Bayesian::Bayesian(string tfile, string tempFile, string method, int ksize, int cutoff, int i) :
Classify(), kmerSize(ksize), confidenceThreshold(cutoff), iters(i) {
try {
-
+
/************calculate the probablity that each word will be in a specific taxonomy*************/
string tfileroot = tfile.substr(0,tfile.find_last_of(".")+1);
string tempfileroot = m->getRootName(m->getSimpleName(tempFile));
/**************************************************************************************************/
Bayesian::~Bayesian() {
try {
+
delete phyloTree;
if (database != NULL) { delete database; }
}
//get words contained in query
//getKmerString returns a string where the index in the string is hte kmer number
//and the character at that index can be converted to be the number of times that kmer was seen
-
+
string queryKmerString = kmer.getKmerString(seq->getUnaligned());
vector<int> queryKmers;
if (queryKmers.size() == 0) { m->mothurOut(seq->getName() + "is bad."); m->mothurOutEndLine(); return "bad seq"; }
+
int index = getMostProbableTaxonomy(queryKmers);
if (m->control_pressed) { return tax; }
-//cout << seq->getName() << '\t' << index << endl;
+
//bootstrap - to set confidenceScore
int numToSelect = queryKmers.size() / 8;
+
tax = bootstrapResults(queryKmers, index, numToSelect);
-
+
return tax;
}
catch(exception& e) {
try {
map<int, int> confidenceScores;
+
+ //initialize confidences to 0
+ int seqIndex = tax;
+ TaxNode seq = phyloTree->get(tax);
+ confidenceScores[tax] = 0;
+
+ while (seq.level != 0) { //while you are not at the root
+ seqIndex = seq.parent;
+ confidenceScores[seqIndex] = 0;
+ seq = phyloTree->get(seq.parent);
+ }
map<int, int>::iterator itBoot;
map<int, int>::iterator itBoot2;
if (m->control_pressed) { return "control"; }
vector<int> temp;
-
for (int j = 0; j < numToSelect; j++) {
int index = int(rand() % kmers.size());
//get taxonomy
int newTax = getMostProbableTaxonomy(temp);
+ //int newTax = 1;
TaxNode taxonomyTemp = phyloTree->get(newTax);
-
+
//add to confidence results
while (taxonomyTemp.level != 0) { //while you are not at the root
-
itBoot2 = confidenceScores.find(newTax); //is this a classification we already have a count on
- if (itBoot2 == confidenceScores.end()) { //not already in confidence scores
- confidenceScores[newTax] = 1;
- }else{
- confidenceScores[newTax]++;
+ if (itBoot2 != confidenceScores.end()) { //this is a classification we need a confidence for
+ (itBoot2->second)++;
}
newTax = taxonomyTemp.parent;
int confidence = 0;
if (itBoot2 != confidenceScores.end()) { //already in confidence scores
- confidence = confidenceScores[seqTaxIndex];
+ confidence = itBoot2->second;
}
if (((confidence/(float)iters) * 100) >= confidenceThreshold) {
for (int i = 0; i < queryKmer.size(); i++) {
prob += wordGenusProb[queryKmer[i]][k];
}
-
+
//is this the taxonomy with the greatest probability?
if (prob > maxProbability) {
indexofGenus = genusNodes[k];
private:
vector< vector<float> > wordGenusProb; //vector of maps from genus to probability
- //wordGenusProb[0][392] = probability that a sequence within genus that's index in the tree is 392 would contain kmer 0;
+ //wordGenusProb[0][392] = probability that a sequence within genus that's index in the tree is 392 would contain kmer 0;
vector<int> genusTotals;
vector<int> genusNodes; //indexes in phyloTree where genus' are located
bool done = false;
int count = 0;
-
+
while (!done) {
if (m->control_pressed) { return 0; }
Sequence* candidateSeq = new Sequence(inFASTA); m->gobble(inFASTA);
if (candidateSeq->getName() != "") {
+
taxonomy = classify->getTaxonomy(candidateSeq);
if (m->control_pressed) { delete candidateSeq; return 0; }
}
//report progress
if((count) % 100 != 0){ m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine(); }
-
+
inFASTA.close();
outTax.close();
outTaxSimple.close();
/**************************************************************************************************/
-EstOutput Parsimony::getValues(Tree* t) {
+EstOutput Parsimony::getValues(Tree* t, int p, string o) {
try {
globaldata = GlobalData::getInstance();
- vector<string> groups;
-
- copyTree = new Tree();
+ processors = p;
+ outputDir = o;
//if the users enters no groups then give them the score of all groups
int numGroups = globaldata->Groups.size();
//calculate number of comparsions
int numComp = 0;
+ vector< vector<string> > namesOfGroupCombos;
for (int r=0; r<numGroups; r++) {
for (int l = r+1; l < numGroups; l++) {
numComp++;
+ vector<string> groups; groups.push_back(globaldata->Groups[r]); groups.push_back(globaldata->Groups[l]);
+ //cout << globaldata->Groups[r] << '\t' << globaldata->Groups[l] << endl;
+ namesOfGroupCombos.push_back(groups);
}
}
//numComp+1 for AB, AC, BC, ABC
- data.resize(numComp+1,0);
-
- int count = 0;
- for (int a=0; a<numGroups; a++) {
- for (int l = 0; l < a; l++) {
- int score = 0;
-
- //groups in this combo
- groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]);
-
- //copy users tree so that you can redo pgroups
- copyTree->getCopy(t);
-
- //create pgroups that reflect the groups the user want to use
- for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
- copyTree->tree[i].pGroups = (copyTree->mergeUserGroups(i, groups));
- }
-
- for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
-
- if (m->control_pressed) { return data; }
-
- int lc = copyTree->tree[i].getLChild();
- int rc = copyTree->tree[i].getRChild();
-
- int iSize = copyTree->tree[i].pGroups.size();
- int rcSize = copyTree->tree[rc].pGroups.size();
- int lcSize = copyTree->tree[lc].pGroups.size();
-
- //if isize are 0 then that branch is to be ignored
- if (iSize == 0) { }
- else if ((rcSize == 0) || (lcSize == 0)) { }
- //if you have more groups than either of your kids then theres been a change.
- else if(iSize > rcSize || iSize > lcSize){
- score++;
- }
- }
-
- data[count] = score;
- count++;
- groups.clear();
- }
- }
-
if (numComp != 1) {
+ vector<string> groups;
if (numGroups == 0) {
//get score for all users groups
for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
if (tmap->namesOfGroups[i] != "xxx") {
groups.push_back(tmap->namesOfGroups[i]);
+ //cout << tmap->namesOfGroups[i] << endl;
}
}
+ namesOfGroupCombos.push_back(groups);
}else {
for (int i = 0; i < globaldata->Groups.size(); i++) {
groups.push_back(globaldata->Groups[i]);
+ //cout << globaldata->Groups[i] << endl;
+ }
+ namesOfGroupCombos.push_back(groups);
+ }
+ }
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ if(processors == 1){
+ data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
+ }else{
+ lines.clear();
+ int numPairs = namesOfGroupCombos.size();
+
+ int numPairsPerProcessor = numPairs / processors;
+
+ for (int i = 0; i < processors; i++) {
+ int startPos = i * numPairsPerProcessor;
+
+ if(i == processors - 1){
+ numPairsPerProcessor = numPairs - i * numPairsPerProcessor;
}
+
+ lines.push_back(linePair(startPos, numPairsPerProcessor));
}
+ data = createProcesses(t, namesOfGroupCombos);
+ }
+ #else
+ data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
+ #endif
+
+ return data;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Parsimony", "getValues");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+
+EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos) {
+ try {
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ int process = 1;
+ int num = 0;
+ vector<int> processIDS;
+
+ EstOutput results;
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+
+ if (pid > 0) {
+ 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){
+ EstOutput myresults;
+ myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num);
+
+ if (m->control_pressed) { exit(0); }
+
+ //pass numSeqs to parent
+ ofstream out;
+ string tempFile = outputDir + toString(getpid()) + ".pars.results.temp";
+ m->openOutputFile(tempFile, out);
+ 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("[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<processIDS.size();i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ if (m->control_pressed) { return results; }
+
+ //get data created by processes
+ for (int i=0;i<processIDS.size();i++) {
+ ifstream in;
+ string s = outputDir + toString(processIDS[i]) + ".pars.results.temp";
+ m->openInputFile(s, in);
+
+ //get scores
+ if (!in.eof()) {
+ int num;
+ in >> num; m->gobble(in);
+
+ if (m->control_pressed) { break; }
+
+ double w;
+ for (int j = 0; j < num; j++) {
+ in >> w;
+ results.push_back(w);
+ }
+ m->gobble(in);
+ }
+ in.close();
+ remove(s.c_str());
+ }
+
+ return results;
+#endif
+ }
+ catch(exception& e) {
+ m->errorOut(e, "Parsimony", "createProcesses");
+ exit(1);
+ }
+}
+/**************************************************************************************************/
+EstOutput Parsimony::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num) {
+ try {
+
+ EstOutput results; results.resize(num);
+
+ Tree* copyTree = new Tree();
+ int count = 0;
+
+ for (int h = start; h < (start+num); h++) {
+
+ if (m->control_pressed) { delete copyTree; return results; }
+
+ int score = 0;
+
+ //groups in this combo
+ vector<string> groups = namesOfGroupCombos[h];
+
//copy users tree so that you can redo pgroups
copyTree->getCopy(t);
- int score = 0;
-
+
//create pgroups that reflect the groups the user want to use
for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
copyTree->tree[i].pGroups = (copyTree->mergeUserGroups(i, groups));
}
-
-// map<string,int>::iterator it;
for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
-
+
if (m->control_pressed) { return data; }
int lc = copyTree->tree[i].getLChild();
int rc = copyTree->tree[i].getRChild();
-
+
int iSize = copyTree->tree[i].pGroups.size();
int rcSize = copyTree->tree[rc].pGroups.size();
int lcSize = copyTree->tree[lc].pGroups.size();
-
//if isize are 0 then that branch is to be ignored
if (iSize == 0) { }
else if ((rcSize == 0) || (lcSize == 0)) { }
score++;
}
}
-
- data[count] = score;
-
+
+ results[count] = score;
+ count++;
}
-
+
delete copyTree;
-
- return data;
+
+ return results;
}
catch(exception& e) {
- m->errorOut(e, "Parsimony", "getValues");
+ m->errorOut(e, "Parsimony", "driver");
exit(1);
}
}
public:
Parsimony(TreeMap* t) : tmap(t) {};
~Parsimony() {};
- EstOutput getValues(Tree*);
+ EstOutput getValues(Tree*, int, string);
//EstOutput getValues(Tree*, string, string) { return data; }
private:
+ struct linePair {
+ int start;
+ int num;
+ linePair(int i, int j) : start(i), num(j) {}
+ };
+ vector<linePair> lines;
+
GlobalData* globaldata;
- Tree* copyTree;
EstOutput data;
TreeMap* tmap;
- map<string, int>::iterator it;
+ int processors;
+ string outputDir;
+
+ EstOutput driver(Tree*, vector< vector<string> >, int, int);
+ EstOutput createProcesses(Tree*, vector< vector<string> >);
};
/***********************************************************************/
//**********************************************************************************************************************
vector<string> ParsimonyCommand::getValidParameters(){
try {
- string Array[] = {"random","groups","iters","outputdir","inputdir"};
+ string Array[] = {"random","groups","iters","processors","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
return myArray;
}
else {
//valid paramters for this command
- string Array[] = {"random","groups","iters","outputdir","inputdir"};
+ string Array[] = {"random","groups","processors","iters","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
}
//if the user changes the output directory command factory will send this info to us in the output parameter
- string outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
+ string outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; if (randomtree == "") { outputDir += m->hasPath(globaldata->inputFileName); } }
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
itersString = validParameter.validFile(parameters, "iters", false); if (itersString == "not found") { itersString = "1000"; }
convert(itersString, iters);
+
+ string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = "1"; }
+ convert(temp, processors);
if (abort == false) {
//randomtree will tell us if user had their own treefile or if they just want the random distribution
void ParsimonyCommand::help(){
try {
m->mothurOut("The parsimony command can only be executed after a successful read.tree command, unless you use the random parameter.\n");
- m->mothurOut("The parsimony command parameters are random, groups and iters. No parameters are required.\n");
+ m->mothurOut("The parsimony command parameters are random, groups, processors and iters. No parameters are required.\n");
m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 1 valid group.\n");
m->mothurOut("The group names are separated by dashes. The iters parameter allows you to specify how many random trees you would like compared to your tree.\n");
m->mothurOut("The parsimony command should be in the following format: parsimony(random=yourOutputFilename, groups=yourGroups, iters=yourIters).\n");
+ m->mothurOut("The processors parameter allows you to specify the number of processors to use. The default is 1.\n");
m->mothurOut("Example parsimony(random=out, iters=500).\n");
m->mothurOut("The default value for random is "" (meaning you want to use the trees in your inputfile, randomtree=out means you just want the random distribution of trees outputted to out.rd_parsimony),\n");
m->mothurOut("and iters is 1000. The parsimony command output two files: .parsimony and .psummary their descriptions are in the manual.\n");
if (randomtree == "") {
//get pscores for users trees
for (int i = 0; i < T.size(); i++) {
- userData = pars->getValues(T[i]); //data = AB, AC, BC, ABC.
+ userData = pars->getValues(T[i], processors, outputDir); //data = AB, AC, BC, ABC.
if (m->control_pressed) {
delete reading; delete pars; delete util; delete output;
randT->assembleRandomTree();
//get pscore of random tree
- randomData = pars->getValues(randT);
+ randomData = pars->getValues(randT, processors, outputDir);
if (m->control_pressed) {
delete reading; delete pars; delete util; delete output; delete randT;
//get pscore of random tree
- randomData = pars->getValues(randT);
+ randomData = pars->getValues(randT, processors, outputDir);
if (m->control_pressed) {
delete reading; delete pars; delete util; delete output; delete randT;
Parsimony* pars;
vector<string> groupComb; // AB. AC, BC...
string sumFile, randomtree, allGroups, outputDir;
- int iters, numGroups, numComp, counter;
+ int iters, numGroups, numComp, counter, processors;
vector<int> numEachGroup; //vector containing the number of sequences in each group the users wants for random distrib.
vector< vector<float> > userTreeScores; //scores for users trees for each comb.
vector< vector<float> > UScoreSig; //tree score signifigance when compared to random trees - percentage of random trees with that score or lower.
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);
D[count] += weightedSum;
}
+
count++;
}
m->mothurOut("Processing combo: " + toString(h)); m->mothurOutEndLine();
int numLeaves = t->getNumLeaves();
- map<int, double> tempTotals; //maps node to total Branch Length
- map<int, int> nodePcountSize; //maps node to pcountSize
string groupA = namesOfGroupCombos[h][0];
string groupB = namesOfGroupCombos[h][1];
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; }
//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;
}
+
}
}
}
int numLeaves = t->getNumLeaves();
- map<int, double> tempTotals; //maps node to total Branch Length
- map<int, int> nodePcountSize; //maps node to pcountSize
//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;
+ //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
try {
double sum = 0.0;
- map<int, double> tempTotals; //maps node to total Branch Length
- map<int, int> nodePcountSize; //maps node to pcountSize
- map<int, int>::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<string> 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<string, int>::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<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) {
- 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) {
/**************************************************************************************************/
-
map<string, double> WScore; //a score for each group combination i.e. AB, AC, BC.
int processors;
string outputDir;
+ map< vector<string>, set<int> > rootForGrouping; //maps a grouping combo to the root for that combo
EstOutput driver(Tree*, vector< vector<string> >, int, int);
EstOutput createProcesses(Tree*, vector< vector<string> >);
projects / mothur.git / commitdiff