+/*
+ * bootstrapsharedcommand.cpp
+ * Mothur
+ *
+ * Created by Sarah Westcott on 4/16/09.
+ * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
+ *
+ */
+
+#include "bootstrapsharedcommand.h"
+#include "sharedjabund.h"
+#include "sharedsorabund.h"
+#include "sharedjclass.h"
+#include "sharedsorclass.h"
+#include "sharedjest.h"
+#include "sharedsorest.h"
+#include "sharedthetayc.h"
+#include "sharedthetan.h"
+#include "sharedmorisitahorn.h"
+
+
+//**********************************************************************************************************************
+
+BootSharedCommand::BootSharedCommand(){
+ try {
+ globaldata = GlobalData::getInstance();
+ format = globaldata->getFormat();
+ convert(globaldata->getIters(), iters);
+ validCalculator = new ValidCalculators();
+ util = new SharedUtil();
+
+
+ int i;
+ for (i=0; i<globaldata->Estimators.size(); i++) {
+ if (validCalculator->isValidCalculator("boot", globaldata->Estimators[i]) == true) {
+ if (globaldata->Estimators[i] == "jabund") {
+ treeCalculators.push_back(new JAbund());
+ }else if (globaldata->Estimators[i] == "sorensonabund") {
+ 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());
+ }
+ }
+ }
+
+ ofstream* temp;
+ for (int i=0; i < treeCalculators.size(); i++) {
+ temp = new ofstream;
+ out.push_back(temp);
+ }
+
+ //reset calc for next command
+ globaldata->setCalc("");
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function BootSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the BootSharedCommand class function BootSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+BootSharedCommand::~BootSharedCommand(){
+ delete input;
+ delete read;
+ delete util;
+}
+
+//**********************************************************************************************************************
+
+int BootSharedCommand::execute(){
+ try {
+ int count = 1;
+ EstOutput data;
+
+ //if the users entered no valid calculators don't execute command
+ if (treeCalculators.size() == 0) { return 0; }
+
+ if (format == "sharedfile") {
+ read = new ReadPhilFile(globaldata->inputFileName);
+ read->read(&*globaldata);
+
+ input = globaldata->ginput;
+ order = input->getSharedOrderVector();
+ }else {
+ //you are using a list and a groupfile
+ read = new ReadPhilFile(globaldata->inputFileName);
+ read->read(&*globaldata);
+
+ input = globaldata->ginput;
+ SharedList = globaldata->gSharedList;
+ order = SharedList->getSharedOrderVector();
+ }
+
+ //set users groups
+ util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "treegroup");
+ 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(order != NULL){
+
+ if(globaldata->allLines == 1 || globaldata->lines.count(count) == 1 || globaldata->labels.count(order->getLabel()) == 1){
+
+ cout << order->getLabel() << '\t' << count << endl;
+
+ //open an ostream for each calc to print to
+ for (int z = 0; z < treeCalculators.size(); z++) {
+ //create a new filename
+ outputFile = getRootName(globaldata->inputFileName) + treeCalculators[z]->getName() + ".boot" + order->getLabel() + ".tre";
+ openOutputFile(outputFile, *(out[z]));
+ }
+
+ //create a file for each calculator with the 1000 trees in it.
+ for (int p = 0; p < iters; p++) {
+
+ util->getSharedVectorswithReplacement(globaldata->Groups, lookup, order); //fills group vectors from order vector.
+
+ //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; }
+
+ for (int k = 0; k < lookup.size(); k++) { // pass cdd each set of groups to commpare
+ 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
+ data = treeCalculators[i]->getValues(lookup[k], lookup[l]); //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(out[i]);
+ }
+ }
+ //close ostream for each calc
+ for (int z = 0; z < treeCalculators.size(); z++) { out[z]->close(); }
+ }
+
+ //get next line to process
+ if (format == "sharedfile") {
+ order = input->getSharedOrderVector();
+ }else {
+ //you are using a list and a groupfile
+ SharedList = input->getSharedListVector(); //get new list vector to process
+ if (SharedList != NULL) {
+ order = SharedList->getSharedOrderVector(); //gets new order vector with group info.
+ }else {
+ break;
+ }
+ }
+ count++;
+ }
+
+ //reset groups parameter
+ globaldata->Groups.clear(); globaldata->setGroups("");
+
+ return 0;
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the BootSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+void BootSharedCommand::createTree(ostream* out){
+ try {
+ //create tree
+ t = new Tree();
+
+ //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;
+ int row, column;
+ //find largest value in sims matrix by searching lower triangle
+ for (int j = 1; j < simMatrix.size(); j++) {
+ for (int k = 0; k < j; k++) {
+ if (simMatrix[j][k] > largest) { largest = simMatrix[j][k]; row = j; column = k; }
+ }
+ }
+
+ //set non-leaf node info and update leaves to know their parents
+ //non-leaf
+ t->tree[numGroups + i].setChildren(index[row], index[column]);
+
+ //parents
+ t->tree[index[row]].setParent(numGroups + i);
+ t->tree[index[column]].setParent(numGroups + i);
+
+ //blength = distance / 2;
+ float blength = ((1.0 - largest) / 2);
+
+ //branchlengths
+ t->tree[index[row]].setBranchLength(blength - t->tree[index[row]].getLengthToLeaves());
+ t->tree[index[column]].setBranchLength(blength - t->tree[index[column]].getLengthToLeaves());
+
+ //set your length to leaves to your childs length plus branchlength
+ t->tree[numGroups + i].setLengthToLeaves(t->tree[index[row]].getLengthToLeaves() + t->tree[index[row]].getBranchLength());
+
+
+ //update index
+ 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;
+
+ //merge values in simsMatrix
+ for (int n = 0; n < simMatrix.size(); n++) {
+ //row becomes merge of 2 groups
+ 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;
+ }
+ }
+
+ //assemble tree
+ t->assembleTree();
+
+ //print newick file
+ t->print(*out);
+
+ //delete tree
+ delete t;
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the BootSharedCommand class function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************/
+void BootSharedCommand::printSims() {
+ try {
+ cout << "simsMatrix" << endl;
+ for (int m = 0; m < simMatrix.size(); m++) {
+ for (int n = 0; n < simMatrix.size(); n++) {
+ cout << simMatrix[m][n] << '\t';
+ }
+ cout << endl;
+ }
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the BootSharedCommand class function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/***********************************************************/
+
+