map<int, float>::iterator itDist;
for(it=thisRowsBlastScores.begin(); it!=thisRowsBlastScores.end(); it++) {
distance = 1.0 - (it->second / refScore);
+
//do we already have the distance calculated for b->a
map<string,int>::iterator itA = nameMap->find(currentRow);
//if we have it then compare
if (itDist != dists[it->first].end()) {
+
//if you want the minimum blast score ratio, then pick max distance
if(minWanted) { distance = max(itDist->second, distance); }
else{ distance = min(itDist->second, distance); }
-
+
//is this distance below cutoff
if (distance < cutoff) {
if (!hclusterWanted) {
ifstream in;
openInputFile(blastfile, in);
+ //ofstream outName;
+ //openOutputFile((blastfile + ".tempOutNames"), outName);
+
//read first line
in >> prevName;
+
for (int i = 0; i < 11; i++) { in >> hold; }
gobble(in);
-
+
//save name in nameMap
nameMap->push_back(prevName);
//read line
in >> name;
+
for (int i = 0; i < 11; i++) { in >> hold; }
gobble(in);
//openOutputFile(outNames, out);
//nameMap->print(out);
//out.close();
+
if (m->control_pressed) { return 0; }
m->mothurOut(toString(num) + " names read."); m->mothurOutEndLine();