abort = false;
filename = fileroot;
- //allow user to run help
- //if(option == "help") { help(); abort = true; }
- //else {
- //if (option != "") { mothurOut("There are no valid parameters for the consensus command."); mothurOutEndLine(); abort = true; }
-
- // //no trees were read
- // if (globaldata->gTree.size() == 0) { mothurOut("You must execute the read.tree command, before you may use the consensus command."); mothurOutEndLine(); abort = true; }
- //else {
- t = globaldata->gTree;
- // }
- //}
+ t = globaldata->gTree;
+
}
catch(exception& e) {
errorOut(e, "ConcensusCommand", "ConcensusCommand");
out2 << "Species in Order: " << endl << endl;
for (int i = 0; i < treeSet.size(); i++) { out2 << i+1 << ". " << treeSet[i] << endl; }
- vector<string> temp;
//output sets included
out2 << endl << "Sets included in the consensus tree:" << endl << endl;
+
+ vector<string> temp;
for (it2 = nodePairsInTree.begin(); it2 != nodePairsInTree.end(); it2++) {
//only output pairs not leaves
if (it2->first.size() > 1) {
//find spot
int index = findSpot(it2->first[i]);
temp[index] = "*";
+ //temp[index] = it2->first[i] + " ";
}
//output temp
//terminate recursion
}else if (count == numNodes) { return 0; }
else {
- leftChildSet = getNextAvailableSet(nodeSet);
- rightChildSet = getRestSet(nodeSet, leftChildSet);
+ //finds best child pair
+ leftChildSet = getNextAvailableSet(nodeSet, rightChildSet);
int left = buildConcensusTree(leftChildSet);
int right = buildConcensusTree(rightChildSet);
consensusTree->tree[count].setChildren(left, right);
}
}
+
//add each leaf to terminate recursion in consensus
//you want the leaves in there but with insignifigant sightings value so it is added last
//for each leaf node get descendant info.
}
sort(treeSet.begin(), treeSet.end());
+
+
+ map< vector<string>, int> nodePairsCopy = nodePairs;
+
+
+ //set initial rating on pairs to sightings + subgroup sightings
+ while (nodePairsCopy.size() != 0) {
+
+ vector<string> small = getSmallest(nodePairsCopy);
+
+ int subgrouprate = getSubgroupRating(small);
+
+ nodePairsInitialRate[small] = nodePairs[small] + subgrouprate;
+
+ nodePairsCopy.erase(small);
+ }
+
}
catch(exception& e) {
errorOut(e, "ConcensusCommand", "getSets");
exit(1);
}
}
+//**********************************************************************************************************************
+vector<string> ConcensusCommand::getSmallest(map< vector<string>, int> nodes) {
+ try{
+ vector<string> smallest = nodes.begin()->first;
+ int smallsize = smallest.size();
+
+ for(it2 = nodes.begin(); it2 != nodes.end(); it2++) {
+ if(it2->first.size() < smallsize) { smallsize = it2->first.size(); smallest = it2->first; }
+ }
+
+ return smallest;
+ }
+ catch(exception& e) {
+ errorOut(e, "ConcensusCommand", "getSmallest");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
-vector<string> ConcensusCommand::getNextAvailableSet(vector<string> bigset) {
+vector<string> ConcensusCommand::getNextAvailableSet(vector<string> bigset, vector<string>& rest) {
try {
+//cout << "new call " << endl << endl << endl;
vector<string> largest; largest.clear();
- int largestSighting = -1;
-
- //go through the sets
- for (it2 = nodePairs.begin(); it2 != nodePairs.end(); it2++) {
- //are you a subset of bigset
- if (isSubset(bigset, it2->first) == true) {
-
- //are you the largest. if you are the same size as current largest refer to sighting
- if (it2->first.size() > largest.size()) { largest = it2->first; largestSighting = it2->second; }
- else if (it2->first.size() == largest.size()) {
- if (it2->second > largestSighting) { largest = it2->first; largestSighting = it2->second; }
- }
-
- }
+ rest.clear();
+
+ //if you are just 2 groups
+ if (bigset.size() == 2) {
+ rest.push_back(bigset[0]);
+ largest.push_back(bigset[1]);
+ }else{
+ rest = bestSplit[bigset][0];
+ largest = bestSplit[bigset][1];
}
+
+ //save for printing out later and for branch lengths
+ nodePairsInTree[rest] = nodePairs[rest];
+
+ //delete whatever set you return because it is no longer available
+ nodePairs.erase(rest);
+
//save for printing out later and for branch lengths
nodePairsInTree[largest] = nodePairs[largest];
}
}
+/**********************************************************************************************************************/
+int ConcensusCommand::getSubgroupRating(vector<string> group) {
+ try {
+ map< vector<string>, int>::iterator ittemp;
+ map< vector< vector<string> > , int >::iterator it3;
+ int rate = 0;
+
+ // ***********************************************************************************//
+ //1. this function must be called passing it littlest sets to biggest
+ // since it the rating is made from your sighting plus you best splits rating
+ //2. it saves the top pair to use later
+ // ***********************************************************************************//
+
+
+ if (group.size() < 3) { return rate; }
+
+ map< vector<string>, int> possiblePairing; //this is all the subsets of group
+
+ //go through the sets
+ for (it2 = nodePairs.begin(); it2 != nodePairs.end(); it2++) {
+ //are you a subset of bigset, then save in possiblePairings
+ if (isSubset(group, it2->first) == true) { possiblePairing[it2->first] = it2->second; }
+ }
+
+ map< vector< vector<string> > , int > rating;
+
+ while (possiblePairing.size() != 0) {
+
+ it2 = possiblePairing.begin();
+ vector<string> temprest = getRestSet(group, it2->first);
+
+ //is the rest a set available in possiblePairings
+ ittemp = possiblePairing.find(temprest);
+ if (ittemp != possiblePairing.end()) { //if the rest is in the possible pairings then add this pair to rating map
+ vector< vector<string> > temprate;
+ temprate.push_back(it2->first); temprate.push_back(temprest);
+
+ rating[temprate] = (nodePairsInitialRate[it2->first] + nodePairsInitialRate[temprest]);
+
+ //erase so you dont add 1,2 and 2,1.
+ possiblePairing.erase(temprest);
+ }
+
+ possiblePairing.erase(it2);
+ }
+
+
+ it3 = rating.begin();
+ rate = it3->second;
+ vector< vector<string> > topPair = it3->first;
+
+ //choose the split with the best rating
+ for (it3 = rating.begin(); it3 != rating.end(); it3++) {
+
+ if (it3->second > rate) { rate = it3->second; topPair = it3->first; }
+ }
+
+ bestSplit[group] = topPair;
+
+ return rate;
+ }
+ catch(exception& e) {
+ errorOut(e, "ConcensusCommand", "getSubgroupRating");
+ exit(1);
+ }
+}
+
//**********************************************************************************************************************
vector<string> ConcensusCommand::getRestSet(vector<string> bigset, vector<string> subset) {
try {
//its not in the subset so put it in the rest
if (inSubset == false) { rest.push_back(bigset[i]); }
}
-
- //save for printing out later and for branch lengths
- nodePairsInTree[rest] = nodePairs[rest];
-
- //delete whatever set you return because it is no longer available
- nodePairs.erase(rest);
return rest;
bool ConcensusCommand::isSubset(vector<string> bigset, vector<string> subset) {
try {
+
+ if (subset.size() > bigset.size()) { return false; }
+
//check if each guy in suset is also in bigset
for (int i = 0; i < subset.size(); i++) {
bool match = false;
projects / mothur.git / blobdiff