TEST(Test_Container_SharedRabundVector, GetSabundVector) {
vector<int> abunds(10, 5);
SharedRAbundVector temp(abunds);
EXPECT_EQ(temp.getNumBins(), 10);
EXPECT_EQ(temp.getNumSeqs(), 50);
EXPECT_EQ(temp.getMaxRank(), 5);
SAbundVector sabund = temp.getSAbundVector();
EXPECT_EQ(sabund.getNumBins(), 10);
EXPECT_EQ(sabund.getNumSeqs(), 50);
EXPECT_EQ(sabund.getMaxRank(), 5);
EXPECT_EQ(sabund.get(5), 10);
}
//**********************************************************************************************************************
int RemoveRareCommand::processSabund(){
try {
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir += m->hasPath(sabundfile); }
string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(sabundfile)) + "pick" + m->getExtension(sabundfile);
outputTypes["sabund"].push_back(outputFileName); outputNames.push_back(outputFileName);
ofstream out;
m->openOutputFile(outputFileName, out);
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
InputData input(sabundfile, "sabund");
SAbundVector* sabund = input.getSAbundVector();
string lastLabel = sabund->getLabel();
set<string> processedLabels;
set<string> userLabels = labels;
while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
if (m->control_pressed) { delete sabund; out.close(); return 0; }
if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
if (sabund->getMaxRank() > nseqs) {
for(int i = 1; i <=nseqs; i++) { sabund->set(i, 0); }
}else { sabund->clear(); }
if (sabund->getNumBins() > 0) { sabund->print(out); }
}
if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = sabund->getLabel();
delete sabund;
sabund = input.getSAbundVector(lastLabel);
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
if (sabund->getMaxRank() > nseqs) {
for(int i = 1; i <=nseqs; i++) { sabund->set(i, 0); }
}else { sabund->clear(); }
if (sabund->getNumBins() > 0) { sabund->print(out); }
//restore real lastlabel to save below
sabund->setLabel(saveLabel);
}
lastLabel = sabund->getLabel();
delete sabund;
sabund = input.getSAbundVector();
}
if (m->control_pressed) { out.close(); 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();
}
}
//run last label if you need to
if (needToRun == true) {
if (sabund != NULL) { delete sabund; }
sabund = input.getSAbundVector(lastLabel);
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
if (sabund->getMaxRank() > nseqs) {
for(int i = 1; i <=nseqs; i++) { sabund->set(i, 0); }
}else { sabund->clear(); }
if (sabund->getNumBins() > 0) { sabund->print(out); }
delete sabund;
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "RemoveRareCommand", "processSabund");
exit(1);
}
}
