*/
#include "phylodiversitycommand.h"
+#include "treereader.h"
//**********************************************************************************************************************
vector<string> PhyloDiversityCommand::setParameters(){
try {
- CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptree);
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pgroup);
- CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq);
- CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
- CommandParameter prarefy("rarefy", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(prarefy);
- CommandParameter psummary("summary", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(psummary);
- CommandParameter pcollect("collect", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pcollect);
- CommandParameter pscale("scale", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pscale);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none","phylodiv",false,true,true); parameters.push_back(ptree);
+ CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
+ CommandParameter pfreq("freq", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pfreq);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+ CommandParameter prarefy("rarefy", "Boolean", "", "F", "", "", "","rarefy",false,false); parameters.push_back(prarefy);
+ CommandParameter psummary("summary", "Boolean", "", "T", "", "", "","summary",false,false); parameters.push_back(psummary);
+ CommandParameter pcollect("collect", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pcollect);
+ CommandParameter pscale("scale", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pscale);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
string PhyloDiversityCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The phylo.diversity command parameters are tree, group, name, groups, iters, freq, processors, scale, rarefy, collect and summary. tree and group are required, unless you have valid current files.\n";
+ helpString += "The phylo.diversity command parameters are tree, group, name, count, groups, iters, freq, processors, scale, rarefy, collect and summary. tree and group are required, unless you have valid current files.\n";
helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. The group names are separated by dashes. By default all groups are used.\n";
helpString += "The iters parameter allows you to specify the number of randomizations to preform, by default iters=1000, if you set rarefy to true.\n";
helpString += "The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n";
exit(1);
}
}
-
+//**********************************************************************************************************************
+string PhyloDiversityCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "phylodiv") { pattern = "[filename],[tag],phylodiv"; }
+ else if (type == "rarefy") { pattern = "[filename],[tag],phylodiv.rarefaction"; }
+ else if (type == "summary") { pattern = "[filename],[tag],phylodiv.summary"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloDiversityCommand", "getOutputPattern");
+ exit(1);
+ }
+}
//**********************************************************************************************************************
PhyloDiversityCommand::PhyloDiversityCommand(){
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["name"] = inputDir + it->second; }
}
+
+ it = parameters.find("count");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["count"] = inputDir + it->second; }
+ }
}
- m->runParse = true;
- m->clearGroups();
- m->clearAllGroups();
- m->Treenames.clear();
- m->names.clear();
-
//check for required parameters
treefile = validParameter.validFile(parameters, "tree", true);
- if (treefile == "not open") { abort = true; }
+ if (treefile == "not open") { treefile = ""; abort = true; }
else if (treefile == "not found") {
//if there is a current design file, use it
treefile = m->getTreeFile();
else { m->setGroupFile(groupfile); }
namefile = validParameter.validFile(parameters, "name", true);
- if (namefile == "not open") { abort = true; }
+ if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
else { m->setNameFile(namefile); }
+ countfile = validParameter.validFile(parameters, "count", true);
+ if (countfile == "not open") { countfile = ""; abort = true; }
+ else if (countfile == "not found") { countfile = ""; }
+ else { m->setCountTableFile(countfile); }
+
+ if ((namefile != "") && (countfile != "")) {
+ m->mothurOut("[ERROR]: you may only use one of the following: name or count."); m->mothurOutEndLine(); abort = true;
+ }
+
+ if ((groupfile != "") && (countfile != "")) {
+ m->mothurOut("[ERROR]: you may only use one of the following: group or count."); m->mothurOutEndLine(); abort=true;
+ }
+
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(treefile); }
string temp;
temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
- convert(temp, freq);
+ m->mothurConvert(temp, freq);
temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
- convert(temp, iters);
+ m->mothurConvert(temp, iters);
temp = validParameter.validFile(parameters, "rarefy", false); if (temp == "not found") { temp = "F"; }
rarefy = m->isTrue(temp);
temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
}
if ((!collect) && (!rarefy) && (!summary)) { m->mothurOut("No outputs selected. You must set either collect, rarefy or summary to true, summary=T by default."); m->mothurOutEndLine(); abort=true; }
+
+ if (countfile=="") {
+ if (namefile == "") {
+ vector<string> files; files.push_back(treefile);
+ parser.getNameFile(files);
+ }
+ }
}
}
if (abort == true) { if (calledHelp) { return 0; } return 2; }
+ int start = time(NULL);
+
m->setTreeFile(treefile);
-
- if (groupfile != "") {
- //read in group map info.
- tmap = new TreeMap(groupfile);
- tmap->readMap();
- }else{ //fake out by putting everyone in one group
- Tree* tree = new Tree(treefile); delete tree; //extracts names from tree to make faked out groupmap
- tmap = new TreeMap();
-
- for (int i = 0; i < m->Treenames.size(); i++) { tmap->addSeq(m->Treenames[i], "Group1"); }
- }
-
- if (namefile != "") { readNamesFile(); }
-
- read = new ReadNewickTree(treefile);
- int readOk = read->read(tmap);
-
- if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); delete tmap; delete read; return 0; }
-
- read->AssembleTrees();
- vector<Tree*> trees = read->getTrees();
- delete read;
-
- //make sure all files match
- //if you provide a namefile we will use the numNames in the namefile as long as the number of unique match the tree names size.
- int numNamesInTree;
- if (namefile != "") {
- if (numUniquesInName == m->Treenames.size()) { numNamesInTree = nameMap.size(); }
- else { numNamesInTree = m->Treenames.size(); }
- }else { numNamesInTree = m->Treenames.size(); }
-
-
- //output any names that are in group file but not in tree
- if (numNamesInTree < tmap->getNumSeqs()) {
- for (int i = 0; i < tmap->namesOfSeqs.size(); i++) {
- //is that name in the tree?
- int count = 0;
- for (int j = 0; j < m->Treenames.size(); j++) {
- if (tmap->namesOfSeqs[i] == m->Treenames[j]) { break; } //found it
- count++;
- }
-
- if (m->control_pressed) {
- delete tmap; for (int i = 0; i < trees.size(); i++) { delete trees[i]; }
- for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
- m->clearGroups();
- return 0;
- }
-
- //then you did not find it so report it
- if (count == m->Treenames.size()) {
- //if it is in your namefile then don't remove
- map<string, string>::iterator it = nameMap.find(tmap->namesOfSeqs[i]);
-
- if (it == nameMap.end()) {
- m->mothurOut(tmap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); m->mothurOutEndLine();
- tmap->removeSeq(tmap->namesOfSeqs[i]);
- i--; //need this because removeSeq removes name from namesOfSeqs
- }
- }
- }
- }
-
- SharedUtil* util = new SharedUtil();
+ TreeReader* reader;
+ if (countfile == "") { reader = new TreeReader(treefile, groupfile, namefile); }
+ else { reader = new TreeReader(treefile, countfile); }
+ vector<Tree*> trees = reader->getTrees();
+ ct = trees[0]->getCountTable();
+ delete reader;
+
+ SharedUtil util;
vector<string> mGroups = m->getGroups();
- vector<string> tGroups = tmap->getNamesOfGroups();
- util->setGroups(mGroups, tGroups, "phylo.diversity"); //sets the groups the user wants to analyze
- delete util;
+ vector<string> tGroups = ct->getNamesOfGroups();
+ util.setGroups(mGroups, tGroups, "phylo.diversity"); //sets the groups the user wants to analyze
//incase the user had some mismatches between the tree and group files we don't want group xxx to be analyzed
for (int i = 0; i < mGroups.size(); i++) { if (mGroups[i] == "xxx") { mGroups.erase(mGroups.begin()+i); break; } }
//for each of the users trees
for(int i = 0; i < trees.size(); i++) {
- if (m->control_pressed) { delete tmap; for (int j = 0; j < trees.size(); j++) { delete trees[j]; } for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
+ if (m->control_pressed) { delete ct; for (int j = 0; j < trees.size(); j++) { delete trees[j]; } for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
ofstream outSum, outRare, outCollect;
- string outSumFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(i+1) + ".phylodiv.summary";
- string outRareFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(i+1) + ".phylodiv.rarefaction";
- string outCollectFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(i+1) + ".phylodiv";
+ map<string, string> variables;
+ variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(treefile));
+ variables["[tag]"] = toString(i+1);
+ string outSumFile = getOutputFileName("summary",variables);
+ string outRareFile = getOutputFileName("rarefy",variables);
+ string outCollectFile = getOutputFileName("phylodiv",variables);
if (summary) { m->openOutputFile(outSumFile, outSum); outputNames.push_back(outSumFile); outputTypes["summary"].push_back(outSumFile); }
if (rarefy) { m->openOutputFile(outRareFile, outRare); outputNames.push_back(outRareFile); outputTypes["rarefy"].push_back(outRareFile); }
randomLeaf.push_back(j);
}
}
+
+ /* float sum = 0;
+ vector<float> sums; sums.resize(m->getGroups().size(), 0);
+ vector<float> sumsAboveRoot; sumsAboveRoot.resize(m->getGroups().size(), 0);
+ for (int j = 0; j < trees[i]->getNumNodes(); j++) {
+ if (trees[i]->tree[j].getBranchLength() < 0) { cout << j << '\t' << trees[i]->tree[j].getName() << '\t' << trees[i]->tree[j].getBranchLength() << endl; }
+
+ sum += abs(trees[i]->tree[j].getBranchLength());
+ for (int k = 0; k < m->getGroups().size(); k++) {
+ map<string, int>::iterator itGroup = trees[i]->tree[j].pcount.find(m->getGroups()[k]);
+ if (itGroup != trees[i]->tree[j].pcount.end()) { //this branch belongs to a group we care about
+ if (j < rootForGroup[m->getGroups()[k]]) {
+ sums[k] += abs(trees[i]->tree[j].getBranchLength());
+ }else {
+ sumsAboveRoot[k] += abs(trees[i]->tree[j].getBranchLength());
+ }
+ }
+ }
+ }
+ cout << sum << endl; //exit(1);
+
+ for (int k = 0; k < m->getGroups().size(); k++) {
+ cout << m->getGroups()[k] << "root node = " << rootForGroup[m->getGroups()[k]] << "sum below root = " << sums[k] << "sum above root = " << sumsAboveRoot[k] << endl;
+ }
+ exit(1); */
numLeafNodes = randomLeaf.size(); //reset the number of leaf nodes you are using
//find largest group total
int largestGroup = 0;
- for (int j = 0; j < mGroups.size(); j++) {
- if (tmap->seqsPerGroup[mGroups[j]] > largestGroup) { largestGroup = tmap->seqsPerGroup[mGroups[j]]; }
+ for (int j = 0; j < mGroups.size(); j++) {
+ int numSeqsThisGroup = ct->getGroupCount(mGroups[j]);
+ if (numSeqsThisGroup > largestGroup) { largestGroup = numSeqsThisGroup; }
//initialize diversity
- diversity[mGroups[j]].resize(tmap->seqsPerGroup[mGroups[j]]+1, 0.0); //numSampled
+ diversity[mGroups[j]].resize(numSeqsThisGroup+1, 0.0); //numSampled
//groupA 0.0 0.0
//initialize sumDiversity
- sumDiversity[mGroups[j]].resize(tmap->seqsPerGroup[mGroups[j]]+1, 0.0);
+ sumDiversity[mGroups[j]].resize(numSeqsThisGroup+1, 0.0);
}
//convert freq percentage to number
if (numSampledList.count(diversity[mGroups[j]].size()-1) == 0) { numSampledList.insert(diversity[mGroups[j]].size()-1); }
}
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- if(processors == 1){
- driver(trees[i], diversity, sumDiversity, iters, increment, randomLeaf, numSampledList, outCollect, outSum, true);
- }else{
- if (rarefy) {
- vector<int> procIters;
-
- int numItersPerProcessor = iters / processors;
-
- //divide iters between processes
- for (int h = 0; h < processors; h++) {
- if(h == processors - 1){
- numItersPerProcessor = iters - h * numItersPerProcessor;
- }
- procIters.push_back(numItersPerProcessor);
- }
-
- createProcesses(procIters, trees[i], diversity, sumDiversity, iters, increment, randomLeaf, numSampledList, outCollect, outSum);
-
- }else{ //no need to paralellize if you dont want to rarefy
- driver(trees[i], diversity, sumDiversity, iters, increment, randomLeaf, numSampledList, outCollect, outSum, true);
- }
- }
-
- #else
- driver(trees[i], diversity, sumDiversity, iters, increment, randomLeaf, numSampledList, outCollect, outSum, true);
- #endif
-
+ if (rarefy) {
+ vector<int> procIters;
+ int numItersPerProcessor = iters / processors;
+
+ //divide iters between processes
+ for (int h = 0; h < processors; h++) {
+ if(h == processors - 1){ numItersPerProcessor = iters - h * numItersPerProcessor; }
+ procIters.push_back(numItersPerProcessor);
+ }
+
+ createProcesses(procIters, trees[i], diversity, sumDiversity, iters, increment, randomLeaf, numSampledList, outCollect, outSum);
+
+ }else{ //no need to paralellize if you dont want to rarefy
+ driver(trees[i], diversity, sumDiversity, iters, increment, randomLeaf, numSampledList, outCollect, outSum, true);
+ }
+
if (rarefy) { printData(numSampledList, sumDiversity, outRare, iters); }
}
if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run phylo.diversity."); m->mothurOutEndLine();
+
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
//**********************************************************************************************************************
int PhyloDiversityCommand::createProcesses(vector<int>& procIters, Tree* t, map< string, vector<float> >& div, map<string, vector<float> >& sumDiv, int numIters, int increment, vector<int>& randomLeaf, set<int>& numSampledList, ofstream& outCollect, ofstream& outSum){
try {
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
- int process = 1;
+ int process = 1;
vector<int> processIDS;
map< string, vector<float> >::iterator itSum;
-
+
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+
//loop through and create all the processes you want
while (process != processors) {
int pid = fork();
in.close();
m->mothurRemove(inTemp);
}
+#else
+
+ //fill in functions
+ vector<phylodivData*> pDataArray;
+ DWORD dwThreadIdArray[processors-1];
+ HANDLE hThreadArray[processors-1];
+ vector<CountTable*> cts;
+ vector<Tree*> trees;
+ map<string, int> rootForGroup = getRootForGroups(t);
+
+ //Create processor worker threads.
+ for( int i=1; i<processors; i++ ){
+ CountTable* copyCount = new CountTable();
+ copyCount->copy(ct);
+ Tree* copyTree = new Tree(copyCount);
+ copyTree->getCopy(t);
+
+ cts.push_back(copyCount);
+ trees.push_back(copyTree);
+
+ map<string, vector<float> > copydiv = div;
+ map<string, vector<float> > copysumDiv = sumDiv;
+ vector<int> copyrandomLeaf = randomLeaf;
+ set<int> copynumSampledList = numSampledList;
+ map<string, int> copyRootForGrouping = rootForGroup;
+
+ phylodivData* temp = new phylodivData(m, procIters[i], copydiv, copysumDiv, copyTree, copyCount, increment, copyrandomLeaf, copynumSampledList, copyRootForGrouping);
+ pDataArray.push_back(temp);
+ processIDS.push_back(i);
+
+ hThreadArray[i-1] = CreateThread(NULL, 0, MyPhyloDivThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
+ }
+
+ driver(t, div, sumDiv, procIters[0], increment, randomLeaf, numSampledList, outCollect, outSum, true);
+
+ //Wait until all threads have terminated.
+ WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
+
+ //Close all thread handles and free memory allocations.
+ for(int i=0; i < pDataArray.size(); i++){
+ for (itSum = pDataArray[i]->sumDiv.begin(); itSum != pDataArray[i]->sumDiv.end(); itSum++) {
+ for (int k = 0; k < (itSum->second).size(); k++) {
+ sumDiv[itSum->first][k] += (itSum->second)[k];
+ }
+ }
+ delete cts[i];
+ delete trees[i];
+ CloseHandle(hThreadArray[i]);
+ delete pDataArray[i];
+ }
#endif
try {
int numLeafNodes = randomLeaf.size();
vector<string> mGroups = m->getGroups();
-
+
+ map<string, int> rootForGroup = getRootForGroups(t); //maps groupName to root node in tree. "root" for group may not be the trees root and we don't want to include the extra branches.
+
for (int l = 0; l < numIters; l++) {
random_shuffle(randomLeaf.begin(), randomLeaf.end());
-
+
//initialize counts
map<string, int> counts;
- map< string, set<int> > countedBranch;
- for (int j = 0; j < mGroups.size(); j++) { counts[mGroups[j]] = 0; countedBranch[mGroups[j]].insert(-2); } //add dummy index to initialize countedBranch sets
+ vector< map<string, bool> > countedBranch;
+ for (int i = 0; i < t->getNumNodes(); i++) {
+ map<string, bool> temp;
+ for (int j = 0; j < mGroups.size(); j++) { temp[mGroups[j]] = false; }
+ countedBranch.push_back(temp);
+ }
+
+ for (int j = 0; j < mGroups.size(); j++) { counts[mGroups[j]] = 0; }
for(int k = 0; k < numLeafNodes; k++){
if (m->control_pressed) { return 0; }
//calc branch length of randomLeaf k
- vector<float> br = calcBranchLength(t, randomLeaf[k], countedBranch);
+ vector<float> br = calcBranchLength(t, randomLeaf[k], countedBranch, rootForGroup);
//for each group in the groups update the total branch length accounting for the names file
vector<string> groups = t->tree[randomLeaf[k]].getGroup();
for (int j = 0; j < groups.size(); j++) {
- int numSeqsInGroupJ = 0;
- map<string, int>::iterator it;
- it = t->tree[randomLeaf[k]].pcount.find(groups[j]);
- if (it != t->tree[randomLeaf[k]].pcount.end()) { //this leaf node contains seqs from group j
- numSeqsInGroupJ = it->second;
- }
-
- if (numSeqsInGroupJ != 0) { div[groups[j]][(counts[groups[j]]+1)] = div[groups[j]][counts[groups[j]]] + br[j]; }
-
- for (int s = (counts[groups[j]]+2); s <= (counts[groups[j]]+numSeqsInGroupJ); s++) {
- div[groups[j]][s] = div[groups[j]][s-1]; //update counts, but don't add in redundant branch lengths
- }
- counts[groups[j]] += numSeqsInGroupJ;
+
+ if (m->inUsersGroups(groups[j], mGroups)) {
+ int numSeqsInGroupJ = 0;
+ map<string, int>::iterator it;
+ it = t->tree[randomLeaf[k]].pcount.find(groups[j]);
+ if (it != t->tree[randomLeaf[k]].pcount.end()) { //this leaf node contains seqs from group j
+ numSeqsInGroupJ = it->second;
+ }
+
+ if (numSeqsInGroupJ != 0) { div[groups[j]][(counts[groups[j]]+1)] = div[groups[j]][counts[groups[j]]] + br[j]; }
+
+ for (int s = (counts[groups[j]]+2); s <= (counts[groups[j]]+numSeqsInGroupJ); s++) {
+ div[groups[j]][s] = div[groups[j]][s-1]; //update counts, but don't add in redundant branch lengths
+ }
+ counts[groups[j]] += numSeqsInGroupJ;
+ }
}
}
else { score = div[mGroups[j]][numSampled] / (float)numIters; }
out << setprecision(4) << score << endl;
+ //cout << mGroups[j] << '\t' << numSampled << '\t'<< setprecision(4) << score << endl;
}
out.close();
}
//**********************************************************************************************************************
//need a vector of floats one branch length for every group the node represents.
-vector<float> PhyloDiversityCommand::calcBranchLength(Tree* t, int leaf, map< string, set<int> >& counted){
+vector<float> PhyloDiversityCommand::calcBranchLength(Tree* t, int leaf, vector< map<string, bool> >& counted, map<string, int> roots){
try {
-
+
//calc the branch length
//while you aren't at root
vector<float> sums;
vector<string> groups = t->tree[leaf].getGroup();
sums.resize(groups.size(), 0.0);
- map<string, map<int, double> > tempTotals; //maps node to total Branch Length
- map< string, set<int> > tempCounted;
- set<int>::iterator it;
-
- //you are a leaf
+
+ //you are a leaf
if(t->tree[index].getBranchLength() != -1){
for (int k = 0; k < groups.size(); k++) {
- sums[k] += abs(t->tree[index].getBranchLength());
- counted[groups[k]].insert(index);
+ sums[k] += abs(t->tree[index].getBranchLength());
}
}
-
- for (int k = 0; k < groups.size(); k++) {
- tempTotals[groups[k]][index] = 0.0;
- }
-
- index = t->tree[index].getParent();
-
+
+
+ index = t->tree[index].getParent();
+
//while you aren't at root
while(t->tree[index].getParent() != -1){
-
+
if (m->control_pressed) { return sums; }
- int pcountSize = 0;
for (int k = 0; k < groups.size(); k++) {
- map<string, int>::iterator itGroup = t->tree[index].pcount.find(groups[k]);
- if (itGroup != t->tree[index].pcount.end()) { pcountSize++; }
-
- //do both your chidren have have descendants from the users groups?
- int lc = t->tree[index].getLChild();
- int rc = t->tree[index].getRChild();
-
- int LpcountSize = 0;
- itGroup = t->tree[lc].pcount.find(groups[k]);
- if (itGroup != t->tree[lc].pcount.end()) { LpcountSize++; }
-
- int RpcountSize = 0;
- itGroup = t->tree[rc].pcount.find(groups[k]);
- if (itGroup != t->tree[rc].pcount.end()) { RpcountSize++; }
-
- //if yes, add your childrens tempTotals
- if ((LpcountSize != 0) && (RpcountSize != 0)) {
- sums[k] += tempTotals[groups[k]][lc] + tempTotals[groups[k]][rc];
-
- for (it = tempCounted[groups[k]].begin(); it != tempCounted[groups[k]].end(); it++) { counted[groups[k]].insert(*it); }
-
- //cout << "added to total " << tempTotals[lc] << '\t' << tempTotals[rc] << endl;
- if (t->tree[index].getBranchLength() != -1) {
- if (counted[groups[k]].count(index) == 0) {
- tempTotals[groups[k]][index] = abs(t->tree[index].getBranchLength());
- tempCounted[groups[k]].insert(index);
- }else{
- tempTotals[groups[k]][index] = 0.0;
- }
- }else {
- tempTotals[groups[k]][index] = 0.0;
- }
- }else { //if no, your tempTotal is your childrens temp totals + your branch length
- tempTotals[groups[k]][index] = tempTotals[groups[k]][lc] + tempTotals[groups[k]][rc];
-
- if (counted[groups[k]].count(index) == 0) {
- tempTotals[groups[k]][index] += abs(t->tree[index].getBranchLength());
- tempCounted[groups[k]].insert(index);
- }
-
- }
- //cout << "temptotal = "<< tempTotals[i] << endl;
- }
-
- index = t->tree[index].getParent();
- }
-
+
+ if (index >= roots[groups[k]]) { counted[index][groups[k]] = true; } //if you are at this groups "root", then say we are done
+
+ if (!counted[index][groups[k]]){ //if counted[index][groups[k] is true this groups has already added all br from here to root, so quit early
+ if (t->tree[index].getBranchLength() != -1) {
+ sums[k] += abs(t->tree[index].getBranchLength());
+ }
+ counted[index][groups[k]] = true;
+ }
+ }
+ index = t->tree[index].getParent();
+ }
+
return sums;
-
+
}
catch(exception& e) {
m->errorOut(e, "PhyloDiversityCommand", "calcBranchLength");
exit(1);
}
}
-/*****************************************************************/
-int PhyloDiversityCommand::readNamesFile() {
+//**********************************************************************************************************************
+map<string, int> PhyloDiversityCommand::getRootForGroups(Tree* t){
try {
- m->names.clear();
- numUniquesInName = 0;
-
- ifstream in;
- m->openInputFile(namefile, in);
-
- string first, second;
- map<string, string>::iterator itNames;
-
- while(!in.eof()) {
- in >> first >> second; m->gobble(in);
-
- numUniquesInName++;
-
- itNames = m->names.find(first);
- if (itNames == m->names.end()) {
- m->names[first] = second;
-
- //we need a list of names in your namefile to use above when removing extra seqs above so we don't remove them
- vector<string> dupNames;
- m->splitAtComma(second, dupNames);
-
- for (int i = 0; i < dupNames.size(); i++) {
- nameMap[dupNames[i]] = dupNames[i];
- if ((groupfile == "") && (i != 0)) { tmap->addSeq(dupNames[i], "Group1"); }
- }
- }else { m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); m->names.clear(); namefile = ""; return 1; }
- }
- in.close();
-
- return 0;
+ map<string, int> roots; //maps group to root for group, may not be root of tree
+ map<string, bool> done;
+
+ //initialize root for all groups to -1
+ for (int k = 0; k < (t->getCountTable())->getNamesOfGroups().size(); k++) { done[(t->getCountTable())->getNamesOfGroups()[k]] = false; }
+
+ for (int i = 0; i < t->getNumLeaves(); i++) {
+
+ vector<string> groups = t->tree[i].getGroup();
+
+ int index = t->tree[i].getParent();
+
+ for (int j = 0; j < groups.size(); j++) {
+
+ if (done[groups[j]] == false) { //we haven't found the root for this group yet, initialize it
+ done[groups[j]] = true;
+ roots[groups[j]] = i; //set root to self to start
+ }
+
+ //while you aren't at root
+ while(t->tree[index].getParent() != -1){
+
+ if (m->control_pressed) { return roots; }
+
+ //do both your chidren have have descendants from the users groups?
+ int lc = t->tree[index].getLChild();
+ int rc = t->tree[index].getRChild();
+
+ int LpcountSize = 0;
+ map<string, int>:: iterator itGroup = t->tree[lc].pcount.find(groups[j]);
+ if (itGroup != t->tree[lc].pcount.end()) { LpcountSize++; }
+
+ int RpcountSize = 0;
+ itGroup = t->tree[rc].pcount.find(groups[j]);
+ if (itGroup != t->tree[rc].pcount.end()) { RpcountSize++; }
+
+ if ((LpcountSize != 0) && (RpcountSize != 0)) { //possible root
+ if (index > roots[groups[j]]) { roots[groups[j]] = index; }
+ }else { ;}
+
+ index = t->tree[index].getParent();
+ }
+ //}
+ }
+ }
+
+
+
+ return roots;
+
}
catch(exception& e) {
- m->errorOut(e, "PhyloDiversityCommand", "readNamesFile");
+ m->errorOut(e, "PhyloDiversityCommand", "getRootForGroups");
exit(1);
}
}
-
//**********************************************************************************************************************
projects / mothur.git / blobdiff