+++ /dev/null
-/*
- * unweighted.cpp
- * Mothur
- *
- * Created by Sarah Westcott on 2/9/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "unweighted.h"
-
-/**************************************************************************************************/
-
-EstOutput Unweighted::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
- int numGroups = m->getNumGroups();
-
- //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((m->getGroups())[r]); groups.push_back((m->getGroups())[l]);
- namesOfGroupCombos.push_back(groups);
- }
- }
-
- if (numComp != 1) {
- vector<string> groups;
- if (numGroups == 0) {
- //get score for all users groups
- for (int i = 0; i < (tmap->getNamesOfGroups()).size(); i++) {
- if ((tmap->getNamesOfGroups())[i] != "xxx") {
- groups.push_back((tmap->getNamesOfGroups())[i]);
- }
- }
- namesOfGroupCombos.push_back(groups);
- }else {
- for (int i = 0; i < m->getNumGroups(); i++) {
- groups.push_back((m->getGroups())[i]);
- }
- 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{
- 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);
- lines.clear();
- }
- #else
- data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), tmap);
- #endif
-
- return data;
- }
- catch(exception& e) {
- m->errorOut(e, "Unweighted", "getValues");
- exit(1);
- }
-}
-/**************************************************************************************************/
-
-EstOutput Unweighted::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); }
-
- m->mothurOut("Merging results."); m->mothurOutEndLine();
-
- //pass numSeqs to parent
- ofstream out;
- string tempFile = outputDir + toString(getpid()) + ".unweighted.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<(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-1);i++) {
- ifstream in;
- string s = outputDir + toString(processIDS[i]) + ".unweighted.results.temp";
- m->openInputFile(s, in);
-
- //get quantiles
- 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);
- }
-
- m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
-
- return results;
-#endif
- }
- catch(exception& e) {
- m->errorOut(e, "Unweighted", "createProcesses");
- exit(1);
- }
-}
-/**************************************************************************************************/
-EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, TreeMap* tmap) {
- try {
-
-
- EstOutput results; results.resize(num);
-
- int count = 0;
- int total = num;
- int twentyPercent = (total * 0.20);
- if (twentyPercent == 0) { twentyPercent = 1; }
-
-
- for (int h = start; h < (start+num); h++) {
-
- if (m->control_pressed) { return results; }
-
- double UniqueBL=0.0000; //a branch length is unique if it's chidren are from the same group
- double totalBL = 0.00; //all branch lengths
- double UW = 0.00; //Unweighted Value = UniqueBL / totalBL;
-
- //find a node that belongs to one of the groups in this combo
- int nodeBelonging = -1;
- for (int g = 0; g < namesOfGroupCombos[h].size(); g++) {
- if (t->groupNodeInfo[namesOfGroupCombos[h][g]].size() != 0) { nodeBelonging = t->groupNodeInfo[namesOfGroupCombos[h][g]][0]; break; }
- }
-
- //sanity check
- if (nodeBelonging == -1) {
- m->mothurOut("[WARNING]: cannot find a nodes in the tree from grouping ");
- for (int g = 0; g < namesOfGroupCombos[h].size()-1; g++) { m->mothurOut(namesOfGroupCombos[h][g] + "-"); }
- m->mothurOut(namesOfGroupCombos[h][namesOfGroupCombos[h].size()-1]);
- m->mothurOut(", skipping."); m->mothurOutEndLine(); results[count] = UW;
- }else{
- //cout << "trying to get root" << endl;
- //if including the root this clears rootForGrouping[namesOfGroupCombos[h]]
- getRoot(t, nodeBelonging, namesOfGroupCombos[h]);
- //cout << "here" << endl;
- for(int i=0;i<t->getNumNodes();i++){
-
- if (m->control_pressed) { return data; }
- //cout << i << endl;
- //pcountSize = 0, they are from a branch that is entirely from a group the user doesn't want
- //pcountSize = 2, not unique to one group
- //pcountSize = 1, unique to one group
-
- int pcountSize = 0;
- for (int j = 0; j < namesOfGroupCombos[h].size(); j++) {
- map<string, int>::iterator itGroup = t->tree[i].pcount.find(namesOfGroupCombos[h][j]);
- if (itGroup != t->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
- }
-
-
- //unique calc
- if (pcountSize == 0) { }
- else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1) && (rootForGrouping[namesOfGroupCombos[h]].count(i) == 0)) { //you have a unique branch length and you are not the root
- UniqueBL += abs(t->tree[i].getBranchLength());
- }
-
- //total calc
- if (pcountSize == 0) { }
- else if ((t->tree[i].getBranchLength() != -1) && (pcountSize != 0) && (rootForGrouping[namesOfGroupCombos[h]].count(i) == 0)) { //you have a branch length and you are not the root
- totalBL += abs(t->tree[i].getBranchLength());
- }
- }
- //cout << UniqueBL << '\t' << totalBL << endl;
- UW = (UniqueBL / totalBL);
-
- if (isnan(UW) || isinf(UW)) { UW = 0; }
-
- results[count] = UW;
- }
- count++;
-
- //report progress
- //if((count % twentyPercent) == 0) { float tempOut = (count / (float)total); if (isnan(tempOut) || isinf(tempOut)) { tempOut = 0.0; } m->mothurOut("Percentage complete: " + toString((int(tempOut) * 100.0))); m->mothurOutEndLine(); }
- }
-
- //report progress
- //if((count % twentyPercent) != 0) { float tempOut = (count / (float)total); if (isnan(tempOut) || isinf(tempOut)) { tempOut = 0.0; } m->mothurOut("Percentage complete: " + toString((int(tempOut) * 100.0))); m->mothurOutEndLine(); }
-
- return results;
- }
- catch(exception& e) {
- m->errorOut(e, "Unweighted", "driver");
- exit(1);
- }
-}
-/**************************************************************************************************/
-
-EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, 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
- int numGroups = m->getNumGroups();
-
- //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((m->getGroups())[r]); groups.push_back((m->getGroups())[l]);
- namesOfGroupCombos.push_back(groups);
- }
- }
-
- if (numComp != 1) {
- vector<string> groups;
- if (numGroups == 0) {
- //get score for all users groups
- for (int i = 0; i < (tmap->getNamesOfGroups()).size(); i++) {
- if ((tmap->getNamesOfGroups())[i] != "xxx") {
- groups.push_back((tmap->getNamesOfGroups())[i]);
- }
- }
- namesOfGroupCombos.push_back(groups);
- }else {
- for (int i = 0; i < m->getNumGroups(); i++) {
- groups.push_back((m->getGroups())[i]);
- }
- namesOfGroupCombos.push_back(groups);
- }
- }
-
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- if(processors == 1){
- data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true, tmap);
- }else{
- 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, true, tmap);
-
- lines.clear();
- }
- #else
- data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true, tmap);
- #endif
-
- return data;
- }
- catch(exception& e) {
- m->errorOut(e, "Unweighted", "getValues");
- exit(1);
- }
-}
-/**************************************************************************************************/
-
-EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, bool usingGroups, 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, usingGroups, tmap);
-
- if (m->control_pressed) { exit(0); }
-
- //pass numSeqs to parent
- ofstream out;
- string tempFile = outputDir + toString(getpid()) + ".unweighted.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, usingGroups, tmap);
-
- //force parent to wait until all the processes are done
- 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-1);i++) {
- ifstream in;
- string s = outputDir + toString(processIDS[i]) + ".unweighted.results.temp";
- m->openInputFile(s, in);
-
- //get quantiles
- 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, "Unweighted", "createProcesses");
- exit(1);
- }
-}
-/**************************************************************************************************/
-EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, bool usingGroups, TreeMap* tmap) {
- try {
-
- EstOutput results; results.resize(num);
-
- int count = 0;
-
- Tree* copyTree = new Tree(tmap);
-
- for (int h = start; h < (start+num); h++) {
-
- if (m->control_pressed) { return results; }
-
- //copy random tree passed in
- copyTree->getCopy(t);
-
- //swap labels in the groups you want to compare
- copyTree->assembleRandomUnifracTree(namesOfGroupCombos[h]);
-
- double UniqueBL=0.0000; //a branch length is unique if it's chidren are from the same group
- double totalBL = 0.00; //all branch lengths
- double UW = 0.00; //Unweighted Value = UniqueBL / totalBL;
- //find a node that belongs to one of the groups in this combo
- int nodeBelonging = -1;
- for (int g = 0; g < namesOfGroupCombos[h].size(); g++) {
- if (copyTree->groupNodeInfo[namesOfGroupCombos[h][g]].size() != 0) { nodeBelonging = copyTree->groupNodeInfo[namesOfGroupCombos[h][g]][0]; break; }
- }
-
- //sanity check
- if (nodeBelonging == -1) {
- m->mothurOut("[WARNING]: cannot find a nodes in the tree from grouping ");
- for (int g = 0; g < namesOfGroupCombos[h].size()-1; g++) { m->mothurOut(namesOfGroupCombos[h][g] + "-"); }
- m->mothurOut(namesOfGroupCombos[h][namesOfGroupCombos[h].size()-1]);
- m->mothurOut(", skipping."); m->mothurOutEndLine(); results[count] = UW;
- }else{
-
- //if including the root this clears rootForGrouping[namesOfGroupCombos[h]]
- getRoot(copyTree, nodeBelonging, namesOfGroupCombos[h]);
-
- for(int i=0;i<copyTree->getNumNodes();i++){
-
- if (m->control_pressed) { return data; }
-
- //pcountSize = 0, they are from a branch that is entirely from a group the user doesn't want
- //pcountSize = 2, not unique to one group
- //pcountSize = 1, unique to one group
-
- int pcountSize = 0;
- for (int j = 0; j < namesOfGroupCombos[h].size(); j++) {
- map<string, int>::iterator itGroup = copyTree->tree[i].pcount.find(namesOfGroupCombos[h][j]);
- if (itGroup != copyTree->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
- }
-
- //unique calc
- if (pcountSize == 0) { }
- else if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize == 1) && (rootForGrouping[namesOfGroupCombos[h]].count(i) == 0)) { //you have a unique branch length and you are not the root
- UniqueBL += abs(copyTree->tree[i].getBranchLength());
- }
-
- //total calc
- if (pcountSize == 0) { }
- else if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize != 0) && (rootForGrouping[namesOfGroupCombos[h]].count(i) == 0)) { //you have a branch length and you are not the root
- totalBL += abs(copyTree->tree[i].getBranchLength());
- }
-
- }
- //cout << UniqueBL << '\t' << totalBL << endl;
- UW = (UniqueBL / totalBL);
-
- if (isnan(UW) || isinf(UW)) { UW = 0; }
-
- results[count] = UW;
- }
- count++;
-
- }
-
- delete copyTree;
-
- return results;
- }
- catch(exception& e) {
- m->errorOut(e, "Unweighted", "driver");
- exit(1);
- }
-}
-/**************************************************************************************************/
-int Unweighted::getRoot(Tree* t, int v, vector<string> grouping) {
- try {
- //you are a leaf so get your parent
- int index = t->tree[v].getParent();
-
- if (includeRoot) {
- rootForGrouping[grouping].clear();
- }else {
-
- //my parent is a potential root
- rootForGrouping[grouping].insert(index);
-
- //while you aren't at root
- while(t->tree[index].getParent() != -1){
- //cout << index << endl;
- if (m->control_pressed) { return 0; }
-
- //am I the root for this grouping? if so I want to stop "early"
- //does my sibling have descendants from the users groups?
- //if so I am not the root
- 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;
- for (int j = 0; j < grouping.size(); j++) {
- map<string, int>::iterator itGroup = t->tree[sib].pcount.find(grouping[j]);
- if (itGroup != t->tree[sib].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
- }
-
- //if yes, I am not the root
- if (pcountSize != 0) {
- rootForGrouping[grouping].clear();
- rootForGrouping[grouping].insert(parent);
- }
-
- 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);
- //cout << parent << " in root" << endl;
- index = parent;
- }
- }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "Unweighted", "getRoot");
- exit(1);
- }
-}
-/**************************************************************************************************/
-
-
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