clusterArray.push_back(temp);
}
- if (method != "average") {
+ if ((method == "furthest") || (method == "nearest")) {
m->openInputFile(distfile, filehandle);
}else{
processFile();
//you don't want to cluster with yourself
if (smallRow != smallCol) {
- if (method != "average") {
+ if ((method == "furthest") || (method == "nearest")) {
//can we cluster???
if (method == "nearest") { cluster = true; }
else{ //assume furthest
try {
vector<seqDist> sameSeqs;
- if(method != "average") {
+ if ((method == "furthest") || (method == "nearest")) {
sameSeqs = getSeqsFNNN();
}else{
sameSeqs = getSeqsAN();
map<string,int>::iterator itA = nameMap->find(firstName);
map<string,int>::iterator itB = nameMap->find(secondName);
- if(itA == nameMap->end()){ cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n"; exit(1); }
- if(itB == nameMap->end()){ cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1); }
+ if(itA == nameMap->end()){ m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the names file, please correct\n"); exit(1); }
+ if(itB == nameMap->end()){ m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the names file, please correct\n"); exit(1); }
//using cutoff
if (distance > cutoff) { break; }
float average;
if (it2Merge != smallRowColValues[1].end()) { //if yes, then average
- //weighted average
- int total = clusterArray[smallRow].numSeq + clusterArray[smallCol].numSeq;
- average = ((clusterArray[smallRow].numSeq * itMerge->second) + (clusterArray[smallCol].numSeq * it2Merge->second)) / (float) total;
+ //average
+ if (method == "average") {
+ int total = clusterArray[smallRow].numSeq + clusterArray[smallCol].numSeq;
+ average = ((clusterArray[smallRow].numSeq * itMerge->second) + (clusterArray[smallCol].numSeq * it2Merge->second)) / (float) total;
+ }else { //weighted
+ average = ((itMerge->second * 1.0) + (it2Merge->second * 1.0)) / (float) 2.0;
+ }
+
smallRowColValues[1].erase(it2Merge);
seqDist temp(clusterArray[smallRow].parent, itMerge->first, average);
map<string,int>::iterator itA = nameMap->find(firstName);
map<string,int>::iterator itB = nameMap->find(secondName);
- if(itA == nameMap->end()){ cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n"; exit(1); }
- if(itB == nameMap->end()){ cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1); }
+ if(itA == nameMap->end()){ m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the names file, please correct\n"); exit(1); }
+ if(itB == nameMap->end()){ m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the names file, please correct\n"); exit(1); }
//using cutoff
if (distance > cutoff) { break; }