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);
string VennCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The venn command parameters are list, shared, groups, calc, abund, nseqs, permute and label. shared, relabund, list, rabund or sabund is required unless you have a valid current file.\n";
+ 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 += "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\n";
+ helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
return helpString;
}
catch(exception& e) {
//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();
listfile = validParameter.validFile(parameters, "list", true);
if (listfile == "not open") { listfile = ""; abort = true; }
else if (listfile == "not found") { listfile = ""; }
- else { format = "list"; inputfile = 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; }
+ else { format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
if ((sharedfile == "") && (listfile == "")) {
//is there are current file available for any of these?
if (groups == "not found") { groups = ""; }
else {
m->splitAtDash(groups, Groups);
- m->Groups = Groups;
+ m->setGroups(Groups);
}
calc = validParameter.validFile(parameters, "calc", false);
}
}
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"; }
+ 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);
}
//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);
+ venn = new Venn(outputDir, nseqs, inputfile, fontsize);
input = new InputData(inputfile, format);
string lastLabel;
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->Groups.clear(); delete venn; delete input;
- 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;
}
if (m->control_pressed) {
for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
- m->Groups.clear(); delete venn; delete input;
- 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;
}
//reset groups parameter
- m->Groups.clear();
+ m->clearGroups();
if (m->control_pressed) {
- m->Groups.clear(); delete venn; delete input;
+ 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; delete venn; delete input;
- 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]; }
- 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;
}
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;
}
}
projects / mothur.git / blobdiff