else {
//valid paramters for this command
- string Array[] = {"iters","label","calc","groups", "jumble","outputdir","inputdir"};
+ string Array[] = {"iters","freq","label","calc","groups", "jumble","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
//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
+ outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
}
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; }
}
else {
if (calc == "default") { calc = "sharedobserved"; }
}
- splitAtDash(calc, Estimators);
+ m->splitAtDash(calc, Estimators);
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else {
- splitAtDash(groups, Groups);
+ 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 (isTrue(temp)) { jumble = true; }
+ if (m->isTrue(temp)) { jumble = true; }
else { jumble = false; }
globaldata->jumble = jumble;
if (abort == false) {
- string fileNameRoot = outputDir + getRootName(getSimpleName(globaldata->inputFileName));
+ string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName));
// format = globaldata->getFormat();
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");
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) {
m->mothurOut("I cannot run the command without at least 2 valid groups.");
//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);
rCurve->getSharedCurve(freq, nIters);
delete rCurve;
- m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
}
- if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ 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();
}
+ 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;
}
}
+ 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]; } }
//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(); }