outputDir = o;
numGroups = globaldata->Groups.size();
-
- vector<double> sums = getBranchLengthSums(t);
if (m->control_pressed) { return data; }
//calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
vector< vector<string> > namesOfGroupCombos;
for (int i=0; i<numGroups; i++) {
- for (int l = i+1; l < numGroups; l++) {
+ for (int l = 0; l < i; l++) {
//initialize weighted scores
//WScore[globaldata->Groups[i]+globaldata->Groups[l]] = 0.0;
vector<string> groups; groups.push_back(globaldata->Groups[i]); groups.push_back(globaldata->Groups[l]);
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
if(processors == 1){
- data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), sums);
+ data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
}else{
int numPairs = namesOfGroupCombos.size();
if(i == processors - 1){
numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
}
- lines.push_back(new linePair(startPos, numPairsPerProcessor));
+ lines.push_back(linePair(startPos, numPairsPerProcessor));
}
- data = createProcesses(t, namesOfGroupCombos, sums);
+ data = createProcesses(t, namesOfGroupCombos);
- for (int i = 0; i < lines.size(); i++) { delete lines[i]; } lines.clear();
+ lines.clear();
}
#else
- data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), sums);
+ data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
#endif
return data;
}
/**************************************************************************************************/
-EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, vector<double>& sums) {
+EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos) {
try {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- int process = 0;
+ int process = 1;
int num = 0;
vector<int> processIDS;
processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
process++;
}else if (pid == 0){
- results = driver(t, namesOfGroupCombos, lines[process]->start, lines[process]->num, sums);
-
- if (m->control_pressed) { exit(0); }
-
+
+ EstOutput Myresults;
+ Myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num);
+
m->mothurOut("Merging results."); m->mothurOutEndLine();
//pass numSeqs to parent
ofstream out;
- string tempFile = outputDir + toString(getpid()) + ".results.temp";
+
+ string tempFile = outputDir + toString(getpid()) + ".weighted.results.temp";
+
m->openOutputFile(tempFile, out);
- out << results.size() << endl;
- for (int i = 0; i < results.size(); i++) { out << results[i] << '\t'; } out << endl;
+
+ out << Myresults.size() << endl;
+ for (int i = 0; i < Myresults.size(); i++) { out << Myresults[i] << '\t'; } out << endl;
out.close();
exit(0);
- }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); exit(0); }
+ }else {
+ m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
+ for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
+ exit(0);
+ }
}
-
+
+ results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num);
+
//force parent to wait until all the processes are done
- for (int i=0;i<processors;i++) {
+ for (int i=0;i<(processors-1);i++) {
int temp = processIDS[i];
wait(&temp);
}
-
+
if (m->control_pressed) { return results; }
//get data created by processes
- for (int i=0;i<processors;i++) {
+ for (int i=0;i<(processors-1);i++) {
ifstream in;
- string s = outputDir + toString(processIDS[i]) + ".results.temp";
+ string s = outputDir + toString(processIDS[i]) + ".weighted.results.temp";
m->openInputFile(s, in);
- vector<double> r;
-
//get quantiles
while (!in.eof()) {
int num;
- in >> num;
+ in >> num; m->gobble(in);
if (m->control_pressed) { break; }
-
- m->gobble(in);
double w;
for (int j = 0; j < num; j++) {
in >> w;
- r.push_back(w);
+ results.push_back(w);
}
m->gobble(in);
}
in.close();
remove(s.c_str());
-
- //save quan in quantiles
- for (int j = 0; j < r.size(); j++) {
- //put all values of r into results
- results.push_back(r[j]);
- }
}
m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
}
}
/**************************************************************************************************/
-EstOutput Weighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, vector<double>& sums) {
+EstOutput Weighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num) {
try {
- globaldata = GlobalData::getInstance();
-
EstOutput results;
vector<double> D;
int count = 0;
- int total = start+num;
- int twentyPercent = (total * 0.20);
-
for (int h = start; h < (start+num); h++) {
if (m->control_pressed) { return results; }
string groupA = namesOfGroupCombos[h][0];
string groupB = namesOfGroupCombos[h][1];
+ set<int> validBranches;
WScore[groupA+groupB] = 0.0;
D.push_back(0.0000); //initialize a spot in D for each combination
map<string, int>::iterator it = t->tree[t->groupNodeInfo[groupA][j]].pcount.find(groupA);
int numSeqsInGroupI = it->second;
- double weightedSum = ((numSeqsInGroupI * sums[t->groupNodeInfo[groupA][j]]) / (double)tmap->seqsPerGroup[groupA]);
+ double sum = getLengthToRoot(t, t->groupNodeInfo[groupA][j], groupA, groupB);
+ double weightedSum = ((numSeqsInGroupI * sum) / (double)tmap->seqsPerGroup[groupA]);
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<string, int>::iterator it = t->tree[t->groupNodeInfo[groupB][j]].pcount.find(groupB);
int numSeqsInGroupL = it->second;
- double weightedSum = ((numSeqsInGroupL * sums[t->groupNodeInfo[groupB][j]]) / (double)tmap->seqsPerGroup[groupB]);
+ double sum = getLengthToRoot(t, t->groupNodeInfo[groupB][j], groupA, groupB);
+ double weightedSum = ((numSeqsInGroupL * sum) / (double)tmap->seqsPerGroup[groupB]);
D[count] += weightedSum;
}
- count++;
- //report progress
- if((h) % twentyPercent == 0){ m->mothurOut("Percentage complete: " + toString(int((h / (float)total) * 100.0))); m->mothurOutEndLine(); }
+ count++;
}
- m->mothurOut("Percentage complete: 100"); m->mothurOutEndLine();
-
//calculate u for the group comb
- for(int i=0;i<t->getNumNodes();i++){
- for (int h = start; h < (start+num); h++) {
+
+ for (int h = start; h < (start+num); h++) {
+ //report progress
+ m->mothurOut("Processing combo: " + toString(h)); m->mothurOutEndLine();
+
+ int numLeaves = t->getNumLeaves();
+
+ string groupA = namesOfGroupCombos[h][0];
+ string groupB = namesOfGroupCombos[h][1];
+
+ //calculate u for the group comb
+ for(int i=0;i<t->getNumNodes();i++){
- string groupA = namesOfGroupCombos[h][0];
- string groupB = namesOfGroupCombos[h][1];
-
- if (m->control_pressed) { return results; }
+ if (m->control_pressed) { return data; }
double u;
+ //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];
}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;
+
+ //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;
+ }
+
}
}
/********************************************************/
-
//calculate weighted score for the group combination
double UN;
count = 0;
}
}
/**************************************************************************************************/
-EstOutput Weighted::getValues(Tree* t, string groupA, string groupB, vector<double>& sums) {
+EstOutput Weighted::getValues(Tree* t, string groupA, string groupB) {
try {
globaldata = GlobalData::getInstance();
//initialize weighted score
WScore[(groupA+groupB)] = 0.0;
double D = 0.0;
+ set<int> validBranches;
vector<string> groups; groups.push_back(groupA); groups.push_back(groupB);
map<string, int>::iterator it = t->tree[t->groupNodeInfo[groups[0]][j]].pcount.find(groups[0]);
int numSeqsInGroupI = it->second;
- double weightedSum = ((numSeqsInGroupI * sums[t->groupNodeInfo[groups[0]][j]]) / (double)tmap->seqsPerGroup[groups[0]]);
+ double sum = getLengthToRoot(t, t->groupNodeInfo[groups[0]][j], groups[0], groups[1]);
+ double weightedSum = ((numSeqsInGroupI * sum) / (double)tmap->seqsPerGroup[groups[0]]);
D += weightedSum;
}
map<string, int>::iterator it = t->tree[t->groupNodeInfo[groups[1]][j]].pcount.find(groups[1]);
int numSeqsInGroupL = it->second;
- double weightedSum = ((numSeqsInGroupL * sums[t->groupNodeInfo[groups[1]][j]]) / (double)tmap->seqsPerGroup[groups[1]]);
+ double sum = getLengthToRoot(t, t->groupNodeInfo[groups[1]][j], groups[0], groups[1]);
+ double weightedSum = ((numSeqsInGroupL * sum) / (double)tmap->seqsPerGroup[groups[1]]);
D += weightedSum;
}
+ int numLeaves = t->getNumLeaves();
+
//calculate u for the group comb
for(int i=0;i<t->getNumNodes();i++){
-
+
if (m->control_pressed) { return data; }
double u;
+ //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];
}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;
- }
-
+
+ //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
}
}
/**************************************************************************************************/
-vector<double> Weighted::getBranchLengthSums(Tree* t) {
+double Weighted::getLengthToRoot(Tree* t, int v, string groupA, string groupB) {
try {
- vector<double> sums;
+ double sum = 0.0;
+ int index = v;
+
+ //you are a leaf
+ if(t->tree[index].getBranchLength() != -1){ sum += abs(t->tree[index].getBranchLength()); }
+ double tempTotal = 0.0;
+ index = t->tree[index].getParent();
+
+ vector<string> grouping; grouping.push_back(groupA); grouping.push_back(groupB);
- for(int v=0;v<t->getNumLeaves();v++){
+ rootForGrouping[grouping].insert(index);
- if (m->control_pressed) { return sums; }
+ //while you aren't at root
+ while(t->tree[index].getParent() != -1){
+
+ if (m->control_pressed) { return sum; }
- 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());
+ //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();
+
+ int sib = lc;
+ if (lc == index) { sib = rc; }
+
+ map<string, int>::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) {
+ sum += abs(t->tree[index].getBranchLength()) + tempTotal;
+ tempTotal = 0.0;
+ }else {
+ 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());
}
- index = t->tree[index].getParent();
- }
-
- //get last breanch length added
- if(t->tree[index].getBranchLength() != -1){
- sum += abs(t->tree[index].getBranchLength());
}
- sums.push_back(sum);
+ 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 sums;
+ return sum;
}
catch(exception& e) {
m->errorOut(e, "Weighted", "getBranchLengthSums");
/**************************************************************************************************/
-