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;
- int num = 0;
vector<int> processIDS;
EstOutput results;
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;
out.close();
exit(0);
- }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); 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);
+ 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 {
-
+
+
EstOutput results; results.resize(num);
int count = 0;
- int numLeaves = t->getNumLeaves();
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;
- map<int, double> tempTotals; //maps node to total Branch Length
- map<int, int> nodePcountSize; //maps node to pcountSize
- map<int, int>::iterator itCount;
-
- for(int i=0;i<t->getNumNodes();i++){
+
+ //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; }
+ }
- 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 = t->tree[i].pcount.find(namesOfGroupCombos[h][j]);
- if (itGroup != t->tree[i].pcount.end()) { pcountSize++; if (pcountSize > 1) { break; } }
- }
-
- nodePcountSize[i] = pcountSize;
-
- if (pcountSize == 0) { ; }
- else if ((t->tree[i].getBranchLength() != -1) && (pcountSize == 1)) { UniqueBL += abs(t->tree[i].getBranchLength()); }
-
- //if you are a leaf from a users group add to total
- if (i < numLeaves) {
- if ((t->tree[i].getBranchLength() != -1) && pcountSize != 0) {
- totalBL += abs(t->tree[i].getBranchLength());
+ //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; } }
}
- tempTotals[i] = 0.0; //we don't care about you, or we have already added you
- }else{ //if you are not a leaf
- //do both your chidren have have descendants from the users groups?
- int lc = t->tree[i].getLChild();
- int rc = t->tree[i].getRChild();
- //if yes, add your childrens tempTotals
- if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) {
- totalBL += tempTotals[lc] + tempTotals[rc];
- if (t->tree[i].getBranchLength() != -1) {
- tempTotals[i] = abs(t->tree[i].getBranchLength());
- }else {
- tempTotals[i] = 0.0;
- }
- }else { //if no, your tempTotal is your childrens temp totals + your branch length
- tempTotals[i] = tempTotals[lc] + tempTotals[rc] + abs(t->tree[i].getBranchLength());
+
+ //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);
+ //cout << UniqueBL << '\t' << totalBL << endl;
+ UW = (UniqueBL / totalBL);
- if (isnan(UW) || isinf(UW)) { UW = 0; }
+ if (isnan(UW) || isinf(UW)) { UW = 0; }
- results[count] = UW;
+ 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(); }
+ //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(); }
+ //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;
}
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;
- int num = 0;
vector<int> processIDS;
EstOutput results;
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); }
out.close();
exit(0);
- }else { m->mothurOut("unable to spawn the necessary processes."); m->mothurOutEndLine(); 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);
+ 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++) {
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();
- 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;
- int total = num;
- int twentyPercent = (total * 0.20);
- int numLeaves = t->getNumLeaves();
- Tree* copyTree = new Tree;
+ Tree* copyTree = new Tree(ct);
for (int h = start; h < (start+num); 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;
- map<int, double> tempTotals; //maps node to total Branch Length
- map<int, int> nodePcountSize; //maps node to pcountSize
-
- for(int i=0;i<copyTree->getNumNodes();i++){
+ //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; }
+ }
- 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; } }
- }
-
- nodePcountSize[i] = pcountSize;
+ //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 (pcountSize == 0) { }
- else if ((copyTree->tree[i].getBranchLength() != -1) && (pcountSize == 1)) { UniqueBL += abs(copyTree->tree[i].getBranchLength()); }
+ //if including the root this clears rootForGrouping[namesOfGroupCombos[h]]
+ getRoot(copyTree, nodeBelonging, namesOfGroupCombos[h]);
- //if you are a leaf from a users group add to total
- if (i < numLeaves) {
- if ((copyTree->tree[i].getBranchLength() != -1) && pcountSize != 0) {
- totalBL += abs(copyTree->tree[i].getBranchLength());
+ 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; } }
}
- tempTotals[i] = 0.0; //we don't care about you, or we have already added you
- }else{ //if you are not a leaf
- //do both your chidren have have descendants from the users groups?
- int lc = copyTree->tree[i].getLChild();
- int rc = copyTree->tree[i].getRChild();
- //if yes, add your childrens tempTotals
- if ((nodePcountSize[lc] != 0) && (nodePcountSize[rc] != 0)) {
- totalBL += tempTotals[lc] + tempTotals[rc];
- if (copyTree->tree[i].getBranchLength() != -1) {
- tempTotals[i] = abs(copyTree->tree[i].getBranchLength());
- }else {
- tempTotals[i] = 0.0;
- }
- }else { //if no, your tempTotal is your childrens temp totals + your branch length
- tempTotals[i] = tempTotals[lc] + tempTotals[rc] + abs(copyTree->tree[i].getBranchLength());
+ //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;
}
-
- UW = (UniqueBL / totalBL);
-
- if (isnan(UW) || isinf(UW)) { UW = 0; }
-
- results[count] = UW;
count++;
-
+
}
delete copyTree;
}
}
/**************************************************************************************************/
+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);
+ }
+}
+/**************************************************************************************************/
projects / mothur.git / blobdiff