue(temp)) { jumble = true; }
else { jumble = false; }
- globaldata->jumble = jumble;
-
- if (abort == false) {
-
- string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName));
-// format = globaldata->getFormat();
-
-
- validCalculator = new ValidCalculators();
-
- for (int i=0; i<Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("sharedrarefaction", Estimators[i]) == true) {
- if (Estimators[i] == "sharedobserved") {
- rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
- outputNames.push_back(fileNameRoot+"shared.rarefaction"); outputTypes["sharedrarefaction"].push_back(fileNameRoot+"shared.rarefaction");
- }else if (Estimators[i] == "sharednseqs") {
- rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.r_nseqs", "")));
- outputNames.push_back(fileNameRoot+"shared.r_nseqs"); outputTypes["sharedr_nseqs"].push_back(fileNameRoot+"shared.r_nseqs");
- }
- }
- }
- }
+ m->jumble = jumble;
}
exit(1);
}
}
-
-//**********************************************************************************************************************
-
-void RareFactSharedCommand::help(){
- try {
- m->mothurOut("The rarefaction.shared command can only be executed after a successful read.otu command.\n");
- m->mothurOut("The rarefaction.shared command parameters are label, iters, groups, jumble and calc. No parameters are required.\n");
- m->mothurOut("The rarefaction command should be in the following format: \n");
- m->mothurOut("rarefaction.shared(label=yourLabel, iters=yourIters, calc=yourEstimators, jumble=yourJumble, groups=yourGroups).\n");
- m->mothurOut("The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n");
- m->mothurOut("Example rarefaction.shared(label=unique-0.01-0.03, iters=10000, groups=B-C, jumble=T, calc=sharedobserved).\n");
- m->mothurOut("The default values for iters is 1000, freq is 100, and calc is sharedobserved which calculates the shared rarefaction curve for the observed richness.\n");
- m->mothurOut("The default value for groups is all the groups in your groupfile, and jumble is true.\n");
- validCalculator->printCalc("sharedrarefaction", cout);
- m->mothurOut("The label parameter is used to analyze specific labels in your input.\n");
- m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups.\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "RareFactSharedCommand", "help");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-
-RareFactSharedCommand::~RareFactSharedCommand(){
- if (abort == false) {
- delete input; globaldata->ginput = NULL;
- delete read;
- delete validCalculator;
- }
-}
-
//**********************************************************************************************************************
int RareFactSharedCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(sharedfile));
+
+ ValidCalculators validCalculator;
+
+ for (int i=0; i<Estimators.size(); i++) {
+ if (validCalculator.isValidCalculator("sharedrarefaction", Estimators[i]) == true) {
+ if (Estimators[i] == "sharedobserved") {
+ rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
+ outputNames.push_back(fileNameRoot+"shared.rarefaction"); outputTypes["sharedrarefaction"].push_back(fileNameRoot+"shared.rarefaction");
+ }else if (Estimators[i] == "sharednseqs") {
+ rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.r_nseqs", "")));
+ outputNames.push_back(fileNameRoot+"shared.r_nseqs"); outputTypes["sharedr_nseqs"].push_back(fileNameRoot+"shared.r_nseqs");
+ }
+ }
+ }
//if the users entered no valid calculators don't execute command
if (rDisplays.size() == 0) { return 0; }
-
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
- input = globaldata->ginput;
+ input = new InputData(sharedfile, "sharedfile");
lookup = input->getSharedRAbundVectors();
string lastLabel = lookup[0]->getLabel();
if (m->control_pressed) {
- globaldata->Groups.clear();
+ m->Groups.clear();
+ delete input;
for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
//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) {
- globaldata->Groups.clear();
+ m->Groups.clear();
+ delete input;
for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
}
if (m->control_pressed) {
- globaldata->Groups.clear();
- for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
- return 0;
+ m->Groups.clear();
+ delete input;
+ for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
}
//output error messages about any remaining user labels
}
if (m->control_pressed) {
- globaldata->Groups.clear();
- for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
- return 0;
+ m->Groups.clear();
+ delete input;
+ for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
}
//run last label if you need to
}
for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
+ m->Groups.clear();
+ delete input;
- //reset groups parameter
- globaldata->Groups.clear();
-
- if (m->control_pressed) {
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
- return 0;
- }
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
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