--- /dev/null
+/*
+ * indicatorcommand.cpp
+ * Mothur
+ *
+ * Created by westcott on 11/12/10.
+ * Copyright 2010 Schloss Lab. All rights reserved.
+ *
+ */
+
+#include "indicatorcommand.h"
+#include "sharedutilities.h"
+
+
+//**********************************************************************************************************************
+vector<string> IndicatorCommand::setParameters(){
+ try {
+ CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
+ CommandParameter pdesign("design", "InputTypes", "", "", "TreeDesign", "TreeDesign", "none",false,false); parameters.push_back(pdesign);
+ CommandParameter pshared("shared", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(pshared);
+ CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRel", "SharedRel", "none",false,false); parameters.push_back(prelabund);
+ CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
+ CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
+ CommandParameter ptree("tree", "InputTypes", "", "", "TreeDesign", "TreeDesign", "none",false,false); parameters.push_back(ptree);
+ CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
+ CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
+
+ 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, "IndicatorCommand", "setParameters");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+string IndicatorCommand::getHelpString(){
+ try {
+ string helpString = "";
+ helpString += "The indicator command can be run in 3 ways: with a shared or relabund file and a design file, or with a shared or relabund file and a tree file, or with a shared or relabund file, tree file and design file. \n";
+ helpString += "The indicator command outputs a .indicator.summary file and a .indicator.tre if a tree is given. \n";
+ helpString += "The new tree contains labels at each internal node. The label is the node number so you can relate the tree to the summary file.\n";
+ helpString += "The summary file lists the indicator value for each OTU for each node.\n";
+ helpString += "The indicator command parameters are tree, groups, shared, relabund, design and label. \n";
+ helpString += "The design parameter allows you to relate the tree to the shared or relabund file, if your tree contains the grouping names, or if no tree is provided to group your groups into groupings.\n";
+ helpString += "The groups parameter allows you to specify which of the groups in your shared or relabund you would like analyzed, or if you provide a design file the groups in your design file. The groups may be entered separated by dashes.\n";
+ helpString += "The label parameter indicates at what distance your tree relates to the shared or relabund.\n";
+ helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n";
+ helpString += "The iters parameter allows you to set number of randomization for the P value. The default is 1000.";
+ helpString += "The indicator command should be used in the following format: indicator(tree=test.tre, shared=test.shared, label=0.03)\n";
+ helpString += "Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n";
+ return helpString;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "getHelpString");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+IndicatorCommand::IndicatorCommand(){
+ try {
+ abort = true; calledHelp = true;
+ setParameters();
+ vector<string> tempOutNames;
+ outputTypes["tree"] = tempOutNames;
+ outputTypes["summary"] = tempOutNames;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "IndicatorCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+IndicatorCommand::IndicatorCommand(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();
+
+ ValidParameters validParameter;
+ map<string, string>::iterator it;
+
+ //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; }
+ }
+
+ m->runParse = true;
+ m->clearGroups();
+ m->clearAllGroups();
+ m->Treenames.clear();
+
+ vector<string> tempOutNames;
+ outputTypes["tree"] = tempOutNames;
+ outputTypes["summary"] = 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("tree");
+ //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["tree"] = inputDir + it->second; }
+ }
+
+ 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; }
+ }
+
+ it = parameters.find("relabund");
+ //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["relabund"] = inputDir + it->second; }
+ }
+
+ it = parameters.find("design");
+ //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["design"] = inputDir + it->second; }
+ }
+ }
+
+ outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
+
+ //check for required parameters
+ treefile = validParameter.validFile(parameters, "tree", true);
+ if (treefile == "not open") { treefile = ""; abort = true; }
+ else if (treefile == "not found") { treefile = ""; }
+ else { m->setTreeFile(treefile); }
+
+ sharedfile = validParameter.validFile(parameters, "shared", true);
+ if (sharedfile == "not open") { abort = true; }
+ else if (sharedfile == "not found") { sharedfile = ""; }
+ else { inputFileName = sharedfile; m->setSharedFile(sharedfile); }
+
+ relabundfile = validParameter.validFile(parameters, "relabund", true);
+ if (relabundfile == "not open") { abort = true; }
+ else if (relabundfile == "not found") { relabundfile = ""; }
+ else { inputFileName = relabundfile; m->setRelAbundFile(relabundfile); }
+
+ designfile = validParameter.validFile(parameters, "design", true);
+ if (designfile == "not open") { designfile = ""; abort = true; }
+ else if (designfile == "not found") { designfile = ""; }
+ else { m->setDesignFile(designfile); }
+
+ groups = validParameter.validFile(parameters, "groups", false);
+ if (groups == "not found") { groups = ""; Groups.push_back("all"); }
+ else { m->splitAtDash(groups, Groups); }
+ m->setGroups(Groups);
+
+ label = validParameter.validFile(parameters, "label", false);
+ if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); label=""; }
+
+ string temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
+ m->mothurConvert(temp, iters);
+
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ m->mothurConvert(temp, processors);
+
+ if ((relabundfile == "") && (sharedfile == "")) {
+ //is there are current file available for either of these?
+ //give priority to shared, then relabund
+ sharedfile = m->getSharedFile();
+ if (sharedfile != "") { inputFileName = sharedfile; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
+ else {
+ relabundfile = m->getRelAbundFile();
+ if (relabundfile != "") { inputFileName = relabundfile; m->mothurOut("Using " + relabundfile + " as input file for the relabund parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("No valid current files. You must provide a shared or relabund."); m->mothurOutEndLine();
+ abort = true;
+ }
+ }
+ }
+
+
+ if ((designfile == "") && (treefile == "")) {
+ treefile = m->getTreeFile();
+ if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
+ else {
+ designfile = m->getDesignFile();
+ if (designfile != "") { m->mothurOut("Using " + designfile + " as input file for the design parameter."); m->mothurOutEndLine(); }
+ else {
+ m->mothurOut("[ERROR]: You must provide either a tree or design file."); m->mothurOutEndLine(); abort = true;
+ }
+ }
+ }
+
+ if ((relabundfile != "") && (sharedfile != "")) { m->mothurOut("[ERROR]: You may not use both a shared and relabund file."); m->mothurOutEndLine(); abort = true; }
+
+
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "IndicatorCommand");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+
+int IndicatorCommand::execute(){
+ try {
+
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+
+ cout.setf(ios::fixed, ios::floatfield); cout.setf(ios::showpoint);
+
+ int start = time(NULL);
+
+ //read designfile if given and set up groups for read of sharedfiles
+ if (designfile != "") {
+ designMap = new GroupMap(designfile);
+ designMap->readDesignMap();
+
+ //fill Groups - checks for "all" and for any typo groups
+ SharedUtil util;
+ vector<string> nameGroups = designMap->getNamesOfGroups();
+ util.setGroups(Groups, nameGroups);
+ designMap->setNamesOfGroups(nameGroups);
+
+ //loop through the Groups and fill Globaldata's Groups with the design file info
+ vector<string> namesSeqs = designMap->getNamesSeqs(Groups);
+ m->setGroups(namesSeqs);
+ }
+
+ /***************************************************/
+ // use smart distancing to get right sharedRabund //
+ /***************************************************/
+ if (sharedfile != "") {
+ getShared();
+ if (m->control_pressed) { if (designfile != "") { delete designMap; } for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } return 0; }
+ if (lookup[0] == NULL) { m->mothurOut("[ERROR] reading shared file."); m->mothurOutEndLine(); return 0; }
+ }else {
+ getSharedFloat();
+ if (m->control_pressed) { if (designfile != "") { delete designMap; } for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } return 0; }
+ if (lookupFloat[0] == NULL) { m->mothurOut("[ERROR] reading relabund file."); m->mothurOutEndLine(); return 0; }
+ }
+
+ //reset groups if needed
+ if (designfile != "") { m->setGroups(Groups); }
+
+ /***************************************************/
+ // reading tree info //
+ /***************************************************/
+ if (treefile != "") {
+ string groupfile = "";
+ m->setTreeFile(treefile);
+ Tree* tree = new Tree(treefile); delete tree; //extracts names from tree to make faked out groupmap
+ treeMap = new TreeMap();
+ bool mismatch = false;
+
+ for (int i = 0; i < m->Treenames.size(); i++) {
+ //sanity check - is this a group that is not in the sharedfile?
+ if (designfile == "") {
+ if (!(m->inUsersGroups(m->Treenames[i], m->getAllGroups()))) {
+ m->mothurOut("[ERROR]: " + m->Treenames[i] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
+ mismatch = true;
+ }
+ treeMap->addSeq(m->Treenames[i], "Group1");
+ }else{
+ vector<string> myGroups; myGroups.push_back(m->Treenames[i]);
+ vector<string> myNames = designMap->getNamesSeqs(myGroups);
+
+ for(int k = 0; k < myNames.size(); k++) {
+ if (!(m->inUsersGroups(myNames[k], m->getAllGroups()))) {
+ m->mothurOut("[ERROR]: " + myNames[k] + " is not a group in your shared or relabund file."); m->mothurOutEndLine();
+ mismatch = true;
+ }
+ }
+ treeMap->addSeq(m->Treenames[i], "Group1");
+ }
+ }
+
+ if ((designfile != "") && (m->Treenames.size() != Groups.size())) { cout << Groups.size() << '\t' << m->Treenames.size() << endl; m->mothurOut("[ERROR]: You design file does not match your tree, aborting."); m->mothurOutEndLine(); mismatch = true; }
+
+ if (mismatch) { //cleanup and exit
+ if (designfile != "") { delete designMap; }
+ if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
+ else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
+ delete treeMap;
+ return 0;
+ }
+
+ read = new ReadNewickTree(treefile);
+ int readOk = read->read(treeMap);
+
+ if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); delete treeMap; delete read; return 0; }
+
+ vector<Tree*> T = read->getTrees();
+
+ delete read;
+
+ if (m->control_pressed) {
+ if (designfile != "") { delete designMap; }
+ if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
+ else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
+ for (int i = 0; i < T.size(); i++) { delete T[i]; } delete treeMap; return 0;
+ }
+
+ map<string, string> nameMap;
+ T[0]->assembleTree(nameMap);
+
+ /***************************************************/
+ // create ouptut tree - respecting pickedGroups //
+ /***************************************************/
+ Tree* outputTree = new Tree(m->getNumGroups(), treeMap);
+
+ outputTree->getSubTree(T[0], m->getGroups());
+ outputTree->assembleTree(nameMap);
+
+ //no longer need original tree, we have output tree to use and label
+ for (int i = 0; i < T.size(); i++) { delete T[i]; }
+
+ if (m->control_pressed) {
+ if (designfile != "") { delete designMap; }
+ if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
+ else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
+ delete outputTree; delete treeMap; return 0;
+ }
+
+ /***************************************************/
+ // get indicator species values //
+ /***************************************************/
+ GetIndicatorSpecies(outputTree);
+ delete outputTree; delete treeMap;
+
+ }else { //run with design file only
+ //get indicator species
+ GetIndicatorSpecies();
+ }
+
+ if (designfile != "") { delete designMap; }
+ if (sharedfile != "") { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } }
+ else { for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; } }
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
+ //set tree file as new current treefile
+ if (treefile != "") {
+ string current = "";
+ itTypes = outputTypes.find("tree");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTreeFile(current); }
+ }
+ }
+
+ m->mothurOutEndLine(); m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to find the indicator species."); m->mothurOutEndLine();
+ 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, "IndicatorCommand", "execute");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//divide shared or relabund file by groupings in the design file
+//report all otu values to file
+int IndicatorCommand::GetIndicatorSpecies(){
+ try {
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(inputFileName); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + "indicator.summary";
+ outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+ m->mothurOutEndLine(); m->mothurOut("Species\tIndicatorValue\tpValue\n");
+
+ int numBins = 0;
+ if (sharedfile != "") { numBins = lookup[0]->getNumBins(); }
+ else { numBins = lookupFloat[0]->getNumBins(); }
+
+ if (m->control_pressed) { out.close(); return 0; }
+
+ /*****************************************************/
+ //create vectors containing rabund info //
+ /*****************************************************/
+
+ vector<float> indicatorValues; //size of numBins
+ vector<float> pValues;
+ map< vector<int>, vector<int> > randomGroupingsMap; //maps location in groupings to location in groupings, ie, [0][0] -> [1][2]. This is so we don't have to actually move the sharedRabundVectors.
+
+ if (sharedfile != "") {
+ vector< vector<SharedRAbundVector*> > groupings;
+ set<string> groupsAlreadyAdded;
+ vector<SharedRAbundVector*> subset;
+
+ //for each grouping
+ for (int i = 0; i < (designMap->getNamesOfGroups()).size(); i++) {
+
+ for (int k = 0; k < lookup.size(); k++) {
+ //are you from this grouping?
+ if (designMap->getGroup(lookup[k]->getGroup()) == (designMap->getNamesOfGroups())[i]) {
+ subset.push_back(lookup[k]);
+ groupsAlreadyAdded.insert(lookup[k]->getGroup());
+ }
+ }
+ if (subset.size() != 0) { groupings.push_back(subset); }
+ subset.clear();
+ }
+
+ if (groupsAlreadyAdded.size() != lookup.size()) { m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
+
+ indicatorValues = getValues(groupings, randomGroupingsMap);
+
+ pValues = getPValues(groupings, randomGroupingsMap, lookup.size(), indicatorValues);
+ }else {
+ vector< vector<SharedRAbundFloatVector*> > groupings;
+ set<string> groupsAlreadyAdded;
+ vector<SharedRAbundFloatVector*> subset;
+
+ //for each grouping
+ for (int i = 0; i < (designMap->getNamesOfGroups()).size(); i++) {
+ for (int k = 0; k < lookupFloat.size(); k++) {
+ //are you from this grouping?
+ if (designMap->getGroup(lookupFloat[k]->getGroup()) == (designMap->getNamesOfGroups())[i]) {
+ subset.push_back(lookupFloat[k]);
+ groupsAlreadyAdded.insert(lookupFloat[k]->getGroup());
+ }
+ }
+ if (subset.size() != 0) { groupings.push_back(subset); }
+ subset.clear();
+ }
+
+ if (groupsAlreadyAdded.size() != lookupFloat.size()) { m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
+
+ indicatorValues = getValues(groupings, randomGroupingsMap);
+
+ pValues = getPValues(groupings, randomGroupingsMap, lookupFloat.size(), indicatorValues);
+ }
+
+ if (m->control_pressed) { out.close(); return 0; }
+
+
+ /******************************************************/
+ //output indicator values to table form //
+ /*****************************************************/
+ out << "OTU\tIndicator_Value\tpValue" << endl;
+ for (int j = 0; j < indicatorValues.size(); j++) {
+
+ if (m->control_pressed) { out.close(); return 0; }
+
+ out << m->currentBinLabels[j] << '\t' << indicatorValues[j] << '\t';
+
+ if (pValues[j] > (1/(float)iters)) { out << pValues[j] << endl; }
+ else { out << "<" << (1/(float)iters) << endl; }
+
+ if (pValues[j] <= 0.05) {
+ cout << m->currentBinLabels[j] << '\t' << indicatorValues[j] << '\t';
+ string pValueString = "<" + toString((1/(float)iters));
+ if (pValues[j] > (1/(float)iters)) { pValueString = toString(pValues[j]); cout << pValues[j];}
+ else { cout << "<" << (1/(float)iters); }
+ m->mothurOutJustToLog(m->currentBinLabels[j] + "\t" + toString(indicatorValues[j]) + "\t" + pValueString);
+ m->mothurOutEndLine();
+ }
+ }
+
+ out.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "GetIndicatorSpecies");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//traverse tree finding indicator species values for each otu at each node
+//label node with otu number that has highest indicator value
+//report all otu values to file
+int IndicatorCommand::GetIndicatorSpecies(Tree*& T){
+ try {
+
+ string thisOutputDir = outputDir;
+ if (outputDir == "") { thisOutputDir += m->hasPath(inputFileName); }
+ string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(inputFileName)) + "indicator.summary";
+ outputNames.push_back(outputFileName); outputTypes["summary"].push_back(outputFileName);
+
+ ofstream out;
+ m->openOutputFile(outputFileName, out);
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+
+ int numBins = 0;
+ if (sharedfile != "") { numBins = lookup[0]->getNumBins(); }
+ else { numBins = lookupFloat[0]->getNumBins(); }
+
+ //print headings
+ out << "TreeNode\t";
+ for (int i = 0; i < numBins; i++) { out << m->currentBinLabels[i] << "_IndValue" << '\t' << "pValue" << '\t'; }
+ out << endl;
+
+ m->mothurOutEndLine(); m->mothurOut("Node\tSpecies\tIndicatorValue\tpValue\n");
+
+ string treeOutputDir = outputDir;
+ if (outputDir == "") { treeOutputDir += m->hasPath(treefile); }
+ string outputTreeFileName = treeOutputDir + m->getRootName(m->getSimpleName(treefile)) + "indicator.tre";
+
+
+ //create a map from tree node index to names of descendants, save time later to know which sharedRabund you need
+ map<int, set<string> > nodeToDescendants;
+ map<int, set<int> > descendantNodes;
+ for (int i = 0; i < T->getNumNodes(); i++) {
+ if (m->control_pressed) { return 0; }
+
+ nodeToDescendants[i] = getDescendantList(T, i, nodeToDescendants, descendantNodes);
+ }
+
+ //you need the distances to leaf to decide grouping below
+ //this will also set branch lengths if the tree does not include them
+ map<int, float> distToRoot = getDistToRoot(T);
+
+ //for each node
+ for (int i = T->getNumLeaves(); i < T->getNumNodes(); i++) {
+ //cout << endl << i+1 << endl;
+ if (m->control_pressed) { out.close(); return 0; }
+
+ /*****************************************************/
+ //create vectors containing rabund info //
+ /*****************************************************/
+
+ vector<float> indicatorValues; //size of numBins
+ vector<float> pValues;
+ map< vector<int>, vector<int> > randomGroupingsMap; //maps location in groupings to location in groupings, ie, [0][0] -> [1][2]. This is so we don't have to actually move the sharedRabundVectors.
+
+ if (sharedfile != "") {
+ vector< vector<SharedRAbundVector*> > groupings;
+
+ //get nodes that will be a valid grouping
+ //you are valid if you are not one of my descendants
+ //AND your distToRoot is >= mine
+ //AND you were not added as part of a larger grouping. Largest nodes are added first.
+
+ set<string> groupsAlreadyAdded;
+ //create a grouping with my grouping
+ vector<SharedRAbundVector*> subset;
+ int count = 0;
+ int doneCount = nodeToDescendants[i].size();
+ for (int k = 0; k < lookup.size(); k++) {
+ //is this descendant of i
+ if ((nodeToDescendants[i].count(lookup[k]->getGroup()) != 0)) {
+ subset.push_back(lookup[k]);
+ groupsAlreadyAdded.insert(lookup[k]->getGroup());
+ count++;
+ }
+ if (count == doneCount) { break; } //quit once you get the rabunds for this grouping
+ }
+ if (subset.size() != 0) { groupings.push_back(subset); }
+
+
+ for (int j = (T->getNumNodes()-1); j >= 0; j--) {
+
+
+ if ((descendantNodes[i].count(j) == 0) && (distToRoot[j] >= distToRoot[i])) {
+ vector<SharedRAbundVector*> subset;
+ int count = 0;
+ int doneCount = nodeToDescendants[j].size();
+ for (int k = 0; k < lookup.size(); k++) {
+ //is this descendant of j, and we didn't already add this as part of a larger grouping
+ if ((nodeToDescendants[j].count(lookup[k]->getGroup()) != 0) && (groupsAlreadyAdded.count(lookup[k]->getGroup()) == 0)) {
+ subset.push_back(lookup[k]);
+ groupsAlreadyAdded.insert(lookup[k]->getGroup());
+ count++;
+ }
+ if (count == doneCount) { break; } //quit once you get the rabunds for this grouping
+ }
+
+ //if subset.size == 0 then the node was added as part of a larger grouping
+ if (subset.size() != 0) { groupings.push_back(subset); }
+ }
+ }
+
+ if (groupsAlreadyAdded.size() != lookup.size()) { m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
+
+ indicatorValues = getValues(groupings, randomGroupingsMap);
+
+ pValues = getPValues(groupings, randomGroupingsMap, lookup.size(), indicatorValues);
+ }else {
+ vector< vector<SharedRAbundFloatVector*> > groupings;
+
+ //get nodes that will be a valid grouping
+ //you are valid if you are not one of my descendants
+ //AND your distToRoot is >= mine
+ //AND you were not added as part of a larger grouping. Largest nodes are added first.
+
+ set<string> groupsAlreadyAdded;
+ //create a grouping with my grouping
+ vector<SharedRAbundFloatVector*> subset;
+ int count = 0;
+ int doneCount = nodeToDescendants[i].size();
+ for (int k = 0; k < lookupFloat.size(); k++) {
+ //is this descendant of i
+ if ((nodeToDescendants[i].count(lookupFloat[k]->getGroup()) != 0)) {
+ subset.push_back(lookupFloat[k]);
+ groupsAlreadyAdded.insert(lookupFloat[k]->getGroup());
+ count++;
+ }
+ if (count == doneCount) { break; } //quit once you get the rabunds for this grouping
+ }
+ if (subset.size() != 0) { groupings.push_back(subset); }
+
+ for (int j = (T->getNumNodes()-1); j >= 0; j--) {
+ if ((descendantNodes[i].count(j) == 0) && (distToRoot[j] >= distToRoot[i])) {
+ vector<SharedRAbundFloatVector*> subset;
+ int count = 0;
+ int doneCount = nodeToDescendants[j].size();
+ for (int k = 0; k < lookupFloat.size(); k++) {
+ //is this descendant of j, and we didn't already add this as part of a larger grouping
+ if ((nodeToDescendants[j].count(lookupFloat[k]->getGroup()) != 0) && (groupsAlreadyAdded.count(lookupFloat[k]->getGroup()) == 0)) {
+ subset.push_back(lookupFloat[k]);
+ groupsAlreadyAdded.insert(lookupFloat[k]->getGroup());
+ count++;
+ }
+ if (count == doneCount) { break; } //quit once you get the rabunds for this grouping
+ }
+
+ //if subset.size == 0 then the node was added as part of a larger grouping
+ if (subset.size() != 0) { groupings.push_back(subset); }
+ }
+ }
+
+ if (groupsAlreadyAdded.size() != lookupFloat.size()) { m->mothurOut("[ERROR]: could not make proper groupings."); m->mothurOutEndLine(); }
+
+ indicatorValues = getValues(groupings, randomGroupingsMap);
+
+ pValues = getPValues(groupings, randomGroupingsMap, lookupFloat.size(), indicatorValues);
+ }
+
+ if (m->control_pressed) { out.close(); return 0; }
+
+
+ /******************************************************/
+ //output indicator values to table form + label tree //
+ /*****************************************************/
+ out << (i+1) << '\t';
+ for (int j = 0; j < indicatorValues.size(); j++) {
+
+ if (m->control_pressed) { out.close(); return 0; }
+
+ if (pValues[j] < (1/(float)iters)) {
+ out << indicatorValues[j] << '\t' << '<' << (1/(float)iters) << '\t';
+ }else {
+ out << indicatorValues[j] << '\t' << pValues[j] << '\t';
+ }
+
+ if (pValues[j] <= 0.05) {
+ cout << i+1 << '\t' << m->currentBinLabels[j] << '\t' << indicatorValues[j] << '\t';
+ string pValueString = "<" + toString((1/(float)iters));
+ if (pValues[j] > (1/(float)iters)) { pValueString = toString(pValues[j]); cout << pValues[j];}
+ else { cout << "<" << (1/(float)iters); }
+ m->mothurOutJustToLog(toString(i) + "\t" + m->currentBinLabels[j] + "\t" + toString(indicatorValues[j]) + "\t" + pValueString);
+ m->mothurOutEndLine();
+ }
+ }
+ out << endl;
+
+ T->tree[i].setLabel((i+1));
+ }
+ out.close();
+
+ ofstream outTree;
+ m->openOutputFile(outputTreeFileName, outTree);
+ outputNames.push_back(outputTreeFileName); outputTypes["tree"].push_back(outputTreeFileName);
+
+ T->print(outTree, "both");
+ outTree.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "GetIndicatorSpecies");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<float> IndicatorCommand::getValues(vector< vector<SharedRAbundFloatVector*> >& groupings, map< vector<int>, vector<int> > groupingsMap){
+ try {
+ vector<float> values;
+ map< vector<int>, vector<int> >::iterator it;
+
+ //for each otu
+ for (int i = 0; i < groupings[0][0]->getNumBins(); i++) {
+
+ if (m->control_pressed) { return values; }
+
+ vector<float> terms;
+ float AijDenominator = 0.0;
+ vector<float> Bij;
+
+ //get overall abundance of each grouping
+ for (int j = 0; j < groupings.size(); j++) {
+
+ float totalAbund = 0;
+ int numNotZero = 0;
+ for (int k = 0; k < groupings[j].size(); k++) {
+ vector<int> temp; temp.push_back(j); temp.push_back(k);
+ it = groupingsMap.find(temp);
+
+ if (it == groupingsMap.end()) { //this one didnt get moved
+ totalAbund += groupings[j][k]->getAbundance(i);
+ if (groupings[j][k]->getAbundance(i) != 0.0) { numNotZero++; }
+ }else {
+ totalAbund += groupings[(it->second)[0]][(it->second)[1]]->getAbundance(i);
+ if (groupings[(it->second)[0]][(it->second)[1]]->getAbundance(i) != 0.0) { numNotZero++; }
+ }
+
+ }
+
+ //mean abundance
+ float Aij = (totalAbund / (float) groupings[j].size());
+ terms.push_back(Aij);
+
+ //percentage of sites represented
+ Bij.push_back(numNotZero / (float) groupings[j].size());
+
+ AijDenominator += Aij;
+ }
+
+ float maxIndVal = 0.0;
+ for (int j = 0; j < terms.size(); j++) {
+ float thisAij = (terms[j] / AijDenominator); //relative abundance
+ float thisValue = thisAij * Bij[j] * 100.0;
+
+ //save largest
+ if (thisValue > maxIndVal) { maxIndVal = thisValue; }
+ }
+
+ values.push_back(maxIndVal);
+ }
+
+ return values;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "getValues");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//same as above, just data type difference
+vector<float> IndicatorCommand::getValues(vector< vector<SharedRAbundVector*> >& groupings, map< vector<int>, vector<int> > groupingsMap){
+ try {
+ vector<float> values;
+
+ /*for (int j = 0; j < groupings.size(); j++) {
+ cout << "grouping " << j << endl;
+ for (int k = 0; k < groupings[j].size(); k++) {
+ cout << groupings[j][k]->getGroup() << endl;
+ }
+ }*/
+ map< vector<int>, vector<int> >::iterator it;
+
+ //for each otu
+ for (int i = 0; i < groupings[0][0]->getNumBins(); i++) {
+ vector<float> terms;
+ float AijDenominator = 0.0;
+ vector<float> Bij;
+ //get overall abundance of each grouping
+ for (int j = 0; j < groupings.size(); j++) {
+
+ int totalAbund = 0.0;
+ int numNotZero = 0;
+ for (int k = 0; k < groupings[j].size(); k++) {
+ vector<int> temp; temp.push_back(j); temp.push_back(k);
+ it = groupingsMap.find(temp);
+
+ if (it == groupingsMap.end()) { //this one didnt get moved
+ totalAbund += groupings[j][k]->getAbundance(i);
+ if (groupings[j][k]->getAbundance(i) != 0.0) { numNotZero++; }
+ }else {
+ totalAbund += groupings[(it->second)[0]][(it->second)[1]]->getAbundance(i);
+ if (groupings[(it->second)[0]][(it->second)[1]]->getAbundance(i) != 0.0) { numNotZero++; }
+ }
+
+ }
+
+ //mean abundance
+ float Aij = (totalAbund / (float) groupings[j].size());
+ terms.push_back(Aij);
+
+ //percentage of sites represented
+ Bij.push_back(numNotZero / (float) groupings[j].size());
+
+ AijDenominator += Aij;
+ }
+
+ float maxIndVal = 0.0;
+ for (int j = 0; j < terms.size(); j++) {
+ float thisAij = (terms[j] / AijDenominator); //relative abundance
+ float thisValue = thisAij * Bij[j] * 100.0;
+
+ //save largest
+ if (thisValue > maxIndVal) { maxIndVal = thisValue; }
+ }
+
+ values.push_back(maxIndVal);
+ }
+
+ return values;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "getValues");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//you need the distances to root to decide groupings
+//this will also set branch lengths if the tree does not include them
+map<int, float> IndicatorCommand::getDistToRoot(Tree*& T){
+ try {
+ map<int, float> dists;
+
+ bool hasBranchLengths = false;
+ for (int i = 0; i < T->getNumNodes(); i++) {
+ if (T->tree[i].getBranchLength() > 0.0) { hasBranchLengths = true; break; }
+ }
+
+ //set branchlengths if needed
+ if (!hasBranchLengths) {
+ for (int i = 0; i < T->getNumNodes(); i++) {
+
+ int lc = T->tree[i].getLChild();
+ int rc = T->tree[i].getRChild();
+
+ if (lc == -1) { // you are a leaf
+ //if you are a leaf set you priliminary length to 1.0, this may adjust later
+ T->tree[i].setBranchLength(1.0);
+ dists[i] = 1.0;
+ }else{ // you are an internal node
+ //look at your children's length to leaf
+ float ldist = dists[lc];
+ float rdist = dists[rc];
+
+ float greater = ldist;
+ if (rdist > greater) { greater = rdist; dists[i] = ldist + 1.0;}
+ else { dists[i] = rdist + 1.0; }
+
+
+ //branch length = difference + 1
+ T->tree[lc].setBranchLength((abs(ldist-greater) + 1.0));
+ T->tree[rc].setBranchLength((abs(rdist-greater) + 1.0));
+ }
+ }
+ }
+
+ dists.clear();
+
+ for (int i = 0; i < T->getNumNodes(); i++) {
+
+ double sum = 0.0;
+ int index = i;
+
+ while(T->tree[index].getParent() != -1){
+ if (T->tree[index].getBranchLength() != -1) {
+ sum += abs(T->tree[index].getBranchLength());
+ }
+ index = T->tree[index].getParent();
+ }
+
+ dists[i] = sum;
+ }
+
+ return dists;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "getLengthToLeaf");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+set<string> IndicatorCommand::getDescendantList(Tree*& T, int i, map<int, set<string> > descendants, map<int, set<int> >& nodes){
+ try {
+ set<string> names;
+
+ set<string>::iterator it;
+
+ int lc = T->tree[i].getLChild();
+ int rc = T->tree[i].getRChild();
+
+ if (lc == -1) { //you are a leaf your only descendant is yourself
+ set<int> temp; temp.insert(i);
+ nodes[i] = temp;
+
+ if (designfile == "") {
+ names.insert(T->tree[i].getName());
+ }else {
+ vector<string> myGroup; myGroup.push_back(T->tree[i].getName());
+ vector<string> myReps = designMap->getNamesSeqs(myGroup);
+ for (int k = 0; k < myReps.size(); k++) {
+ names.insert(myReps[k]);
+ }
+ }
+
+ }else{ //your descedants are the combination of your childrens descendants
+ names = descendants[lc];
+ nodes[i] = nodes[lc];
+ for (it = descendants[rc].begin(); it != descendants[rc].end(); it++) {
+ names.insert(*it);
+ }
+ for (set<int>::iterator itNum = nodes[rc].begin(); itNum != nodes[rc].end(); itNum++) {
+ nodes[i].insert(*itNum);
+ }
+ //you are your own descendant
+ nodes[i].insert(i);
+ }
+
+ return names;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "getDescendantList");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int IndicatorCommand::getShared(){
+ try {
+ InputData* input = new InputData(sharedfile, "sharedfile");
+ lookup = input->getSharedRAbundVectors();
+ string lastLabel = lookup[0]->getLabel();
+
+ if (label == "") { label = lastLabel; delete input; 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> labels; labels.insert(label);
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((lookup[0] != NULL) && (userLabels.size() != 0)) {
+ if (m->control_pressed) { delete input; return 0; }
+
+ if(labels.count(lookup[0]->getLabel()) == 1){
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+ break;
+ }
+
+ if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = lookup[0]->getLabel();
+
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+
+ processedLabels.insert(lookup[0]->getLabel());
+ userLabels.erase(lookup[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
+ break;
+ }
+
+ lastLabel = lookup[0]->getLabel();
+
+ //get next line to process
+ //prevent memory leak
+ for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ lookup = input->getSharedRAbundVectors();
+ }
+
+
+ if (m->control_pressed) { delete input; 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();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
+ lookup = input->getSharedRAbundVectors(lastLabel);
+ }
+
+ delete input;
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "getShared");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+int IndicatorCommand::getSharedFloat(){
+ try {
+ InputData* input = new InputData(relabundfile, "relabund");
+ lookupFloat = input->getSharedRAbundFloatVectors();
+ string lastLabel = lookupFloat[0]->getLabel();
+
+ if (label == "") { label = lastLabel; delete input; 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> labels; labels.insert(label);
+ set<string> processedLabels;
+ set<string> userLabels = labels;
+
+ //as long as you are not at the end of the file or done wih the lines you want
+ while((lookupFloat[0] != NULL) && (userLabels.size() != 0)) {
+
+ if (m->control_pressed) { delete input; return 0; }
+
+ if(labels.count(lookupFloat[0]->getLabel()) == 1){
+ processedLabels.insert(lookupFloat[0]->getLabel());
+ userLabels.erase(lookupFloat[0]->getLabel());
+ break;
+ }
+
+ if ((m->anyLabelsToProcess(lookupFloat[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = lookupFloat[0]->getLabel();
+
+ for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
+ lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
+
+ processedLabels.insert(lookupFloat[0]->getLabel());
+ userLabels.erase(lookupFloat[0]->getLabel());
+
+ //restore real lastlabel to save below
+ lookupFloat[0]->setLabel(saveLabel);
+ break;
+ }
+
+ lastLabel = lookupFloat[0]->getLabel();
+
+ //get next line to process
+ //prevent memory leak
+ for (int i = 0; i < lookupFloat.size(); i++) { delete lookupFloat[i]; }
+ lookupFloat = input->getSharedRAbundFloatVectors();
+ }
+
+
+ if (m->control_pressed) { delete input; 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();
+ }
+ }
+
+ //run last label if you need to
+ if (needToRun == true) {
+ for (int i = 0; i < lookupFloat.size(); i++) { if (lookupFloat[i] != NULL) { delete lookupFloat[i]; } }
+ lookupFloat = input->getSharedRAbundFloatVectors(lastLabel);
+ }
+
+ delete input;
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "getShared");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<float> IndicatorCommand::driver(vector< vector<SharedRAbundFloatVector*> >& groupings, map< vector<int>, vector<int> > groupingsMap, int num, vector<float> indicatorValues, int numIters){
+ try {
+ vector<float> pvalues;
+ pvalues.resize(indicatorValues.size(), 0);
+
+ for(int i=0;i<numIters;i++){
+ if (m->control_pressed) { break; }
+ groupingsMap = randomizeGroupings(groupings, num);
+ vector<float> randomIndicatorValues = getValues(groupings, groupingsMap);
+
+ for (int j = 0; j < indicatorValues.size(); j++) {
+ if (randomIndicatorValues[j] >= indicatorValues[j]) { pvalues[j]++; }
+ }
+ }
+
+ return pvalues;
+
+ }catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "driver");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+vector<float> IndicatorCommand::getPValues(vector< vector<SharedRAbundFloatVector*> >& groupings, map< vector<int>, vector<int> > groupingsMap, int num, vector<float> indicatorValues){
+ try {
+ vector<float> pvalues;
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ if(processors == 1){
+ pvalues = driver(groupings, groupingsMap, num, indicatorValues, iters);
+ for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; }
+ }else{
+
+ //divide iters between processors
+ int numItersPerProcessor = iters / processors;
+
+ vector<int> processIDS;
+ int process = 1;
+ int num = 0;
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+
+ if (pid > 0) {
+ processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
+ process++;
+ }else if (pid == 0){
+ pvalues = driver(groupings, groupingsMap, num, indicatorValues, numItersPerProcessor);
+
+ //pass pvalues to parent
+ ofstream out;
+ string tempFile = toString(getpid()) + ".pvalues.temp";
+ m->openOutputFile(tempFile, out);
+
+ //pass values
+ for (int i = 0; i < pvalues.size(); i++) {
+ out << pvalues[i] << '\t';
+ }
+ out << endl;
+
+ out.close();
+
+ 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);
+ }
+ }
+
+ //do my part
+ //special case for last processor in case it doesn't divide evenly
+ numItersPerProcessor = iters - ((processors-1) * numItersPerProcessor);
+ pvalues = driver(groupings, groupingsMap, num, indicatorValues, numItersPerProcessor);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processIDS.size();i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ //combine results
+ for (int i = 0; i < processIDS.size(); i++) {
+ ifstream in;
+ string tempFile = toString(processIDS[i]) + ".pvalues.temp";
+ m->openInputFile(tempFile, in);
+
+ ////// to do ///////////
+ int numTemp; numTemp = 0;
+ for (int j = 0; j < pvalues.size(); j++) {
+ in >> numTemp; m->gobble(in);
+ pvalues[j] += numTemp;
+ }
+ in.close(); m->mothurRemove(tempFile);
+ }
+ for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; }
+ }
+#else
+ pvalues = driver(groupings, groupingsMap, num, indicatorValues, iters);
+ for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; }
+#endif
+
+ return pvalues;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "getPValues");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+//same as above, just data type difference
+vector<float> IndicatorCommand::driver(vector< vector<SharedRAbundVector*> >& groupings, map< vector<int>, vector<int> > groupingsMap, int num, vector<float> indicatorValues, int numIters){
+ try {
+ vector<float> pvalues;
+ pvalues.resize(indicatorValues.size(), 0);
+
+ for(int i=0;i<numIters;i++){
+ if (m->control_pressed) { break; }
+ groupingsMap = randomizeGroupings(groupings, num);
+ vector<float> randomIndicatorValues = getValues(groupings, groupingsMap);
+
+ for (int j = 0; j < indicatorValues.size(); j++) {
+ if (randomIndicatorValues[j] >= indicatorValues[j]) { pvalues[j]++; }
+ }
+ }
+
+ return pvalues;
+
+ }catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "driver");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//same as above, just data type difference
+vector<float> IndicatorCommand::getPValues(vector< vector<SharedRAbundVector*> >& groupings, map< vector<int>, vector<int> > groupingsMap, int num, vector<float> indicatorValues){
+ try {
+ vector<float> pvalues;
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ if(processors == 1){
+ pvalues = driver(groupings, groupingsMap, num, indicatorValues, iters);
+ for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; }
+ }else{
+
+ //divide iters between processors
+ int numItersPerProcessor = iters / processors;
+
+ vector<int> processIDS;
+ int process = 1;
+
+ //loop through and create all the processes you want
+ while (process != processors) {
+ int pid = fork();
+
+ if (pid > 0) {
+ processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
+ process++;
+ }else if (pid == 0){
+ pvalues = driver(groupings, groupingsMap, num, indicatorValues, numItersPerProcessor);
+
+ //pass pvalues to parent
+ ofstream out;
+ string tempFile = toString(getpid()) + ".pvalues.temp";
+ m->openOutputFile(tempFile, out);
+
+ //pass values
+ for (int i = 0; i < pvalues.size(); i++) {
+ out << pvalues[i] << '\t';
+ }
+ out << endl;
+
+ out.close();
+
+ 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);
+ }
+ }
+
+ //do my part
+ //special case for last processor in case it doesn't divide evenly
+ numItersPerProcessor = iters - ((processors-1) * numItersPerProcessor);
+ pvalues = driver(groupings, groupingsMap, num, indicatorValues, numItersPerProcessor);
+
+ //force parent to wait until all the processes are done
+ for (int i=0;i<processIDS.size();i++) {
+ int temp = processIDS[i];
+ wait(&temp);
+ }
+
+ //combine results
+ for (int i = 0; i < processIDS.size(); i++) {
+ ifstream in;
+ string tempFile = toString(processIDS[i]) + ".pvalues.temp";
+ m->openInputFile(tempFile, in);
+
+ ////// to do ///////////
+ int numTemp; numTemp = 0;
+ for (int j = 0; j < pvalues.size(); j++) {
+ in >> numTemp; m->gobble(in);
+ pvalues[j] += numTemp;
+ }
+ in.close(); m->mothurRemove(tempFile);
+ }
+ for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; }
+ }
+#else
+ pvalues = driver(groupings, groupingsMap, num, indicatorValues, iters);
+ for (int i = 0; i < pvalues.size(); i++) { pvalues[i] /= (double)iters; }
+#endif
+
+ return pvalues;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "getPValues");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//swap groups between groupings, in essence randomizing the second column of the design file
+map< vector<int>, vector<int> > IndicatorCommand::randomizeGroupings(vector< vector<SharedRAbundVector*> >& groupings, int numLookupGroups){
+ try {
+
+ map< vector<int>, vector<int> > randomGroupings;
+
+ for (int i = 0; i < numLookupGroups; i++) {
+ if (m->control_pressed) {break;}
+
+ //get random groups to swap to switch with
+ //generate random int between 0 and groupings.size()-1
+ int z = m->getRandomIndex(groupings.size()-1);
+ int x = m->getRandomIndex(groupings.size()-1);
+ int a = m->getRandomIndex(groupings[z].size()-1);
+ int b = m->getRandomIndex(groupings[x].size()-1);
+ //cout << i << '\t' << z << '\t' << x << '\t' << a << '\t' << b << endl;
+ //if ((z < 0) || (z > 1) || x<0 || x>1 || a <0 || a>groupings[z].size()-1 || b<0 || b>groupings[x].size()-1) { cout << "probelm" << i << '\t' << z << '\t' << x << '\t' << a << '\t' << b << endl; }
+
+ vector<int> from;
+ vector<int> to;
+
+ from.push_back(z); from.push_back(a);
+ to.push_back(x); to.push_back(b);
+
+ randomGroupings[from] = to;
+ }
+ //cout << "done" << endl;
+ return randomGroupings;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "randomizeGroupings");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
+//swap groups between groupings, in essence randomizing the second column of the design file
+map< vector<int>, vector<int> > IndicatorCommand::randomizeGroupings(vector< vector<SharedRAbundFloatVector*> >& groupings, int numLookupGroups){
+ try {
+
+ map< vector<int>, vector<int> > randomGroupings;
+
+ for (int i = 0; i < numLookupGroups; i++) {
+
+ //get random groups to swap to switch with
+ //generate random int between 0 and groupings.size()-1
+ int z = m->getRandomIndex(groupings.size()-1);
+ int x = m->getRandomIndex(groupings.size()-1);
+ int a = m->getRandomIndex(groupings[z].size()-1);
+ int b = m->getRandomIndex(groupings[x].size()-1);
+ //cout << i << '\t' << z << '\t' << x << '\t' << a << '\t' << b << endl;
+
+ vector<int> from;
+ vector<int> to;
+
+ from.push_back(z); from.push_back(a);
+ to.push_back(x); to.push_back(b);
+
+ randomGroupings[from] = to;
+ }
+
+ return randomGroupings;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "IndicatorCommand", "randomizeGroupings");
+ exit(1);
+ }
+}
+
+/*****************************************************************/
+
+
projects / mothur.git / blobdiff