#include "sharedsobscollectsummary.h"
#include "sharedchao1.h"
#include "sharedace.h"
+#include "nseqs.h"
//**********************************************************************************************************************
-VennCommand::VennCommand(string option){
+VennCommand::VennCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
allLines = 1;
labels.clear();
-
+
//allow user to run help
if(option == "help") { help(); abort = true; }
else {
//valid paramters for this command
- string AlignArray[] = {"groups","label","calc", "abund"};
+ string AlignArray[] = {"groups","label","calc", "abund","nseqs","outputdir","inputdir"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
OptionParser parser(option);
//make sure the user has already run the read.otu command
if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
- mothurOut("You must read a list, or a list and a group, or a shared before you can use the venn command."); mothurOutEndLine(); abort = true;
+ 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 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 optional parameter and set defaults
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; }
}
groups = validParameter.validFile(parameters, "groups", false);
if (groups == "not found") { groups = ""; }
else {
- splitAtDash(groups, Groups);
+ m->splitAtDash(groups, Groups);
globaldata->Groups = Groups;
}
else { calc = "sharedsobs"; }
}
}
- splitAtDash(calc, Estimators);
+ m->splitAtDash(calc, Estimators);
string temp;
temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
convert(temp, abund);
+
+ temp = validParameter.validFile(parameters, "nseqs", false); if (temp == "not found"){ temp = "f"; }
+ nseqs = m->isTrue(temp);
+
if (abort == false) {
validCalculator = new ValidCalculators();
}
}
- venn = new Venn();
+ //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); }
}
+
}
}
catch(exception& e) {
- errorOut(e, "VennCommand", "VennCommand");
+ m->errorOut(e, "VennCommand", "VennCommand");
exit(1);
}
}
void VennCommand::help(){
try {
- mothurOut("The venn command can only be executed after a successful read.otu command.\n");
- mothurOut("The venn command parameters are groups, calc, abund and label. No parameters are required.\n");
- 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");
- 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");
- mothurOut("The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, label=yourLabels, abund=yourAbund).\n");
- mothurOut("Example venn(groups=A-B-C, calc=sharedsobs-sharedchao, abund=20).\n");
- 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");
- 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");
- 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");
- mothurOut("The only estmiator available four 4 groups is sharedsobs.\n");
- mothurOut("The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n");
- mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
+ 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 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("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) {
- errorOut(e, "VennCommand", "help");
+ m->errorOut(e, "VennCommand", "help");
exit(1);
}
}
delete read;
delete venn;
globaldata->sabund = NULL;
+ delete validCalculator;
}
}
if (abort == true) { return 0; }
string lastLabel;
-
- //if the users entered no valid calculators don't execute command
- if (vennCalculators.size() == 0) { return 0; }
+ vector<string> outputNames;
if (format == "sharedfile") {
//you have groups
//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]; }
+ globaldata->Groups.clear();
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
if (lookup.size() > 4) {
- 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."); mothurOutEndLine();
+ 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();
for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
}
- venn->getPic(lookup, vennCalculators);
+
+ vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
+ for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.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]; }
lookup = input->getSharedRAbundVectors(lastLabel);
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
if (lookup.size() > 4) {
- 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."); mothurOutEndLine();
+ 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();
for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
}
- venn->getPic(lookup, vennCalculators);
+ vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
+ for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.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]; }
+ globaldata->Groups.clear();
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ 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++) {
- mothurOut("Your file does not include the label " + *it);
+ m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
- mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
- mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
lookup = input->getSharedRAbundVectors(lastLabel);
- mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
+ m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
if (lookup.size() > 4) {
- 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."); mothurOutEndLine();
+ 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();
for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
}
- venn->getPic(lookup, vennCalculators);
+ 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 < lookup.size(); i++) { delete lookup[i]; }
}
//reset groups parameter
globaldata->Groups.clear();
+ 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()); }
+ 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;
+ for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); }
+ return 0;
+ }
if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
- mothurOut(sabund->getLabel()); mothurOutEndLine();
- venn->getPic(sabund, vennCalculators);
+ 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]); } }
+
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;
sabund = input->getSAbundVector(lastLabel);
- mothurOut(sabund->getLabel()); mothurOutEndLine();
- venn->getPic(sabund, vennCalculators);
+ 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]); } }
+
processedLabels.insert(sabund->getLabel());
userLabels.erase(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++) { remove(outputNames[i].c_str()); }
+ 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++) {
- mothurOut("Your file does not include the label " + *it);
+ m->mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
- mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
needToRun = true;
}else {
- mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
+ m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
}
}
if (sabund != NULL) { delete sabund; }
sabund = input->getSAbundVector(lastLabel);
- mothurOut(sabund->getLabel()); mothurOutEndLine();
- venn->getPic(sabund, vennCalculators);
+ 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]); } }
+
delete sabund;
}
+ 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()); }
+ return 0;
+ }
}
for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
+
+ 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) {
- errorOut(e, "VennCommand", "execute");
+ m->errorOut(e, "VennCommand", "execute");
exit(1);
}
}
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