X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=weighted.cpp;h=1ce6230df933eab46bee132a76ec32c2c4e9a666;hb=c53ef46b40b97c00e32bfd8c3924ce8c51b5cd7b;hp=1ac274619bf2c8971ea7f17ddb03c8cf98dde0ed;hpb=3fd6dd6e4f19a458ac2966ee5458787e998a1bde;p=mothur.git diff --git a/weighted.cpp b/weighted.cpp index 1ac2746..1ce6230 100644 --- a/weighted.cpp +++ b/weighted.cpp @@ -184,7 +184,7 @@ EstOutput Weighted::driver(Tree* t, vector< vector > namesOfGroupCombos, D[count] += weightedSum; } - + //adding the wieghted sums from group l for (int j = 0; j < t->groupNodeInfo[groupB].size(); j++) { //the leaf nodes that have seqs from group l map::iterator it = t->tree[t->groupNodeInfo[groupB][j]].pcount.find(groupB); @@ -195,6 +195,7 @@ EstOutput Weighted::driver(Tree* t, vector< vector > namesOfGroupCombos, D[count] += weightedSum; } + count++; } @@ -205,8 +206,6 @@ EstOutput Weighted::driver(Tree* t, vector< vector > namesOfGroupCombos, m->mothurOut("Processing combo: " + toString(h)); m->mothurOutEndLine(); int numLeaves = t->getNumLeaves(); - map tempTotals; //maps node to total Branch Length - map nodePcountSize; //maps node to pcountSize string groupA = namesOfGroupCombos[h][0]; string groupB = namesOfGroupCombos[h][1]; @@ -217,13 +216,12 @@ EstOutput Weighted::driver(Tree* t, vector< vector > namesOfGroupCombos, if (m->control_pressed) { return data; } double u; - int pcountSize = 0; + //int pcountSize = 0; //does this node have descendants from groupA it = t->tree[i].pcount.find(groupA); //if it does u = # of its descendants with a certain group / total number in tree with a certain group if (it != t->tree[i].pcount.end()) { u = (double) t->tree[i].pcount[groupA] / (double) tmap->seqsPerGroup[groupA]; - pcountSize++; }else { u = 0.00; } @@ -232,40 +230,14 @@ EstOutput Weighted::driver(Tree* t, vector< vector > namesOfGroupCombos, //if it does subtract their percentage from u if (it != t->tree[i].pcount.end()) { u -= (double) t->tree[i].pcount[groupB] / (double) tmap->seqsPerGroup[groupB]; - pcountSize++; } - u = abs(u * t->tree[i].getBranchLength()); - - nodePcountSize[i] = pcountSize; - - //if you are a leaf from a users group add to total - if (i < numLeaves) { - if ((t->tree[i].getBranchLength() != -1) && pcountSize != 0) { - //cout << "added to total" << endl; - WScore[(groupA+groupB)] += u; - } - tempTotals[i] = 0.0; //we don't care about you, or we have already added you - }else{ //if you are not a leaf - //do both your chidren have have descendants from the users groups? - int lc = t->tree[i].getLChild(); - int rc = t->tree[i].getRChild(); - - //if yes, add your childrens tempTotals - if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) { - WScore[(groupA+groupB)] += tempTotals[lc] + tempTotals[rc]; - //cout << "added to total " << tempTotals[lc] << '\t' << tempTotals[rc] << endl; - if (t->tree[i].getBranchLength() != -1) { - tempTotals[i] = u; - }else { - tempTotals[i] = 0.0; - } - }else if ((nodePcountSize[lc] == 0) && (nodePcountSize[rc] == 0)) { tempTotals[i] = 0.0; //we don't care about you - }else { //if no, your tempTotal is your childrens temp totals + your branch length - tempTotals[i] = tempTotals[lc] + tempTotals[rc] + u; - } - //cout << "temptotal = "<< tempTotals[i] << endl; + //if this is not the root then add it + if (rootForGrouping[namesOfGroupCombos[h]].count(i) == 0) { + u = abs(u * t->tree[i].getBranchLength()); + WScore[(groupA+groupB)] += u; } + } } @@ -327,66 +299,35 @@ EstOutput Weighted::getValues(Tree* t, string groupA, string groupB) { } int numLeaves = t->getNumLeaves(); - map tempTotals; //maps node to total Branch Length - map nodePcountSize; //maps node to pcountSize //calculate u for the group comb for(int i=0;igetNumNodes();i++){ - + if (m->control_pressed) { return data; } double u; - int pcountSize = 0; + //int pcountSize = 0; //does this node have descendants from groupA it = t->tree[i].pcount.find(groupA); //if it does u = # of its descendants with a certain group / total number in tree with a certain group if (it != t->tree[i].pcount.end()) { u = (double) t->tree[i].pcount[groupA] / (double) tmap->seqsPerGroup[groupA]; - pcountSize++; }else { u = 0.00; } - - + + //does this node have descendants from group l it = t->tree[i].pcount.find(groupB); //if it does subtract their percentage from u if (it != t->tree[i].pcount.end()) { u -= (double) t->tree[i].pcount[groupB] / (double) tmap->seqsPerGroup[groupB]; - pcountSize++; } - - u = abs(u * t->tree[i].getBranchLength()); - nodePcountSize[i] = pcountSize; - - //if you are a leaf from a users group add to total - if (i < numLeaves) { - if ((t->tree[i].getBranchLength() != -1) && pcountSize != 0) { - //cout << "added to total" << endl; - WScore[(groupA+groupB)] += u; - } - tempTotals[i] = 0.0; //we don't care about you, or we have already added you - }else{ //if you are not a leaf - //do both your chidren have have descendants from the users groups? - int lc = t->tree[i].getLChild(); - int rc = t->tree[i].getRChild(); - - //if yes, add your childrens tempTotals - if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) { - WScore[(groupA+groupB)] += tempTotals[lc] + tempTotals[rc]; - //cout << "added to total " << tempTotals[lc] << '\t' << tempTotals[rc] << endl; - if (t->tree[i].getBranchLength() != -1) { - tempTotals[i] = u; - }else { - tempTotals[i] = 0.0; - } - }else if ((nodePcountSize[lc] == 0) && (nodePcountSize[rc] == 0)) { tempTotals[i] = 0.0; //we don't care about you - }else { //if no, your tempTotal is your childrens temp totals + your branch length - tempTotals[i] = tempTotals[lc] + tempTotals[rc] + u; - } - //cout << "temptotal = "<< tempTotals[i] << endl; + //if this is not the root then add it + if (rootForGrouping[groups].count(i) == 0) { + u = abs(u * t->tree[i].getBranchLength()); + WScore[(groupA+groupB)] += u; } - } - + } /********************************************************/ //calculate weighted score for the group combination @@ -408,72 +349,66 @@ double Weighted::getLengthToRoot(Tree* t, int v, string groupA, string groupB) { try { double sum = 0.0; - map tempTotals; //maps node to total Branch Length - map nodePcountSize; //maps node to pcountSize - map::iterator itCount; - int index = v; //you are a leaf if(t->tree[index].getBranchLength() != -1){ sum += abs(t->tree[index].getBranchLength()); } - tempTotals[index] = 0.0; + double tempTotal = 0.0; index = t->tree[index].getParent(); + + vector grouping; grouping.push_back(groupA); grouping.push_back(groupB); + + rootForGrouping[grouping].insert(index); //while you aren't at root while(t->tree[index].getParent() != -1){ if (m->control_pressed) { return sum; } - int pcountSize = 0; - map::iterator itGroup = t->tree[index].pcount.find(groupA); - if (itGroup != t->tree[index].pcount.end()) { pcountSize++; } - itGroup = t->tree[index].pcount.find(groupB); - if (itGroup != t->tree[index].pcount.end()) { pcountSize++; } - - nodePcountSize[index] = pcountSize; - - //do both your chidren have have descendants from the users groups? - int lc = t->tree[index].getLChild(); - int rc = t->tree[index].getRChild(); + //am I the root for this grouping? if so I want to stop "early" + //does my sibling have descendants from the users groups? + int parent = t->tree[index].getParent(); + int lc = t->tree[parent].getLChild(); + int rc = t->tree[parent].getRChild(); - itCount = nodePcountSize.find(lc); - if (itCount == nodePcountSize.end()) { - int LpcountSize = 0; - itGroup = t->tree[lc].pcount.find(groupA); - if (itGroup != t->tree[lc].pcount.end()) { LpcountSize++; } - itGroup = t->tree[lc].pcount.find(groupB); - if (itGroup != t->tree[lc].pcount.end()) { LpcountSize++; } - nodePcountSize[lc] = LpcountSize; - } + int sib = lc; + if (lc == index) { sib = rc; } - itCount = nodePcountSize.find(rc); - if (itCount == nodePcountSize.end()) { - int RpcountSize = 0; - itGroup = t->tree[rc].pcount.find(groupA); - if (itGroup != t->tree[rc].pcount.end()) { RpcountSize++; } - itGroup = t->tree[rc].pcount.find(groupB); - if (itGroup != t->tree[rc].pcount.end()) { RpcountSize++; } - nodePcountSize[rc] = RpcountSize; - } - - //if yes, add your childrens tempTotals - if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) { - sum += tempTotals[lc] + tempTotals[rc]; - - //cout << "added to total " << tempTotals[lc] << '\t' << tempTotals[rc] << endl; + map::iterator itGroup; + int pcountSize = 0; + itGroup = t->tree[sib].pcount.find(groupA); + if (itGroup != t->tree[sib].pcount.end()) { pcountSize++; } + itGroup = t->tree[sib].pcount.find(groupB); + if (itGroup != t->tree[sib].pcount.end()) { pcountSize++; } + + //if yes, I am not the root so add me + if (pcountSize != 0) { if (t->tree[index].getBranchLength() != -1) { - tempTotals[index] = abs(t->tree[index].getBranchLength()); + sum += abs(t->tree[index].getBranchLength()) + tempTotal; + tempTotal = 0.0; }else { - tempTotals[index] = 0.0; + sum += tempTotal; + tempTotal = 0.0; + } + rootForGrouping[grouping].clear(); + rootForGrouping[grouping].insert(parent); + }else { //if no, I may be the root so add my br to tempTotal until I am proven innocent + if (t->tree[index].getBranchLength() != -1) { + tempTotal += abs(t->tree[index].getBranchLength()); } - }else { //if no, your tempTotal is your childrens temp totals + your branch length - tempTotals[index] = tempTotals[lc] + tempTotals[rc] + abs(t->tree[index].getBranchLength()); } - //cout << "temptotal = "<< tempTotals[i] << endl; - index = t->tree[index].getParent(); + index = parent; } - + + //get all nodes above the root to add so we don't add their u values above + index = *(rootForGrouping[grouping].begin()); + while(t->tree[index].getParent() != -1){ + int parent = t->tree[index].getParent(); + rootForGrouping[grouping].insert(parent); + index = parent; + } + return sum; } catch(exception& e) { @@ -484,4 +419,3 @@ double Weighted::getLengthToRoot(Tree* t, int v, string groupA, string groupB) { /**************************************************************************************************/ -