//**********************************************************************************************************************
-RareFactSharedCommand::RareFactSharedCommand(string option){
+RareFactSharedCommand::RareFactSharedCommand(string option) {
try {
globaldata = GlobalData::getInstance();
+
abort = false;
allLines = 1;
- lines.clear();
labels.clear();
Estimators.clear();
-
+ Groups.clear();
+
//allow user to run help
if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
else {
//valid paramters for this command
- string Array[] = {"iters","line","label","calc","groups"};
+ string Array[] = {"iters","label","calc","groups", "jumble","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
- parser = new OptionParser();
- parser->parse(option, parameters); delete parser;
+ OptionParser parser(option);
+ map<string,string> parameters = parser.getParameters();
+
+ ValidParameters validParameter;
- ValidParameters* validParameter = new ValidParameters();
-
//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; }
+ for (map<string,string>::iterator 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->getSharedFile() == "") {
- if (globaldata->getListFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared command." << endl; abort = true; }
- else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group, or a shared before you can use the collect.shared command." << endl; abort = true; }
+ 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 += 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...
- line = validParameter->validFile(parameters, "line", false);
- if (line == "not found") { line = ""; }
- else {
- if(line != "all") { splitAtDash(line, lines); allLines = 0; }
- else { allLines = 1; }
- }
-
- label = validParameter->validFile(parameters, "label", false);
+ label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
if(label != "all") { splitAtDash(label, labels); allLines = 0; }
else { allLines = 1; }
}
- //make sure user did not use both the line and label parameters
- if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; }
- //if the user has not specified any line or labels use the ones from read.otu
- else if((line == "") && (label == "")) {
+ //if the user has not specified any labels use the ones from read.otu
+ if(label == "") {
allLines = globaldata->allLines;
labels = globaldata->labels;
- lines = globaldata->lines;
}
- calc = validParameter->validFile(parameters, "calc", false);
+ calc = validParameter.validFile(parameters, "calc", false);
if (calc == "not found") { calc = "sharedobserved"; }
else {
if (calc == "default") { calc = "sharedobserved"; }
}
splitAtDash(calc, Estimators);
- groups = validParameter->validFile(parameters, "groups", false);
+ groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else {
splitAtDash(groups, Groups);
- globaldata->Groups = Groups;
}
+ globaldata->Groups = Groups;
string temp;
- temp = validParameter->validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
+ temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
convert(temp, nIters);
- delete validParameter;
+ temp = validParameter.validFile(parameters, "jumble", false); if (temp == "not found") { temp = "T"; }
+ if (isTrue(temp)) { jumble = true; }
+ else { jumble = false; }
+ globaldata->jumble = jumble;
if (abort == false) {
- string fileNameRoot = getRootName(globaldata->inputFileName);
- format = globaldata->getFormat();
- int i;
+ string fileNameRoot = outputDir + getRootName(getSimpleName(globaldata->inputFileName));
+// format = globaldata->getFormat();
+
validCalculator = new ValidCalculators();
- for (i=0; i<Estimators.size(); i++) {
+ 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");
}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");
}
}
}
}
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";
- exit(1);
- }
-
}
//**********************************************************************************************************************
void RareFactSharedCommand::help(){
try {
- cout << "The rarefaction.shared command can only be executed after a successful read.otu command." << "\n";
- cout << "The rarefaction.shared command parameters are label, line, iters, groups and calc. No parameters are required, but you may not use " << "\n";
- cout << "both the line and label parameters at the same time. The rarefaction command should be in the following format: " << "\n";
- cout << "rarefaction.shared(label=yourLabel, line=yourLines, iters=yourIters, calc=yourEstimators, groups=yourGroups)." << "\n";
- cout << "Example rarefaction.shared(label=unique-.01-.03, line=0-5-10, iters=10000, groups=B-C, calc=sharedobserved)." << "\n";
- cout << "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";
- cout << "The default value for groups is all the groups in your groupfile." << "\n";
+ 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("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);
- cout << "The label and line parameters are used to analyze specific lines in your input." << "\n";
- cout << "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";
- cout << "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq)." << "\n" << "\n";
+ 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) {
- cout << "Standard Error: " << e.what() << " has occurred in the RareFactSharedCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "RareFactSharedCommand", "help");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the RareFactSharedCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
RareFactSharedCommand::~RareFactSharedCommand(){
- delete input;
- delete rCurve;
- delete read;
- delete validCalculator;
+ if (abort == false) {
+ delete input; globaldata->ginput = NULL;
+ delete read;
+ delete validCalculator;
+ }
}
//**********************************************************************************************************************
if (abort == true) { return 0; }
- int count = 1;
-
//if the users entered no valid calculators don't execute command
if (rDisplays.size() == 0) { return 0; }
input = globaldata->ginput;
lookup = input->getSharedRAbundVectors();
- vector<SharedRAbundVector*> lastLookup = lookup;
+ 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;
}
//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;
//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) || (userLines.size() != 0))) {
+ 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 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
-
+ if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
rCurve = new Rarefact(lookup, rDisplays);
rCurve->getSharedCurve(freq, nIters);
delete rCurve;
- cout << lookup[0]->getLabel() << '\t' << count << endl;
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
- userLines.erase(count);
}
- if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- rCurve = new Rarefact(lastLookup, rDisplays);
+ if ((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(lastLookup[0]->getLabel());
- userLabels.erase(lastLookup[0]->getLabel());
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
}
- //prevent memory leak
- if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
- lastLookup = lookup;
+
+ 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++) {
- cout << "Your file does not include the label "<< *it;
- if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
- cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
+ 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 {
- cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
- //run last line if you need to
+ 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) {
- cout << lastLookup[0]->getLabel() << '\t' << count << endl;
- rCurve = new Rarefact(lastLookup, rDisplays);
+ 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 < lastLookup.size(); i++) { delete lastLookup[i]; }
-
for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
//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;
+ }
+
+ 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