vector<string> PhyloDiversityCommand::setParameters(){
try {
- CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptree);
- CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount);
- CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); 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); 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::getOutputFileNameTag(string type, string inputName=""){
- try {
- string outputFileName = "";
- map<string, vector<string> >::iterator it;
+string PhyloDiversityCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
- //is this a type this command creates
- it = outputTypes.find(type);
- if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
- else {
- if (type == "phylodiv") { outputFileName = "phylodiv"; }
- else if (type == "rarefy") { outputFileName = "phylodiv.rarefaction"; }
- else if (type == "summary") { outputFileName = "phylodiv.summary"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
- }
- return outputFileName;
- }
- catch(exception& e) {
- m->errorOut(e, "PhyloDiversityCommand", "getOutputFileNameTag");
- exit(1);
- }
+ 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);
+ }
}
//**********************************************************************************************************************
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) + "." + getOutputFileNameTag("summary");
- string outRareFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(i+1) + "." + getOutputFileNameTag("rarefy");
- string outCollectFile = outputDir + m->getRootName(m->getSimpleName(treefile)) + toString(i+1) + "." + getOutputFileNameTag("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
if (numSampledList.count(diversity[mGroups[j]].size()-1) == 0) { numSampledList.insert(diversity[mGroups[j]].size()-1); }
}
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- 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); }
}
//**********************************************************************************************************************
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) || (__linux__) || (__unix__) || (__unix)
- 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
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();
//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());
+ sums[k] += abs(t->tree[index].getBranchLength());
}
}
for (int j = 0; j < groups.size(); j++) {
- if (done[groups[j]] == false) { //we haven't found the root for this group yet
-
- done[groups[j]] = true;
- roots[groups[j]] = i; //set root to self to start
+ 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 (itGroup != t->tree[rc].pcount.end()) { RpcountSize++; }
if ((LpcountSize != 0) && (RpcountSize != 0)) { //possible root
- roots[groups[j]] = index;
+ if (index > roots[groups[j]]) { roots[groups[j]] = index; }
}else { ;}
index = t->tree[index].getParent();
}
- }
+ //}
}
}
+
+
return roots;
}
projects / mothur.git / blobdiff