+++ /dev/null
-/*
- * parsimony.cpp
- * Mothur
- *
- * Created by Sarah Westcott on 1/26/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "parsimony.h"
-
-/**************************************************************************************************/
-
-EstOutput Parsimony::getValues(Tree* t, int p, string o) {
- try {
- processors = p;
- outputDir = o;
- TreeMap* tmap = t->getTreeMap();
-
- //if the users enters no groups then give them the score of all groups
- vector<string> mGroups = m->getGroups();
- int numGroups = mGroups.size();
-
- //calculate number of comparsions
- int numComp = 0;
- vector< vector<string> > namesOfGroupCombos;
- for (int r=0; r<numGroups; r++) {
- for (int l = 0; l < r; l++) {
- numComp++;
- vector<string> groups; groups.push_back(mGroups[r]); groups.push_back(mGroups[l]);
- //cout << globaldata->Groups[r] << '\t' << globaldata->Groups[l] << endl;
- namesOfGroupCombos.push_back(groups);
- }
- }
-
- //numComp+1 for AB, AC, BC, ABC
- if (numComp != 1) {
- vector<string> groups;
- if (numGroups == 0) {
- //get score for all users groups
- vector<string> tGroups = tmap->getNamesOfGroups();
- for (int i = 0; i < tGroups.size(); i++) {
- if (tGroups[i] != "xxx") {
- groups.push_back(tGroups[i]);
- //cout << tmap->namesOfGroups[i] << endl;
- }
- }
- namesOfGroupCombos.push_back(groups);
- }else {
- for (int i = 0; i < mGroups.size(); i++) {
- groups.push_back(mGroups[i]);
- //cout << globaldata->Groups[i] << endl;
- }
- namesOfGroupCombos.push_back(groups);
- }
- }
-
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- if(processors == 1){
- data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), tmap);
- }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, tmap);
- }
- #else
- data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), tmap);
- #endif
-
- return data;
-
- }
- catch(exception& e) {
- m->errorOut(e, "Parsimony", "getValues");
- exit(1);
- }
-}
-/**************************************************************************************************/
-
-EstOutput Parsimony::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, TreeMap* tmap) {
- try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- int process = 1;
- 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, tmap);
-
- 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, tmap);
-
- //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();
- m->mothurRemove(s);
- }
-
- 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, TreeMap* tmap) {
- try {
-
- EstOutput results; results.resize(num);
-
- Tree* copyTree = new Tree(tmap);
- 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);
-
- //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++;
- }
- }
-
- results[count] = score;
- count++;
- }
-
- delete copyTree;
-
- return results;
- }
- catch(exception& e) {
- m->errorOut(e, "Parsimony", "driver");
- exit(1);
- }
-}
-
-/**************************************************************************************************/
-
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