#include "sharedsobs.h"
#include "sharednseqs.h"
+//**********************************************************************************************************************
+vector<string> RareFactSharedCommand::getValidParameters(){
+ try {
+ string Array[] = {"iters","freq","label","calc","groups", "jumble","outputdir","inputdir"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RareFactSharedCommand", "getValidParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+RareFactSharedCommand::RareFactSharedCommand(){
+ try {
+ abort = true;
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ outputTypes["sharedrarefaction"] = tempOutNames;
+ outputTypes["sharedr_nseqs"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> RareFactSharedCommand::getRequiredParameters(){
+ try {
+ vector<string> myArray;
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RareFactSharedCommand", "getRequiredParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<string> RareFactSharedCommand::getRequiredFiles(){
+ try {
+ string Array[] = {"shared"};
+ vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ return myArray;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "RareFactSharedCommand", "getRequiredFiles");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
-RareFactSharedCommand::RareFactSharedCommand(){
+RareFactSharedCommand::RareFactSharedCommand(string option) {
try {
globaldata = GlobalData::getInstance();
- string fileNameRoot;
- fileNameRoot = getRootName(globaldata->inputFileName);
- format = globaldata->getFormat();
- validCalculator = new ValidCalculators();
+
+ abort = false;
+ allLines = 1;
+ labels.clear();
+ Estimators.clear();
+ Groups.clear();
- int i;
- for (i=0; i<globaldata->Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("sharedrarefaction", globaldata->Estimators[i]) == true) {
- if (globaldata->Estimators[i] == "sharedobserved") {
- rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
- }else if (globaldata->Estimators[i] == "sharednseqs") {
- rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.r_nseqs", "")));
- }
+ //allow user to run help
+ if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = 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)));
+
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
+
+ //check to make sure all parameters are valid for command
+ for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
+ if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
+ }
+
+ //initialize outputTypes
+ vector<string> tempOutNames;
+ 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 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
+ }
+
+ //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; }
+ }
+
+ //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 {
+ if (calc == "default") { calc = "sharedobserved"; }
+ }
+ m->splitAtDash(calc, Estimators);
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; }
+ else {
+ m->splitAtDash(groups, Groups);
+ }
+ globaldata->Groups = Groups;
+
+ string temp;
+ temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
+ convert(temp, freq);
+
+ temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
+ convert(temp, nIters);
+
+ 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");
+ }
+ }
+ }
+ }
+
}
-
- //reset calc for next command
- globaldata->setCalc("");
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the RareFactSharedCommand class function RareFactSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+
+//**********************************************************************************************************************
+
+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(){
- delete input;
- delete rCurve;
- delete read;
+ if (abort == false) {
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ delete validCalculator;
+ }
}
//**********************************************************************************************************************
int RareFactSharedCommand::execute(){
try {
- int count = 1;
+
+ if (abort == true) { return 0; }
//if the users entered no valid calculators don't execute command
if (rDisplays.size() == 0) { return 0; }
input = globaldata->ginput;
lookup = input->getSharedRAbundVectors();
+ string lastLabel = lookup[0]->getLabel();
+ 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()); }
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ return 0;
+ }
+
+
if (lookup.size() < 2) {
- cout << "I cannot run the command without at least 2 valid groups.";
+ m->mothurOut("I cannot run the command without at least 2 valid groups.");
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
return 0;
}
-
- while(lookup[0] != NULL){
-
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
- //create collectors curve
+ //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;
+
+ //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();
+ 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]; }
+ return 0;
+ }
+
+ if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
rCurve = new Rarefact(lookup, rDisplays);
- convert(globaldata->getFreq(), freq);
- convert(globaldata->getIters(), nIters);
rCurve->getSharedCurve(freq, nIters);
-
delete rCurve;
- cout << lookup[0]->getLabel() << '\t' << count << endl;
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
}
- //prevent memory leak
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = 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();
+ rCurve = new Rarefact(lookup, rDisplays);
+ rCurve->getSharedCurve(freq, nIters);
+ delete rCurve;
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
+ }
+
+ lastLabel = lookup[0]->getLabel();
+
//get next line to process
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors();
- count++;
}
-
+
+ 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;
+ }
+
+ //output error messages about any remaining user labels
+ set<string>::iterator it;
+ bool needToRun = false;
+ for (it = userLabels.begin(); it != userLabels.end(); it++) {
+ m->mothurOut("Your file does not include the label " + *it);
+ if (processedLabels.count(lastLabel) != 1) {
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
+ needToRun = true;
+ }else {
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
+ }
+ }
+
+ 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;
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
+ rCurve = new Rarefact(lookup, rDisplays);
+ rCurve->getSharedCurve(freq, nIters);
+ delete rCurve;
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ }
+
for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
//reset groups parameter
- globaldata->Groups.clear(); globaldata->setGroups("");
+ globaldata->Groups.clear();
+
+ 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();
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
+ m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "RareFactSharedCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the RareFactSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
projects / mothur.git / blobdiff