#include "sharedsobscollectsummary.h"
#include "sharedchao1.h"
#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", "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, 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, 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 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", "abund","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 += 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...
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
- if(label != "all") { splitAtDash(label, labels); allLines = 0; }
+ if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
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 {
- splitAtDash(groups, Groups);
- globaldata->Groups = Groups;
+ m->splitAtDash(groups, Groups);
+ m->setGroups(Groups);
}
- format = globaldata->getFormat();
calc = validParameter.validFile(parameters, "calc", false);
if (calc == "not found") {
if(format == "list") { calc = "sobs"; }
else { calc = "sharedsobs"; }
}
}
- splitAtDash(calc, Estimators);
+ 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);
- 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());
- }
- }
- }
- }
-
- venn = new Venn(outputDir);
- }
- }
+ temp = validParameter.validFile(parameters, "permute", false); if (temp == "not found"){ temp = "f"; }
+ perm = m->isTrue(temp);
+
+ 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 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 only estmiator available four 4 groups is sharedsobs.\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;
- }
-
-}
-
//**********************************************************************************************************************
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; }
- string lastLabel;
- vector<string> outputNames;
+ venn = new Venn(outputDir, nseqs, inputfile, fontsize, sharedOtus);
+ input = new InputData(inputfile, format);
- //if the users entered no valid calculators don't execute command
- if (vennCalculators.size() == 0) { return 0; }
+ string lastLabel;
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()); }
}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.
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) {
- 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."); m->mothurOutEndLine();
+ 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++) { outputNames.push_back(outfilenames[i]); }
+ 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 ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ 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]; }
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
- if (lookup.size() > 4) {
- 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."); m->mothurOutEndLine();
+ 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++) { outputNames.push_back(outfilenames[i]); }
+ 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);
}
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;
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
- if (lookup.size() > 4) {
- 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."); m->mothurOutEndLine();
+ 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++) { outputNames.push_back(outfilenames[i]); }
+
+ 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
- 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++) { 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++) { 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());
userLabels.erase(sabund->getLabel());
}
- if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
string saveLabel = sabund->getLabel();
delete sabund;
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
- for(int i = 0; i < outfilenames.size(); i++) { 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());
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;
m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
- for(int i = 0; i < outfilenames.size(); i++) { 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++) { 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();
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