//**********************************************************************************************************************
-Venn::Venn(){
+Venn::Venn(string o) : outputDir(o) {
try {
globaldata = GlobalData::getInstance();
try {
for(int i=0;i<vCalcs.size();i++){
- string filenamesvg = globaldata->inputFileName + ".venn." + sabund->getLabel() + vCalcs[i]->getName() + ".svg";
+ string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + ".venn." + sabund->getLabel() + vCalcs[i]->getName() + ".svg";
openOutputFile(filenamesvg, outsvg);
vector<double> data = vCalcs[i]->getValues(sabund);
//make a file for each calculator
for(int i=0;i<vCalcs.size();i++){
- string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
+ string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
openOutputFile(filenamesvg, outsvg);
//in essence you want to run it like a single
//make a file for each calculator
for(int i=0;i<vCalcs.size();i++){
- string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
+ string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
openOutputFile(filenamesvg, outsvg);
//get estimates for sharedAB
}else { outsvg << "</text>\n"; }
outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"500\">The number of sepecies shared between groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString(shared[0]) + "</text>\n";
- outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"520\">Percentage of species that are shared in groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString((shared[0] / (float)(numA[0] + numB[0] - shared[0]))) + "</text>\n";
+ outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"520\">Percentage of species that are shared in groups " + lookup[0]->getGroup() + " and " + lookup[1]->getGroup() + " is " + toString((shared[0] / (float)(numA[0] + numB[0] - shared[0]))*100) + "</text>\n";
outsvg << "<text fill=\"black\" class=\"seri\" x=\"175\" y=\"540\">The total richness for all groups is " + toString((float)(numA[0] + numB[0] - shared[0])) + "</text>\n";
//close file
for(int i=0;i<vCalcs.size();i++){
- string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
+ string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
openOutputFile(filenamesvg, outsvg);
if (vCalcs[i]->getName() == "sharedace") {
//merge BC and estimate with shared with A
SharedRAbundVector* merge = new SharedRAbundVector();
for (int j = 0; j < lookup[1]->size(); j++) {
- merge->push_back((lookup[1]->getAbundance(j) + lookup[2]->getAbundance(j)), j, "");
+ merge->push_back((lookup[1]->getAbundance(j) + lookup[2]->getAbundance(j)), "");
}
subset.clear();
//merge AC and estimate with shared with B
merge = new SharedRAbundVector();
for (int j = 0; j < lookup[0]->size(); j++) {
- merge->push_back((lookup[0]->getAbundance(j) + lookup[2]->getAbundance(j)), j, "");
+ merge->push_back((lookup[0]->getAbundance(j) + lookup[2]->getAbundance(j)), "");
}
subset.clear();
//merge AB and estimate with shared with C
merge = new SharedRAbundVector();
for (int j = 0; j < lookup[0]->size(); j++) {
- merge->push_back((lookup[0]->getAbundance(j) + lookup[1]->getAbundance(j)), j, "");
+ merge->push_back((lookup[0]->getAbundance(j) + lookup[1]->getAbundance(j)), "");
}
subset.clear();
if ((vCalcs[i]->getName() != "sharedsobs") && (vCalcs[i]->getName() != "sharedchao")) { mothurOut(vCalcs[i]->getName() + " is not a valid calculator with four groups. It will be disregarded. "); mothurOutEndLine(); }
else{
- string filenamesvg = getRootName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
+ string filenamesvg = outputDir + getSimpleName(globaldata->inputFileName) + lookup[0]->getLabel() + ".venn." + vCalcs[i]->getName() + ".svg";
openOutputFile(filenamesvg, outsvg);