X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=weighted.cpp;h=a114d2ca0756c6fe671dc135acf0254ad1d5bf92;hb=2df35fdeea85f574630d75b11fb5b08c39aec31a;hp=a0d2f5ef4117191886cb3abcc078a4620b609abc;hpb=e90d9faedeb685773c9582674dee75884e2e69b4;p=mothur.git diff --git a/weighted.cpp b/weighted.cpp index a0d2f5e..a114d2c 100644 --- a/weighted.cpp +++ b/weighted.cpp @@ -17,29 +17,25 @@ EstOutput Weighted::getValues(Tree* t) { int numGroups; vector D; - //if the user has not entered specific groups to analyze then do them all - if (globaldata->Groups.size() == 0) { - numGroups = tmap->getNumGroups(); - }else { - numGroups = globaldata->Groups.size(); - } + numGroups = globaldata->Groups.size(); //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3; - int n = 1; - for (int i=1; iGroups.size() == 0) { - WScore[tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]] = 0.0; - D.push_back(0.0000); //initialize a spot in D for each combination - }else { - WScore[globaldata->Groups[i-1]+globaldata->Groups[l]] = 0.0; - D.push_back(0.0000); //initialize a spot in D for each combination - } + WScore[globaldata->Groups[i]+globaldata->Groups[l]] = 0.0; + + vector groups; groups.push_back(globaldata->Groups[i]); groups.push_back(globaldata->Groups[l]); + + D.push_back(0.0000); //initialize a spot in D for each combination /********************************************************/ //calculate a D value for each group combo for(int v=0;vgetNumLeaves();v++){ + + if (m->control_pressed) { return data; } + int index = v; double sum = 0.0000; @@ -48,128 +44,208 @@ EstOutput Weighted::getValues(Tree* t) { //if you have a BL if(t->tree[index].getBranchLength() != -1){ - sum += t->tree[index].getBranchLength(); + sum += abs(t->tree[index].getBranchLength()); } index = t->tree[index].getParent(); } //get last breanch length added if(t->tree[index].getBranchLength() != -1){ - sum += t->tree[index].getBranchLength(); + sum += abs(t->tree[index].getBranchLength()); } - if (globaldata->Groups.size() == 0) { - //is this sum from a sequence which is in one of the users groups - if (inUsersGroups(t->tree[v].getGroup(), tmap->namesOfGroups) == true) { - //is this sum from a sequence which is in this groupCombo - if ((t->tree[v].getGroup() == tmap->namesOfGroups[i-1]) || (t->tree[v].getGroup() == tmap->namesOfGroups[l])) { - sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()]; - D[n-1] += sum; - } - } - }else { - //is this sum from a sequence which is in one of the users groups - if (inUsersGroups(t->tree[v].getGroup(), globaldata->Groups) == true) { - //is this sum from a sequence which is in this groupCombo - if ((t->tree[v].getGroup() == globaldata->Groups[i-1]) || (t->tree[v].getGroup() == globaldata->Groups[l])) { - sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()]; - D[n-1] += sum; - } + //is this sum from a sequence which is in one of the users groups + if (inUsersGroups(t->tree[v].getGroup(), globaldata->Groups) == true) { + //is this sum from a sequence which is in this groupCombo + if (inUsersGroups(t->tree[v].getGroup(), groups)) { + int numSeqsInGroupI, numSeqsInGroupL; + + map::iterator it; + it = t->tree[v].pcount.find(groups[0]); + if (it != t->tree[v].pcount.end()) { //this leaf node contains seqs from group i + numSeqsInGroupI = it->second; + }else{ numSeqsInGroupI = 0; } + + it = t->tree[v].pcount.find(groups[1]); + if (it != t->tree[v].pcount.end()) { //this leaf node contains seqs from group l + numSeqsInGroupL = it->second; + }else{ numSeqsInGroupL = 0; } + + double weightedSum = ((numSeqsInGroupI * sum) / (double)tmap->seqsPerGroup[groups[0]]) + ((numSeqsInGroupL * sum) / (double)tmap->seqsPerGroup[groups[1]]); + + //sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()]; + + D[count] += weightedSum; } } } /*********************************************************/ + count++; } } - data.clear(); //clear out old values for(int i=0;igetNumNodes();i++){ //calculate weighted score for each of the group comb i.e. with groups A,B,C = AB, AC, BC. - n = 1; - for (int b=1; bcontrol_pressed) { return data; } + //calculate a u value for each combo double u; - //the user has not entered specific groups - if (globaldata->Groups.size() == 0) { - //does this node have descendants from group b-1 - it = t->tree[i].pcount.find(tmap->namesOfGroups[b-1]); - //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[tmap->namesOfGroups[b-1]] / (double) tmap->seqsPerGroup[tmap->namesOfGroups[b-1]]; - }else { u = 0.00; } - - //does this node have descendants from group l - it = t->tree[i].pcount.find(tmap->namesOfGroups[l]); - //if it does subtract their percentage from u - if (it != t->tree[i].pcount.end()) { - u -= (double) t->tree[i].pcount[tmap->namesOfGroups[l]] / (double) tmap->seqsPerGroup[tmap->namesOfGroups[l]]; - } - - u = abs(u) * t->tree[i].getBranchLength(); - - //save groupcombs u value - WScore[tmap->namesOfGroups[b-1]+tmap->namesOfGroups[l]] += u; - - //the user has entered specific groups - }else { - //does this node have descendants from group b-1 - it = t->tree[i].pcount.find(globaldata->Groups[b-1]); - //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[globaldata->Groups[b-1]] / (double) tmap->seqsPerGroup[globaldata->Groups[b-1]]; - }else { u = 0.00; } - - //does this node have descendants from group l - it = t->tree[i].pcount.find(globaldata->Groups[l]); - //if it does subtract their percentage from u - if (it != t->tree[i].pcount.end()) { - u -= (double) t->tree[i].pcount[globaldata->Groups[l]] / (double) tmap->seqsPerGroup[globaldata->Groups[l]]; - } + //does this node have descendants from group b-1 + it = t->tree[i].pcount.find(globaldata->Groups[b]); + //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[globaldata->Groups[b]] / (double) tmap->seqsPerGroup[globaldata->Groups[b]]; + }else { u = 0.00; } + + //does this node have descendants from group l + it = t->tree[i].pcount.find(globaldata->Groups[l]); + //if it does subtract their percentage from u + if (it != t->tree[i].pcount.end()) { + u -= (double) t->tree[i].pcount[globaldata->Groups[l]] / (double) tmap->seqsPerGroup[globaldata->Groups[l]]; + } - u = abs(u) * t->tree[i].getBranchLength(); + u = abs(u * t->tree[i].getBranchLength()); - //save groupcombs u value - WScore[globaldata->Groups[b-1]+globaldata->Groups[l]] += u; - } + //save groupcombs u value + WScore[globaldata->Groups[b]+globaldata->Groups[l]] += u; /*********************************************************/ } - n++; } } //calculate weighted score for each group combination double UN; - n = 1; - for (int i=1; iGroups.size() == 0) { - UN = (WScore[tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]] / D[n-1]); -cout << "W score = " << WScore[tmap->namesOfGroups[i-1]+tmap->namesOfGroups[l]] << endl; - }else {//they have entered specific groups - UN = (WScore[globaldata->Groups[i-1]+globaldata->Groups[l]] / D[n-1]); -cout << "W score = " << WScore[globaldata->Groups[i-1]+globaldata->Groups[l]] << endl; - } -cout << " D = "<< D[n-1] << endl; + count = 0; + for (int i=0; iGroups[i]+globaldata->Groups[l]] / D[count]); + if (isnan(UN) || isinf(UN)) { UN = 0; } data.push_back(UN); + count++; } } - return data; } catch(exception& e) { - cout << "Standard Error: " << e.what() << " has occurred in the Weighted class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; + m->errorOut(e, "Weighted", "getValues"); exit(1); } - catch(...) { - cout << "An unknown error has occurred in the Weighted class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n"; +} + +/**************************************************************************************************/ +EstOutput Weighted::getValues(Tree* t, string groupA, string groupB) { + try { + globaldata = GlobalData::getInstance(); + + data.clear(); //clear out old values + + //initialize weighted score + WScore[(groupA+groupB)] = 0.0; + float D = 0.0; + + vector groups; groups.push_back(groupA); groups.push_back(groupB); + + /********************************************************/ + //calculate a D value for the group combo + for(int v=0;vgetNumLeaves();v++){ + if (m->control_pressed) { return data; } + + int index = v; + double sum = 0.0000; + + //while you aren't at root + while(t->tree[index].getParent() != -1){ + + //if you have a BL + if(t->tree[index].getBranchLength() != -1){ + sum += abs(t->tree[index].getBranchLength()); + } + index = t->tree[index].getParent(); + } + + //get last breanch length added + if(t->tree[index].getBranchLength() != -1){ + sum += abs(t->tree[index].getBranchLength()); + } + + if (inUsersGroups(t->tree[v].getGroup(), groups)) { + int numSeqsInGroupI, numSeqsInGroupL; + + map::iterator it; + it = t->tree[v].pcount.find(groups[0]); + if (it != t->tree[v].pcount.end()) { //this leaf node contains seqs from group i + numSeqsInGroupI = it->second; + }else{ numSeqsInGroupI = 0; } + + it = t->tree[v].pcount.find(groups[1]); + if (it != t->tree[v].pcount.end()) { //this leaf node contains seqs from group l + numSeqsInGroupL = it->second; + }else{ numSeqsInGroupL = 0; } + + double weightedSum = ((numSeqsInGroupI * sum) / (double)tmap->seqsPerGroup[groups[0]]) + ((numSeqsInGroupL * sum) / (double)tmap->seqsPerGroup[groups[1]]); + + //sum /= (double)tmap->seqsPerGroup[t->tree[v].getGroup()]; + + D += weightedSum; + } + } + /********************************************************/ + + //calculate u for the group comb + for(int i=0;igetNumNodes();i++){ + + if (m->control_pressed) { return data; } + + double u; + //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]; + }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]; + } + + u = abs(u * t->tree[i].getBranchLength()); + + //save groupcombs u value + WScore[(groupA+groupB)] += u; + } + + /********************************************************/ + + //calculate weighted score for the group combination + double UN; + UN = (WScore[(groupA+groupB)] / D); + + if (isnan(UN) || isinf(UN)) { UN = 0; } + data.push_back(UN); + + return data; + } + catch(exception& e) { + m->errorOut(e, "Weighted", "getValues"); exit(1); } - } -/**************************************************************************************************/ \ No newline at end of file + + + + + + + +