EstOutput Unweighted::getValues(Tree* t, int p, string o) {
try {
- globaldata = GlobalData::getInstance();
processors = p;
outputDir = o;
-
+
+ CountTable* ct = t->getCountTable();
+
//if the users enters no groups then give them the score of all groups
- int numGroups = globaldata->Groups.size();
+ int numGroups = m->getNumGroups();
//calculate number of comparsions
int numComp = 0;
for (int r=0; r<numGroups; r++) {
for (int l = 0; l < r; l++) {
numComp++;
- vector<string> groups; groups.push_back(globaldata->Groups[r]); groups.push_back(globaldata->Groups[l]);
+ vector<string> groups; groups.push_back((m->getGroups())[r]); groups.push_back((m->getGroups())[l]);
namesOfGroupCombos.push_back(groups);
}
}
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]);
+ for (int i = 0; i < (ct->getNamesOfGroups()).size(); i++) {
+ if ((ct->getNamesOfGroups())[i] != "xxx") {
+ groups.push_back((ct->getNamesOfGroups())[i]);
}
}
namesOfGroupCombos.push_back(groups);
}else {
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- groups.push_back(globaldata->Groups[i]);
+ for (int i = 0; i < m->getNumGroups(); i++) {
+ groups.push_back((m->getGroups())[i]);
}
namesOfGroupCombos.push_back(groups);
}
}
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
if(processors == 1){
- data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
+ data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), ct);
}else{
int numPairs = namesOfGroupCombos.size();
lines.push_back(linePair(startPos, numPairsPerProcessor));
}
- data = createProcesses(t, namesOfGroupCombos);
+ data = createProcesses(t, namesOfGroupCombos, ct);
lines.clear();
}
#else
- data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size());
+ data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), ct);
#endif
return data;
}
/**************************************************************************************************/
-EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos) {
+EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, CountTable* ct) {
try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
int process = 1;
vector<int> processIDS;
process++;
}else if (pid == 0){
EstOutput myresults;
- myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num);
+ myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, ct);
if (m->control_pressed) { exit(0); }
- m->mothurOut("Merging results."); m->mothurOutEndLine();
+ //m->mothurOut("Merging results."); m->mothurOutEndLine();
//pass numSeqs to parent
ofstream out;
}
}
- results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num);
+ results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, ct);
//force parent to wait until all the processes are done
for (int i=0;i<(processors-1);i++) {
m->gobble(in);
}
in.close();
- remove(s.c_str());
+ m->mothurRemove(s);
}
- m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
+ //m->mothurOut("DONE."); m->mothurOutEndLine(); m->mothurOutEndLine();
return results;
#endif
}
}
/**************************************************************************************************/
-EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num) {
+EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, CountTable* ct) {
try {
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
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);
EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB, int p, string o) {
try {
- globaldata = GlobalData::getInstance();
processors = p;
outputDir = o;
+ CountTable* ct = t->getCountTable();
+
//if the users enters no groups then give them the score of all groups
- int numGroups = globaldata->Groups.size();
+ int numGroups = m->getNumGroups();
//calculate number of comparsions
int numComp = 0;
for (int r=0; r<numGroups; r++) {
for (int l = 0; l < r; l++) {
numComp++;
- vector<string> groups; groups.push_back(globaldata->Groups[r]); groups.push_back(globaldata->Groups[l]);
+ vector<string> groups; groups.push_back((m->getGroups())[r]); groups.push_back((m->getGroups())[l]);
namesOfGroupCombos.push_back(groups);
}
}
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]);
+ for (int i = 0; i < (ct->getNamesOfGroups()).size(); i++) {
+ if ((ct->getNamesOfGroups())[i] != "xxx") {
+ groups.push_back((ct->getNamesOfGroups())[i]);
}
}
namesOfGroupCombos.push_back(groups);
}else {
- for (int i = 0; i < globaldata->Groups.size(); i++) {
- groups.push_back(globaldata->Groups[i]);
+ for (int i = 0; i < m->getNumGroups(); i++) {
+ groups.push_back((m->getGroups())[i]);
}
namesOfGroupCombos.push_back(groups);
}
}
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
if(processors == 1){
- data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true);
+ data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true, ct);
}else{
int numPairs = namesOfGroupCombos.size();
lines.push_back(linePair(startPos, numPairsPerProcessor));
}
- data = createProcesses(t, namesOfGroupCombos, true);
+ data = createProcesses(t, namesOfGroupCombos, true, ct);
lines.clear();
}
#else
- data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true);
+ data = driver(t, namesOfGroupCombos, 0, namesOfGroupCombos.size(), true, ct);
#endif
return data;
}
/**************************************************************************************************/
-EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, bool usingGroups) {
+EstOutput Unweighted::createProcesses(Tree* t, vector< vector<string> > namesOfGroupCombos, bool usingGroups, CountTable* ct) {
try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
int process = 1;
vector<int> processIDS;
process++;
}else if (pid == 0){
EstOutput myresults;
- myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, usingGroups);
+ myresults = driver(t, namesOfGroupCombos, lines[process].start, lines[process].num, usingGroups, ct);
if (m->control_pressed) { exit(0); }
}
}
- results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, usingGroups);
+ results = driver(t, namesOfGroupCombos, lines[0].start, lines[0].num, usingGroups, ct);
//force parent to wait until all the processes are done
for (int i=0;i<(processors-1);i++) {
m->gobble(in);
}
in.close();
- remove(s.c_str());
+ m->mothurRemove(s);
}
return results;
}
}
/**************************************************************************************************/
-EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, bool usingGroups) {
+EstOutput Unweighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos, int start, int num, bool usingGroups, CountTable* ct) {
try {
EstOutput results; results.resize(num);
int count = 0;
- Tree* copyTree = new Tree;
+ Tree* copyTree = new Tree(ct);
for (int h = start; h < (start+num); h++) {
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++){
int Unweighted::getRoot(Tree* t, int v, vector<string> grouping) {
try {
//you are a leaf so get your parent
- int index = t->tree[index].getParent();
+ int index = t->tree[v].getParent();
- //my parent is a potential root
- rootForGrouping[grouping].insert(index);
-
- //while you aren't at root
- while(t->tree[index].getParent() != -1){
-
- if (m->control_pressed) { return 0; }
+ if (includeRoot) {
+ rootForGrouping[grouping].clear();
+ }else {
- //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();
+ //my parent is a potential root
+ rootForGrouping[grouping].insert(index);
- 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; } }
+ //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;
}
- //if yes, I am not the root
- if (pcountSize != 0) {
- rootForGrouping[grouping].clear();
+ //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;
}
-
- 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;
projects / mothur.git / blobdiff