#include "sharedace.h"
#include "nseqs.h"
+//**********************************************************************************************************************
+vector<string> VennCommand::setParameters(){
+ try {
+ CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); parameters.push_back(plist);
+ CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none","svg",false,false,true); 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 psharedotus("sharedotus", "Boolean", "", "t", "", "", "","",false,false); parameters.push_back(psharedotus);
+ CommandParameter pfontsize("fontsize", "Number", "", "24", "", "", "","",false,false); parameters.push_back(pfontsize);
+ CommandParameter ppermute("permute", "Multiple", "1-2-3-4", "4", "", "", "","",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, sharedotus, 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, you can use the permute parameter to set the number of groups you would like mothur to divide the samples into to draw the venn diagrams for all possible combos. Default=4.\n";
+ helpString += "The only estimators available four 4 groups are sharedsobs and sharedchao.\n";
+ helpString += "The sharedotus parameter can be used with the sharedsobs calculator to get the names of the OTUs in each section of the venn diagram. Default=t.\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);
+ }
+}
+//**********************************************************************************************************************
+string VennCommand::getOutputPattern(string type) {
+ try {
+ string pattern = "";
+
+ if (type == "svg") { pattern = "[filename],svg"; }
+ else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
+
+ return pattern;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "VennCommand", "getOutputPattern");
+ 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 {
- globaldata = GlobalData::getInstance();
- abort = false;
+ abort = false; calledHelp = false;
allLines = 1;
- labels.clear();
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string AlignArray[] = {"groups","label","calc","permute", "abund","nseqs","outputdir","inputdir"};
- vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
+ map<string,string>::iterator it;
ValidParameters validParameter;
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
- //make sure the user has already run the read.otu command
- if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
- m->mothurOut("You must read a list, or a list and a group, or a shared before you can use the venn command."); m->mothurOutEndLine(); 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; }
+ }
}
- //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(globaldata->inputFileName); //if user entered a file with a path then preserve it
+ //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...
else { allLines = 1; }
}
- //if the user has not specified any labels use the ones from read.otu
- if (label == "") {
- allLines = globaldata->allLines;
- labels = globaldata->labels;
- }
-
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else {
m->splitAtDash(groups, Groups);
- globaldata->Groups = Groups;
+ m->setGroups(Groups);
}
- format = globaldata->getFormat();
calc = validParameter.validFile(parameters, "calc", false);
if (calc == "not found") {
if(format == "list") { calc = "sobs"; }
}
}
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"; }
- convert(temp, abund);
+ 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);
-
- if (abort == false) {
- validCalculator = new ValidCalculators();
-
- int i;
-
- if (format == "list") {
- for (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 (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(); abort = true; }
- else { venn = new Venn(outputDir, nseqs); }
- }
+ temp = validParameter.validFile(parameters, "permute", false); if (temp == "not found"){ temp = "4"; }
+ m->mothurConvert(temp, perm);
+ if ((perm == 1) || (perm == 2) || (perm == 3) || (perm == 4)) { }
+ else { m->mothurOut("[ERROR]: Not a valid permute value. Valid values are 1, 2, 3, and 4."); m->mothurOutEndLine(); abort = true; }
+
+ temp = validParameter.validFile(parameters, "sharedotus", false); if (temp == "not found"){ temp = "t"; }
+ sharedOtus = m->isTrue(temp);
- }
+ temp = validParameter.validFile(parameters, "fontsize", false); if (temp == "not found") { temp = "24"; }
+ m->mothurConvert(temp, fontsize);
-
+ }
}
catch(exception& e) {
exit(1);
}
}
-
-//**********************************************************************************************************************
-
-void VennCommand::help(){
- try {
- m->mothurOut("The venn command can only be executed after a successful read.otu command.\n");
- m->mothurOut("The venn command parameters are groups, calc, abund, nseqs, permute and label. No parameters are required.\n");
- m->mothurOut("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");
- m->mothurOut("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");
- m->mothurOut("The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, label=yourLabels, abund=yourAbund).\n");
- m->mothurOut("Example venn(groups=A-B-C, calc=sharedsobs-sharedchao, abund=20).\n");
- m->mothurOut("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");
- m->mothurOut("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");
- m->mothurOut("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 list and group file or a shared file.\n");
- m->mothurOut("The nseqs parameter will output the number of sequences represented by the otus in the picture, default=F.\n");
- m->mothurOut("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");
- m->mothurOut("The only estimators available four 4 groups are sharedsobs and sharedchao.\n");
- m->mothurOut("The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n");
- m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
- }
- catch(exception& e) {
- m->errorOut(e, "VennCommand", "help");
- exit(1);
- }
-}
-
-
-//**********************************************************************************************************************
-
-VennCommand::~VennCommand(){
- if (abort == false) {
- delete input; globaldata->ginput = NULL;
- delete read;
- delete venn;
- globaldata->sabund = NULL;
- delete validCalculator;
- }
-
-}
-
//**********************************************************************************************************************
int VennCommand::execute(){
try {
- if (abort == true) { return 0; }
+ 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, sharedOtus);
+ input = new InputData(inputfile, format);
string lastLabel;
- vector<string> outputNames;
if (format == "sharedfile") {
- //you have groups
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
- input = globaldata->ginput;
lookup = input->getSharedRAbundVectors();
lastLabel = lookup[0]->getLabel();
- if ((lookup.size() > 4) && (perm)) { combosOfFour = findCombinations(lookup.size()); }
+ if ((lookup.size() > 4)) { combos = findCombinations(lookup.size()); }
}else if (format == "list") {
- //you are using just a list file and have only one group
- read = new ReadOTUFile(globaldata->inputFileName);
- read->read(&*globaldata);
-
- sabund = globaldata->sabund;
+ sabund = input->getSAbundVector();
lastLabel = sabund->getLabel();
- input = globaldata->ginput;
}
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
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]; }
- globaldata->Groups.clear();
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ m->clearGroups(); delete venn; delete input;
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
return 0;
}
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]); } }
- }else if ((lookup.size() > 4) && (perm)) {
+ if (lookup.size() > 4) {
set< set<int> >::iterator it3;
set<int>::iterator it2;
- for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
+ for (it3 = combos.begin(); it3 != combos.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]); } }
+ 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]); } }
+ 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(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]); } }
-
- }else if ((lookup.size() > 4) && (perm)) {
+ if (lookup.size() > 4) {
set< set<int> >::iterator it3;
set<int>::iterator it2;
- for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
+ for (it3 = combos.begin(); it3 != combos.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]); } }
+ 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]); } }
+ 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
if (m->control_pressed) {
for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
- globaldata->Groups.clear();
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ m->clearGroups(); delete venn; delete input;
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
return 0;
}
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]); } }
-
- }else if ((lookup.size() > 4) && (perm)) {
+ if (lookup.size() > 4) {
set< set<int> >::iterator it3;
set<int>::iterator it2;
- for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
+ for (it3 = combos.begin(); it3 != combos.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]); } }
+ 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]); } }
+ 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
- globaldata->Groups.clear();
+ 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++) { remove(outputNames[i].c_str()); }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
return 0;
}
if (m->control_pressed) {
for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
- delete sabund;
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ delete sabund; delete venn; delete input;
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
return 0;
}
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]); } }
+ 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());
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]); } }
+ 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());
if (m->control_pressed) {
for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
- for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); }
+ delete venn; delete input;
return 0;
}
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]); } }
+ 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++) { remove(outputNames[i].c_str()); }
+ 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();
}
}
//**********************************************************************************************************************
-//returns a vector of sets containing the 4 group combinations
+//returns a vector of sets containing the group combinations
set< set<int> > VennCommand::findCombinations(int lookupSize){
try {
set< set<int> > combos;
for (int i = 0; i < lookupSize; i++) { possibles.insert(i); }
getCombos(possibles, combos);
-
+
return combos;
}
}
}
//**********************************************************************************************************************
-//recusively finds combos of 4
+//recusively finds combos of length perm
int VennCommand::getCombos(set<int> possibles, set< set<int> >& combos){
try {
- if (possibles.size() == 4) { //done
+ if (possibles.size() == perm) { //done
if (combos.count(possibles) == 0) { //no dups
combos.insert(possibles);
}
projects / mothur.git / blobdiff