-/*
- * 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"
-#include "sharedbraycurtis.h"
-
-
-//**********************************************************************************************************************
-vector<string> BootSharedCommand::setParameters(){
- try {
- CommandParameter pshared("shared", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pshared);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
- CommandParameter pcalc("calc", "Multiple", "jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-morisitahorn-braycurtis", "jclass-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
-
- vector<string> myArray;
- for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "BootSharedCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string BootSharedCommand::getHelpString(){
- try {
- string helpString = "";
- helpString += "The bootstrap.shared command parameters are shared, groups, calc, iters and label. shared is required.\n";
- helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n";
- helpString += "The group names are separated by dashes. The label parameter allows you to select what distance levels you would like trees created for, and is also separated by dashes.\n";
- helpString += "The bootstrap.shared command should be in the following format: bootstrap.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels, iters=yourIters).\n";
- helpString += "Example bootstrap.shared(groups=A-B-C, calc=jabund-sorabund, iters=100).\n";
- helpString += "The default value for groups is all the groups in your groupfile.\n";
- helpString += "The default value for calc is jclass-thetayc. The default for iters is 1000.\n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "BootSharedCommand", "getHelpString");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-BootSharedCommand::BootSharedCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["tree"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "BootSharedCommand", "BootSharedCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-BootSharedCommand::BootSharedCommand(string option) {
- try {
- abort = false; calledHelp = false;
-
- //allow user to run help
- if(option == "help") { help(); abort = true; calledHelp = true; }
- else if(option == "citation") { citation(); abort = true; calledHelp = true;}
-
- else {
- vector<string> myArray = setParameters();
-
- OptionParser parser(option);
- map<string,string> parameters = parser.getParameters();
- map<string,string>::iterator it;
-
- ValidParameters validParameter;
-
- //check to make sure all parameters are valid for command
- for (it = parameters.begin(); it != parameters.end(); it++) {
- if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
- }
-
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["tree"] = tempOutNames;
-
- //if the user changes the input directory command factory will send this info to us in the output parameter
- string inputDir = validParameter.validFile(parameters, "inputdir", false);
- if (inputDir == "not found"){ inputDir = ""; }
- else {
- string path;
- it = parameters.find("shared");
- //user has given a template file
- if(it != parameters.end()){
- path = m->hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["shared"] = inputDir + it->second; }
- }
- }
-
- sharedfile = validParameter.validFile(parameters, "shared", true);
- if (sharedfile == "not found") {
- sharedfile = m->getSharedFile();
- if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
- else { m->mothurOut("You have no current shared file and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
- }
- else if (sharedfile == "not open") { sharedfile = ""; abort = true; }
- else { m->setSharedFile(sharedfile); }
-
- //if the user changes the output directory command factory will send this info to us in the output parameter
- outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
- outputDir = "";
- outputDir += m->hasPath(sharedfile); //if user entered a file with a path then preserve it
- }
-
- //check for optional parameter and set defaults
- // ...at some point should added some additional type checking...
- label = validParameter.validFile(parameters, "label", false);
- if (label == "not found") { label = ""; }
- else {
- if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
- else { allLines = 1; }
- }
-
- groups = validParameter.validFile(parameters, "groups", false);
- if (groups == "not found") { groups = ""; }
- else {
- m->splitAtDash(groups, Groups);
- m->setGroups(Groups);
- }
-
- calc = validParameter.validFile(parameters, "calc", false);
- if (calc == "not found") { calc = "jclass-thetayc"; }
- else {
- if (calc == "default") { calc = "jclass-thetayc"; }
- }
- m->splitAtDash(calc, Estimators);
- if (m->inUsersGroups("citation", Estimators)) {
- ValidCalculators validCalc; validCalc.printCitations(Estimators);
- //remove citation from list of calcs
- for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } }
- }
-
- string temp;
- temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
- m->mothurConvert(temp, iters);
-
- if (abort == false) {
-
- //used in tree constructor
- m->runParse = false;
-
- validCalculator = new ValidCalculators();
-
-
- //NOTE: if you add a calc to this if statement you must add it to the setParameters function
- //or it will not be visible in the gui
- int i;
- for (i=0; i<Estimators.size(); i++) {
- if (validCalculator->isValidCalculator("boot", Estimators[i]) == true) {
- if (Estimators[i] == "jabund") {
- treeCalculators.push_back(new JAbund());
- }else if (Estimators[i] == "sorabund") {
- treeCalculators.push_back(new SorAbund());
- }else if (Estimators[i] == "jclass") {
- treeCalculators.push_back(new Jclass());
- }else if (Estimators[i] == "sorclass") {
- treeCalculators.push_back(new SorClass());
- }else if (Estimators[i] == "jest") {
- treeCalculators.push_back(new Jest());
- }else if (Estimators[i] == "sorest") {
- treeCalculators.push_back(new SorEst());
- }else if (Estimators[i] == "thetayc") {
- treeCalculators.push_back(new ThetaYC());
- }else if (Estimators[i] == "thetan") {
- treeCalculators.push_back(new ThetaN());
- }else if (Estimators[i] == "morisitahorn") {
- treeCalculators.push_back(new MorHorn());
- }else if (Estimators[i] == "braycurtis") {
- treeCalculators.push_back(new BrayCurtis());
- }
- }
- }
-
- delete validCalculator;
-
- ofstream* tempo;
- for (int i=0; i < treeCalculators.size(); i++) {
- tempo = new ofstream;
- out.push_back(tempo);
- }
-
- //make a vector of tree* for each calculator
- trees.resize(treeCalculators.size());
- }
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "BootSharedCommand", "BootSharedCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-BootSharedCommand::~BootSharedCommand(){}
-//**********************************************************************************************************************
-
-int BootSharedCommand::execute(){
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- m->mothurOut("bootstrap.shared command is no longer available."); m->mothurOutEndLine();
- /*
- //read first line
- input = new InputData(sharedfile, "sharedfile");
- order = input->getSharedOrderVector();
- string lastLabel = order->getLabel();
-
- //if the users entered no valid calculators don't execute command
- if (treeCalculators.size() == 0) { return 0; }
-
- //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
- set<string> processedLabels;
- set<string> userLabels = labels;
-
- //set users groups
- util = new SharedUtil();
- util->setGroups(m->Groups, m->namesOfGroups, "treegroup");
-
- numGroups = m->Groups.size();
-
- //clear globaldatas old tree names if any
- globaldata->Treenames.clear();
-
- //fills globaldatas tree names
- globaldata->Treenames = m->Groups;
-
- //create treemap class from groupmap for tree class to use
- tmap = new TreeMap();
- tmap->makeSim(globaldata->gGroupmap);
- globaldata->gTreemap = tmap;
-
- while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } globaldata->Groups.clear(); delete input;delete util; return 0; }
-
- if(allLines == 1 || labels.count(order->getLabel()) == 1){
-
- m->mothurOut(order->getLabel()); m->mothurOutEndLine();
- int error = process(order);
- if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } globaldata->Groups.clear(); delete input;delete util; return 0; }
-
- processedLabels.insert(order->getLabel());
- userLabels.erase(order->getLabel());
- }
-
- //you have a label the user want that is smaller than this label and the last label has not already been processed
- if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- string saveLabel = order->getLabel();
-
- delete order;
- order = input->getSharedOrderVector(lastLabel);
- m->mothurOut(order->getLabel()); m->mothurOutEndLine();
- int error = process(order);
- if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } globaldata->Groups.clear(); delete input;delete util; return 0; }
-
- processedLabels.insert(order->getLabel());
- userLabels.erase(order->getLabel());
-
- //restore real lastlabel to save below
- order->setLabel(saveLabel);
- }
-
-
- lastLabel = order->getLabel();
-
- //get next line to process
- delete order;
- order = input->getSharedOrderVector();
- }
-
-
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } globaldata->Groups.clear(); delete input; delete util; return 0; }
-
- //output error messages about any remaining user labels
- set<string>::iterator it;
- bool needToRun = false;
- for (it = userLabels.begin(); it != userLabels.end(); it++) {
- m->mothurOut("Your file does not include the label " + *it);
- if (processedLabels.count(lastLabel) != 1) {
- m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
- needToRun = true;
- }else {
- m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
- }
- }
-
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } globaldata->Groups.clear(); delete input; delete util; return 0; }
-
- //run last line if you need to
- if (needToRun == true) {
- if (order != NULL) { delete order; }
- order = input->getSharedOrderVector(lastLabel);
- m->mothurOut(order->getLabel()); m->mothurOutEndLine();
- int error = process(order);
- if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } globaldata->Groups.clear(); delete input; delete util; return 0; }
-
- delete order;
-
- }
-
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } globaldata->Groups.clear();delete input; delete util; return 0; }
-
- //reset groups parameter
- globaldata->Groups.clear();
-
- //set first tree file as new current treefile
- string currentTree = "";
- itTypes = outputTypes.find("tree");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { currentTree = (itTypes->second)[0]; m->setTreeFile(currentTree); }
- }
-
- delete input;
- delete util;
-
- m->mothurOutEndLine();
- m->mothurOut("Output File Names: "); m->mothurOutEndLine();
- for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
- m->mothurOutEndLine();
-*/
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "BootSharedCommand", "execute");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int BootSharedCommand::createTree(ostream* out, Tree* t){
- try {
- /*
- //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++) {
-
- if (m->control_pressed) { return 1; }
-
- 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++) {
- 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] = -1000.0;
- simMatrix[column][row] = -1000.0;
-
- //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] = -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();
-
- if (m->control_pressed) { return 1; }
-
- //print newick file
- t->print(*out);*/
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "BootSharedCommand", "createTree");
- exit(1);
- }
-}
-/***********************************************************/
-void BootSharedCommand::printSims() {
- try {
- m->mothurOut("simsMatrix"); m->mothurOutEndLine();
- for (int k = 0; k < simMatrix.size(); k++) {
- for (int n = 0; n < simMatrix.size(); n++) {
- m->mothurOut(toString(simMatrix[k][n])); m->mothurOut("\t");
- }
- m->mothurOutEndLine();
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "BootSharedCommand", "printSims");
- exit(1);
- }
-}
-/***********************************************************/
-int BootSharedCommand::process(SharedOrderVector* order) {
- try{
- /* EstOutput data;
- vector<SharedRAbundVector*> subset;
-
- //open an ostream for each calc to print to
- for (int z = 0; z < treeCalculators.size(); z++) {
- //create a new filename
- outputFile = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + treeCalculators[z]->getName() + ".boot" + order->getLabel() + ".tre";
- m->openOutputFile(outputFile, *(out[z]));
- outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
- }
-
- m->mothurOut("Generating bootstrap trees..."); cout.flush();
-
- //create a file for each calculator with the 1000 trees in it.
- for (int p = 0; p < iters; p++) {
-
- if (m->control_pressed) { return 1; }
-
- util->getSharedVectorswithReplacement(m->Groups, lookup, order); //fills group vectors from order vector.
-
-
- //for each calculator
- for(int i = 0 ; i < treeCalculators.size(); i++) {
-
- if (m->control_pressed) { return 1; }
-
- //initialize simMatrix
- simMatrix.clear();
- simMatrix.resize(numGroups);
- for (int o = 0; o < simMatrix.size(); o++) {
- for (int j = 0; j < simMatrix.size(); j++) {
- simMatrix[o].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
- subset.clear(); //clear out old pair of sharedrabunds
- //add new pair of sharedrabunds
- subset.push_back(lookup[k]); subset.push_back(lookup[l]);
-
- //get estimated similarity between 2 groups
- data = treeCalculators[i]->getValues(subset); //saves the calculator outputs
- //save values in similarity matrix
- simMatrix[k][l] = data[0];
- simMatrix[l][k] = data[0];
- }
- }
- }
-
- tempTree = new Tree();
-
- if (m->control_pressed) { delete tempTree; return 1; }
-
- //creates tree from similarity matrix and write out file
- createTree(out[i], tempTree);
-
- if (m->control_pressed) { delete tempTree; return 1; }
-
- //save trees for consensus command.
- trees[i].push_back(tempTree);
- }
- }
-
- m->mothurOut("\tDone."); m->mothurOutEndLine();
-
-
- //create consensus trees for each bootstrapped tree set
- for (int k = 0; k < trees.size(); k++) {
-
- m->mothurOut("Generating consensus tree for " + treeCalculators[k]->getName()); m->mothurOutEndLine();
-
- if (m->control_pressed) { return 1; }
-
- //set global data to calc trees
- globaldata->gTree = trees[k];
-
- string filename = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + treeCalculators[k]->getName() + ".boot" + order->getLabel();
- consensus = new ConcensusCommand(filename);
- consensus->execute();
- delete consensus;
-
- outputNames.push_back(filename + ".cons.pairs");
- outputNames.push_back(filename + ".cons.tre");
-
- }
-
-
-
- //close ostream for each calc
- for (int z = 0; z < treeCalculators.size(); z++) { out[z]->close(); }
- */
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "BootSharedCommand", "process");
- exit(1);
- }
-}
-/***********************************************************/
-
-
-