globaldata = GlobalData::getInstance();
abort = false;
allLines = 1;
- lines.clear();
labels.clear();
//allow user to run help
else {
//valid paramters for this command
- string AlignArray[] = {"groups","line","label","calc", "abund"};
+ string AlignArray[] = {"groups","label","calc", "abund","outputdir","inputdir"};
vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
OptionParser parser(option);
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;
}
+
+ //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 optional parameter and set defaults
// ...at some point should added some additional type checking...
- line = validParameter.validFile(parameters, "line", false);
- if (line == "not found") { line = ""; }
- else {
- if(line != "all") { splitAtDash(line, lines); allLines = 0; }
- else { allLines = 1; }
- }
-
label = validParameter.validFile(parameters, "label", false);
if (label == "not found") { label = ""; }
else {
else { allLines = 1; }
}
- //make sure user did not use both the line and label parameters
- if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; }
- //if the user has not specified any line or labels use the ones from read.otu
- else if ((line == "") && (label == "")) {
+ //if the user has not specified any labels use the ones from read.otu
+ if (label == "") {
allLines = globaldata->allLines;
labels = globaldata->labels;
- lines = globaldata->lines;
}
groups = validParameter.validFile(parameters, "groups", false);
}
}
- venn = new Venn();
+ venn = new Venn(outputDir);
}
}
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, line and label. No parameters are required, but you may not use line and label at the same time.\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 line and label allow 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, line=yourLines, label=yourLabels, abund=yourAbund).\n");
- mothurOut("Example venn(groups=A-B-C, line=1-3-5, calc=sharedsobs-sharedchao, abund=20).\n");
- mothurOut("The default value for groups is all the groups in your groupfile up to 4, and all lines in your inputfile will be used.\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");
if (abort == true) { return 0; }
- int count = 1;
string lastLabel;
//if the users entered no valid calculators don't execute command
//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;
- set<int> userLines = lines;
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) || (userLines.size() != 0))) {
+ while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
- mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
+ mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
- userLines.erase(count);
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();
}
if ((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() + "\t" + toString(count)); mothurOutEndLine();
+ mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
}
venn->getPic(lookup, vennCalculators);
+
+ //restore real lastlabel to save below
+ lookup[0]->setLabel(saveLabel);
}
//get next line to process
for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
lookup = input->getSharedRAbundVectors();
- count++;
}
//output error messages about any remaining user labels
}
}
- //run last line if you need to
+ //run last label if you need to
if (needToRun == true) {
- for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
+ for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
lookup = input->getSharedRAbundVectors(lastLabel);
- mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
processedLabels.insert(lookup[0]->getLabel());
userLabels.erase(lookup[0]->getLabel());
}else{
- while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+ while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if(allLines == 1 || lines.count(count) == 1 || labels.count(sabund->getLabel()) == 1){
+ if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
- mothurOut(sabund->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ mothurOut(sabund->getLabel()); mothurOutEndLine();
venn->getPic(sabund, vennCalculators);
processedLabels.insert(sabund->getLabel());
userLabels.erase(sabund->getLabel());
- userLines.erase(count);
}
if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = sabund->getLabel();
+
delete sabund;
sabund = input->getSAbundVector(lastLabel);
- mothurOut(sabund->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ mothurOut(sabund->getLabel()); mothurOutEndLine();
venn->getPic(sabund, vennCalculators);
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();
- count++;
}
//output error messages about any remaining user labels
}
}
- //run last line if you need to
+ //run last label if you need to
if (needToRun == true) {
- delete sabund;
+ if (sabund != NULL) { delete sabund; }
sabund = input->getSAbundVector(lastLabel);
- mothurOut(sabund->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ mothurOut(sabund->getLabel()); mothurOutEndLine();
venn->getPic(sabund, vennCalculators);
delete sabund;
projects / mothur.git / blobdiff