+++ /dev/null
-/*
- * venncommand.cpp
- * Mothur
- *
- * Created by Sarah Westcott on 3/30/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "venncommand.h"
-#include "ace.h"
-#include "sobs.h"
-#include "chao1.h"
-//#include "jackknife.h"
-#include "sharedsobscollectsummary.h"
-#include "sharedchao1.h"
-#include "sharedace.h"
-#include "nseqs.h"
-
-//**********************************************************************************************************************
-vector<string> VennCommand::setParameters(){
- try {
- CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
- CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
- CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
- CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
- CommandParameter pcalc("calc", "String", "", "", "", "", "",false,false); parameters.push_back(pcalc);
- CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
- CommandParameter pnseqs("nseqs", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pnseqs);
- CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "",false,false); parameters.push_back(pfontsize);
- CommandParameter ppermute("permute", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(ppermute);
- 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, "VennCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string VennCommand::getHelpString(){
- try {
- string helpString = "";
- helpString += "The venn command parameters are list, shared, groups, calc, abund, nseqs, permute, fontsize and label. shared, relabund, list, rabund or sabund is required unless you have a valid current file.\n";
- helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your venn diagram, you may only use a maximum of 4 groups.\n";
- helpString += "The group names are separated by dashes. The label allows you to select what distance levels you would like a venn diagram created for, and are also separated by dashes.\n";
- helpString += "The fontsize parameter allows you to adjust the font size of the picture created, default=24.\n";
- helpString += "The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, label=yourLabels, abund=yourAbund).\n";
- helpString += "Example venn(groups=A-B-C, calc=sharedsobs-sharedchao, abund=20).\n";
- helpString += "The default value for groups is all the groups in your groupfile up to 4, and all labels in your inputfile will be used.\n";
- helpString += "The default value for calc is sobs if you have only read a list file or if you have selected only one group, and sharedsobs if you have multiple groups.\n";
- helpString += "The default available estimators for calc are sobs, chao and ace if you have only read a list file, and sharedsobs, sharedchao and sharedace if you have read a shared file.\n";
- helpString += "The nseqs parameter will output the number of sequences represented by the otus in the picture, default=F.\n";
- helpString += "If you have more than 4 groups, the permute parameter will find all possible combos of 4 of your groups and create pictures for them, default=F.\n";
- helpString += "The only estimators available four 4 groups are sharedsobs and sharedchao.\n";
- helpString += "The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n";
- helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "VennCommand", "getHelpString");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-VennCommand::VennCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["svg"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "VennCommand", "VennCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-VennCommand::VennCommand(string option) {
- try {
- abort = false; calledHelp = false;
- allLines = 1;
-
- //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 (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
- if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
- }
-
- //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; }
- }
-
- it = parameters.find("list");
- //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["list"] = inputDir + it->second; }
- }
- }
-
- //check for required parameters
- listfile = validParameter.validFile(parameters, "list", true);
- if (listfile == "not open") { listfile = ""; abort = true; }
- else if (listfile == "not found") { listfile = ""; }
- else { format = "list"; inputfile = listfile; m->setListFile(listfile); }
-
- sharedfile = validParameter.validFile(parameters, "shared", true);
- if (sharedfile == "not open") { sharedfile = ""; abort = true; }
- else if (sharedfile == "not found") { sharedfile = ""; }
- else { format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
-
- if ((sharedfile == "") && (listfile == "")) {
- //is there are current file available for any of these?
- //give priority to shared, then list, then rabund, then sabund
- //if there is a current shared file, use it
- sharedfile = m->getSharedFile();
- if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
- else {
- listfile = m->getListFile();
- if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
- else {
- m->mothurOut("No valid current files. You must provide a list or shared file."); m->mothurOutEndLine();
- abort = true;
- }
- }
- }
-
- //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 = m->hasPath(inputfile); }
-
- //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") {
- if(format == "list") { calc = "sobs"; }
- else { calc = "sharedsobs"; }
- }
- else {
- if (calc == "default") {
- if(format == "list") { calc = "sobs"; }
- else { calc = "sharedsobs"; }
- }
- }
- 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, "abund", false); if (temp == "not found") { temp = "10"; }
- m->mothurConvert(temp, abund);
-
- temp = validParameter.validFile(parameters, "nseqs", false); if (temp == "not found"){ temp = "f"; }
- nseqs = m->isTrue(temp);
-
- temp = validParameter.validFile(parameters, "permute", false); if (temp == "not found"){ temp = "f"; }
- perm = m->isTrue(temp);
-
- temp = validParameter.validFile(parameters, "fontsize", false); if (temp == "not found") { temp = "24"; }
- m->mothurConvert(temp, fontsize);
-
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "VennCommand", "VennCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int VennCommand::execute(){
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- ValidCalculators validCalculator;
-
- if (format == "list") {
- for (int i=0; i<Estimators.size(); i++) {
- if (validCalculator.isValidCalculator("vennsingle", Estimators[i]) == true) {
- if (Estimators[i] == "sobs") {
- vennCalculators.push_back(new Sobs());
- }else if (Estimators[i] == "chao") {
- vennCalculators.push_back(new Chao1());
- }else if (Estimators[i] == "ace") {
- if(abund < 5)
- abund = 10;
- vennCalculators.push_back(new Ace(abund));
- }
- }
- }
- }else {
- for (int i=0; i<Estimators.size(); i++) {
- if (validCalculator.isValidCalculator("vennshared", Estimators[i]) == true) {
- if (Estimators[i] == "sharedsobs") {
- vennCalculators.push_back(new SharedSobsCS());
- }else if (Estimators[i] == "sharedchao") {
- vennCalculators.push_back(new SharedChao1());
- }else if (Estimators[i] == "sharedace") {
- vennCalculators.push_back(new SharedAce());
- }
- }
- }
- }
-
- //if the users entered no valid calculators don't execute command
- if (vennCalculators.size() == 0) { m->mothurOut("No valid calculators given, please correct."); m->mothurOutEndLine(); return 0; }
-
- venn = new Venn(outputDir, nseqs, inputfile, fontsize);
- input = new InputData(inputfile, format);
-
- string lastLabel;
-
- if (format == "sharedfile") {
- lookup = input->getSharedRAbundVectors();
- lastLabel = lookup[0]->getLabel();
-
- if ((lookup.size() > 4) && (perm)) { combosOfFour = findCombinations(lookup.size()); }
- }else if (format == "list") {
- sabund = input->getSAbundVector();
- lastLabel = sabund->getLabel();
- }
-
- //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;
-
- if (format != "list") {
-
- //as long as you are not at the end of the file or done wih the lines you want
- while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
-
- if (m->control_pressed) {
- for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
- m->clearGroups(); delete venn; delete input;
- for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
- return 0;
- }
-
- if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
- m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- processedLabels.insert(lookup[0]->getLabel());
- userLabels.erase(lookup[0]->getLabel());
-
- if ((lookup.size() > 4) && (!perm)){
- m->mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile. If you set perm=t, I will find all possible combos of 4 groups."); m->mothurOutEndLine();
- for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
-
- vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
- for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
-
- }else if ((lookup.size() > 4) && (perm)) {
- set< set<int> >::iterator it3;
- set<int>::iterator it2;
- for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
-
- set<int> poss = *it3;
- vector<SharedRAbundVector*> subset;
- for (it2 = poss.begin(); it2 != poss.end(); it2++) { subset.push_back(lookup[*it2]); }
-
- vector<string> outfilenames = venn->getPic(subset, vennCalculators);
- for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
- }
- }else {
- vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
- for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
- }
- }
-
- 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);
-
- m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- processedLabels.insert(lookup[0]->getLabel());
- userLabels.erase(lookup[0]->getLabel());
-
- if ((lookup.size() > 4) && (!perm)){
- m->mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile. If you set perm=t, I will find all possible combos of 4 groups."); m->mothurOutEndLine();
- for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
-
- vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
- for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
-
- }else if ((lookup.size() > 4) && (perm)) {
- set< set<int> >::iterator it3;
- set<int>::iterator it2;
- for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
-
- set<int> poss = *it3;
- vector<SharedRAbundVector*> subset;
- for (it2 = poss.begin(); it2 != poss.end(); it2++) { subset.push_back(lookup[*it2]); }
-
- vector<string> outfilenames = venn->getPic(subset, vennCalculators);
- for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
- }
- }else {
- vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
- for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
- }
-
- //restore real lastlabel to save below
- lookup[0]->setLabel(saveLabel);
- }
-
-
- lastLabel = lookup[0]->getLabel();
-
- //get next line to process
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
- lookup = input->getSharedRAbundVectors();
- }
-
- if (m->control_pressed) {
- for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
- m->clearGroups(); delete venn; delete input;
- for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
- 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);
-
- m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
- processedLabels.insert(lookup[0]->getLabel());
- userLabels.erase(lookup[0]->getLabel());
-
- if ((lookup.size() > 4) && (!perm)){
- m->mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile. If you set perm=t, I will find all possible combos of 4 groups."); m->mothurOutEndLine();
- for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
-
- vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
- for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
-
- }else if ((lookup.size() > 4) && (perm)) {
- set< set<int> >::iterator it3;
- set<int>::iterator it2;
- for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
-
- set<int> poss = *it3;
- vector<SharedRAbundVector*> subset;
- for (it2 = poss.begin(); it2 != poss.end(); it2++) { subset.push_back(lookup[*it2]); }
-
- vector<string> outfilenames = venn->getPic(subset, vennCalculators);
- for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
- }
- }else {
- vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
- for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
- }
-
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
- }
-
-
- //reset groups parameter
- m->clearGroups();
-
- if (m->control_pressed) {
- m->clearGroups(); delete venn; delete input;
- for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
- for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
- return 0;
- }
-
-
- }else{
-
- while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
-
- if (m->control_pressed) {
- for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
- delete sabund; delete venn; delete input;
- for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
- return 0;
- }
-
- if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
-
- m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
- vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
- for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
-
-
- processedLabels.insert(sabund->getLabel());
- userLabels.erase(sabund->getLabel());
- }
-
- if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- string saveLabel = sabund->getLabel();
-
- delete sabund;
- sabund = input->getSAbundVector(lastLabel);
-
- m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
- vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
- for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
-
-
- processedLabels.insert(sabund->getLabel());
- userLabels.erase(sabund->getLabel());
-
- //restore real lastlabel to save below
- sabund->setLabel(saveLabel);
- }
-
- lastLabel = sabund->getLabel();
-
- delete sabund;
- sabund = input->getSAbundVector();
- }
-
- if (m->control_pressed) {
- for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
- for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
- delete venn; 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) {
- if (sabund != NULL) { delete sabund; }
- sabund = input->getSAbundVector(lastLabel);
-
- m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
- vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
- for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); outputTypes["svg"].push_back(outfilenames[i]); } }
-
- delete sabund;
-
- }
-
- if (m->control_pressed) {
- delete venn; delete input;
- for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
- for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
- return 0;
- }
- }
-
- for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
- delete venn; delete input;
-
- 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, "VennCommand", "execute");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-//returns a vector of sets containing the 4 group combinations
-set< set<int> > VennCommand::findCombinations(int lookupSize){
- try {
- set< set<int> > combos;
-
- set<int> possibles;
- for (int i = 0; i < lookupSize; i++) { possibles.insert(i); }
-
- getCombos(possibles, combos);
-
- return combos;
-
- }
- catch(exception& e) {
- m->errorOut(e, "VennCommand", "findCombinations");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-//recusively finds combos of 4
-int VennCommand::getCombos(set<int> possibles, set< set<int> >& combos){
- try {
-
- if (possibles.size() == 4) { //done
- if (combos.count(possibles) == 0) { //no dups
- combos.insert(possibles);
- }
- }else { //we still have work to do
- set<int>::iterator it;
- set<int>::iterator it2;
- for (it = possibles.begin(); it != possibles.end(); it++) {
-
- set<int> newPossibles;
- for (it2 = possibles.begin(); it2 != possibles.end(); it2++) { //all possible combos of one length smaller
- if (*it != *it2) {
- newPossibles.insert(*it2);
- }
- }
- getCombos(newPossibles, combos);
- }
- }
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "VennCommand", "getCombos");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
projects / mothur.git / blobdiff