globaldata = GlobalData::getInstance();
format = globaldata->getFormat();
validCalculator = new ValidCalculators();
-
- int i;
- for (i=0; i<globaldata->Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("treegroup", globaldata->Estimators[i]) == true) {
- if (globaldata->Estimators[i] == "jabund") {
- treeCalculators.push_back(new JAbund());
- }else if (globaldata->Estimators[i] == "sorabund") {
- treeCalculators.push_back(new SorAbund());
- }else if (globaldata->Estimators[i] == "jclass") {
- treeCalculators.push_back(new Jclass());
- }else if (globaldata->Estimators[i] == "sorclass") {
- treeCalculators.push_back(new SorClass());
- }else if (globaldata->Estimators[i] == "jest") {
- treeCalculators.push_back(new Jest());
- }else if (globaldata->Estimators[i] == "sorest") {
- treeCalculators.push_back(new SorEst());
- }else if (globaldata->Estimators[i] == "thetayc") {
- treeCalculators.push_back(new ThetaYC());
- }else if (globaldata->Estimators[i] == "thetan") {
- treeCalculators.push_back(new ThetaN());
- }else if (globaldata->Estimators[i] == "morisitahorn") {
- treeCalculators.push_back(new MorHorn());
- }else if (globaldata->Estimators[i] == "braycurtis") {
- treeCalculators.push_back(new BrayCurtis());
+
+ if (format == "sharedfile") {
+ int i;
+ for (i=0; i<globaldata->Estimators.size(); i++) {
+ if (validCalculator->isValidCalculator("treegroup", globaldata->Estimators[i]) == true) {
+ if (globaldata->Estimators[i] == "jabund") {
+ treeCalculators.push_back(new JAbund());
+ }else if (globaldata->Estimators[i] == "sorabund") {
+ treeCalculators.push_back(new SorAbund());
+ }else if (globaldata->Estimators[i] == "jclass") {
+ treeCalculators.push_back(new Jclass());
+ }else if (globaldata->Estimators[i] == "sorclass") {
+ treeCalculators.push_back(new SorClass());
+ }else if (globaldata->Estimators[i] == "jest") {
+ treeCalculators.push_back(new Jest());
+ }else if (globaldata->Estimators[i] == "sorest") {
+ treeCalculators.push_back(new SorEst());
+ }else if (globaldata->Estimators[i] == "thetayc") {
+ treeCalculators.push_back(new ThetaYC());
+ }else if (globaldata->Estimators[i] == "thetan") {
+ treeCalculators.push_back(new ThetaN());
+ }else if (globaldata->Estimators[i] == "morisitahorn") {
+ treeCalculators.push_back(new MorHorn());
+ }else if (globaldata->Estimators[i] == "braycurtis") {
+ treeCalculators.push_back(new BrayCurtis());
+ }
}
}
}
TreeGroupCommand::~TreeGroupCommand(){
delete input;
- delete read;
+ if (format == "sharedfile") {delete read;}
+ else { delete readMatrix; delete matrix; delete list; }
+ delete tmap;
+
}
//**********************************************************************************************************************
int TreeGroupCommand::execute(){
try {
- int count = 1;
- EstOutput data;
- vector<SharedRAbundVector*> subset;
-
- //if the users entered no valid calculators don't execute command
- if (treeCalculators.size() == 0) { return 0; }
+ if (format == "sharedfile") {
+ //if the users entered no valid calculators don't execute command
+ if (treeCalculators.size() == 0) { cout << "You have given no valid calculators." << endl; return 0; }
- //you have groups
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
+ //you have groups
+ read = new ReadOTUFile(globaldata->inputFileName);
+ read->read(&*globaldata);
- input = globaldata->ginput;
- lookup = input->getSharedRAbundVectors();
-
- if (lookup.size() < 2) { cout << "You have not provided enough valid groups. I cannot run the command." << endl; return 0; }
-
- numGroups = globaldata->Groups.size();
- groupNames = "";
- for (int i = 0; i < numGroups; i++) { groupNames += globaldata->Groups[i]; }
-
- //clear globaldatas old tree names if any
- globaldata->Treenames.clear();
-
- //fills globaldatas tree names
- globaldata->Treenames = globaldata->Groups;
-
- //create treemap class from groupmap for tree class to use
- tmap = new TreeMap();
- tmap->makeSim(globaldata->gGroupmap);
- globaldata->gTreemap = tmap;
+ input = globaldata->ginput;
+ lookup = input->getSharedRAbundVectors();
- while(lookup[0] != NULL){
+ if (lookup.size() < 2) { cout << "You have not provided enough valid groups. I cannot run the command." << endl; return 0; }
- if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
-
- cout << lookup[0]->getLabel() << '\t' << count << endl;
-
- //for each calculator
- for(int i = 0 ; i < treeCalculators.size(); i++) {
-
- //initialize simMatrix
- simMatrix.clear();
- simMatrix.resize(numGroups);
- for (int m = 0; m < simMatrix.size(); m++) {
- for (int j = 0; j < simMatrix.size(); j++) {
- simMatrix[m].push_back(0.0);
- }
- }
+ //create tree file
+ makeSimsShared();
+ }else{
+ //read in dist file
+ filename = globaldata->inputFileName;
+
+ if (format == "column") { readMatrix = new ReadColumnMatrix(filename); }
+ else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(filename); }
- //initialize index
- index.clear();
- for (int g = 0; g < numGroups; g++) { index[g] = g; }
+ if(globaldata->getPrecision() != ""){
+ convert(globaldata->getPrecision(), precision);
+ }
- //create a new filename
- outputFile = getRootName(globaldata->inputFileName) + treeCalculators[i]->getName() + "." + lookup[0]->getLabel() + ".tre";
-
-
- for (int k = 0; k < lookup.size(); k++) {
- for (int l = k; l < lookup.size(); l++) {
- if (k != l) { //we dont need to similiarity of a groups to itself
- //get estimated similarity between 2 groups
-
- subset.clear(); //clear out old pair of sharedrabunds
- //add new pair of sharedrabunds
- subset.push_back(lookup[k]); subset.push_back(lookup[l]);
-
- data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
- //save values in similarity matrix
- simMatrix[k][l] = data[0];
- simMatrix[l][k] = data[0];
- }
- }
- }
-
- //creates tree from similarity matrix and write out file
- createTree();
- }
+ if(globaldata->getCutOff() != ""){
+ convert(globaldata->getCutOff(), cutoff);
+ cutoff += (5 / (precision * 10.0));
}
+ readMatrix->setCutoff(cutoff);
+
+ if(globaldata->getNameFile() != ""){
+ nameMap = new NameAssignment(globaldata->getNameFile());
+ nameMap->readMap(1,2);
+ }
+ else{
+ nameMap = NULL;
+ }
+
+ readMatrix->read(nameMap);
+ list = readMatrix->getListVector();
+ matrix = readMatrix->getMatrix();
+
+ //make treemap
+ tmap = new TreeMap();
+ tmap->makeSim(list);
+ globaldata->gTreemap = tmap;
- //prevent memory leak
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
-
- //get next line to process
- lookup = input->getSharedRAbundVectors();
- count++;
- }
+ globaldata->Groups = tmap->namesOfGroups;
+
+ //clear globaldatas old tree names if any
+ globaldata->Treenames.clear();
+ //fills globaldatas tree names
+ globaldata->Treenames = globaldata->Groups;
+
+ makeSimsDist();
+
+ //create a new filename
+ outputFile = getRootName(globaldata->inputFileName) + "tre";
+
+ createTree();
+ }
+
//reset groups parameter
globaldata->Groups.clear(); globaldata->setGroups("");
//do merges and create tree structure by setting parents and children
//there are numGroups - 1 merges to do
for (int i = 0; i < (numGroups - 1); i++) {
-
- float largest = 0.0;
+ float largest = -1000.0;
+
int row, column;
//find largest value in sims matrix by searching lower triangle
for (int j = 1; j < simMatrix.size(); j++) {
index[row] = numGroups+i;
index[column] = numGroups+i;
- //zero out highest value that caused the merge.
- simMatrix[row][column] = 0.0;
- simMatrix[column][row] = 0.0;
+ //remove highest value that caused the merge.
+ simMatrix[row][column] = -1000.0;
+ simMatrix[column][row] = -1000.0;
//merge values in simsMatrix
for (int n = 0; n < simMatrix.size(); n++) {
simMatrix[row][n] = (simMatrix[row][n] + simMatrix[column][n]) / 2;
simMatrix[n][row] = simMatrix[row][n];
//delete column
- simMatrix[column][n] = 0.0;
- simMatrix[n][column] = 0.0;
+ simMatrix[column][n] = -1000.0;
+ simMatrix[n][column] = -1000.0;
}
}
-
+
+ //adjust tree to make sure root to tip length is .5
+ int root = t->findRoot();
+ t->tree[root].setBranchLength((0.5 - t->tree[root].getLengthToLeaves()));
+
//assemble tree
t->assembleTree();
try {
//output column headers
- out << '\t';
- for (int i = 0; i < lookup.size(); i++) { out << lookup[i]->getGroup() << '\t'; }
- out << endl;
+ //out << '\t';
+ //for (int i = 0; i < lookup.size(); i++) { out << lookup[i]->getGroup() << '\t'; }
+ //out << endl;
for (int m = 0; m < simMatrix.size(); m++) {
- out << lookup[m]->getGroup() << '\t';
+ //out << lookup[m]->getGroup() << '\t';
for (int n = 0; n < simMatrix.size(); n++) {
out << simMatrix[m][n] << '\t';
}
}
}
/***********************************************************/
+void TreeGroupCommand::makeSimsDist() {
+ try {
+ numGroups = list->size();
+
+ //initialize index
+ index.clear();
+ for (int g = 0; g < numGroups; g++) { index[g] = g; }
+
+ //initialize simMatrix
+ simMatrix.clear();
+ simMatrix.resize(numGroups);
+ for (int m = 0; m < simMatrix.size(); m++) {
+ for (int j = 0; j < simMatrix.size(); j++) {
+ simMatrix[m].push_back(0.0);
+ }
+ }
+
+ //go through sparse matrix and fill sims
+ //go through each cell in the sparsematrix
+ for(MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++){
+ //similairity = -(distance-1)
+ simMatrix[currentCell->row][currentCell->column] = -(currentCell->dist -1.0);
+ simMatrix[currentCell->column][currentCell->row] = -(currentCell->dist -1.0);
+ }
+
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function makeSimsDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the TreeGroupCommand class function makeSimsDist. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************/
+void TreeGroupCommand::makeSimsShared() {
+ try {
+ int count = 1;
+ EstOutput data;
+ vector<SharedRAbundVector*> subset;
+
+ numGroups = globaldata->Groups.size();
+
+ //clear globaldatas old tree names if any
+ globaldata->Treenames.clear();
+
+ //fills globaldatas tree names
+ globaldata->Treenames = globaldata->Groups;
+
+ //create treemap class from groupmap for tree class to use
+ tmap = new TreeMap();
+ tmap->makeSim(globaldata->gGroupmap);
+ globaldata->gTreemap = tmap;
+
+ while(lookup[0] != NULL){
+
+ if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(lookup[0]->getLabel()) == 1){
+
+ cout << lookup[0]->getLabel() << '\t' << count << endl;
+
+ //for each calculator
+ for(int i = 0 ; i < treeCalculators.size(); i++) {
+ //initialize simMatrix
+ simMatrix.clear();
+ simMatrix.resize(numGroups);
+ for (int m = 0; m < simMatrix.size(); m++) {
+ for (int j = 0; j < simMatrix.size(); j++) {
+ simMatrix[m].push_back(0.0);
+ }
+ }
+
+ //initialize index
+ index.clear();
+ for (int g = 0; g < numGroups; g++) { index[g] = g; }
+
+ //create a new filename
+ outputFile = getRootName(globaldata->inputFileName) + treeCalculators[i]->getName() + "." + lookup[0]->getLabel() + ".tre";
+
+ for (int k = 0; k < lookup.size(); k++) {
+ for (int l = k; l < lookup.size(); l++) {
+ if (k != l) { //we dont need to similiarity of a groups to itself
+ //get estimated similarity between 2 groups
+
+ subset.clear(); //clear out old pair of sharedrabunds
+ //add new pair of sharedrabunds
+ subset.push_back(lookup[k]); subset.push_back(lookup[l]);
+
+ data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
+ //save values in similarity matrix
+ simMatrix[k][l] = data[0];
+ simMatrix[l][k] = data[0];
+ }
+ }
+ }
+
+ //creates tree from similarity matrix and write out file
+ createTree();
+ }
+ }
+
+ //prevent memory leak
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+
+ //get next line to process
+ lookup = input->getSharedRAbundVectors();
+ count++;
+ }
+
+ for(int i = 0 ; i < treeCalculators.size(); i++) { delete treeCalculators[i]; }
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the TreeGroupCommand class Function makeSimsShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the TreeGroupCommand class function makeSimsShared. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/***********************************************************/
projects / mothur.git / blobdiff