globaldata = GlobalData::getInstance();
abort = false;
allLines = 1;
- lines.clear();
labels.clear();
Groups.clear();
Estimators.clear();
else {
//valid paramters for this command
- string Array[] = {"line","label","calc","groups","iters"};
+ string Array[] = {"label","calc","groups","iters","outputdir","inputdir"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { 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
+ }
+
+
//make sure the user has already run the read.otu command
if (globaldata->getSharedFile() == "") {
if (globaldata->getListFile() == "") { mothurOut("You must read a list and a group, or a shared before you can use the bootstrap.shared command."); mothurOutEndLine(); abort = true; }
//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);
void BootSharedCommand::help(){
try {
mothurOut("The bootstrap.shared command can only be executed after a successful read.otu command.\n");
- mothurOut("The bootstrap.shared command parameters are groups, calc, iters, line and label. You may not use line and label at the same time.\n");
+ mothurOut("The bootstrap.shared command parameters are groups, calc, iters and label.\n");
mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n");
- mothurOut("The group names are separated by dashes. The line and label allow you to select what distance levels you would like trees created for, and are also separated by dashes.\n");
- mothurOut("The bootstrap.shared command should be in the following format: bootstrap.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels, iters=yourIters).\n");
- mothurOut("Example bootstrap.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund, iters=100).\n");
+ mothurOut("The group names are separated by dashes. The label parameter allows you to select what distance levels you would like trees created for, and is also separated by dashes.\n");
+ mothurOut("The bootstrap.shared command should be in the following format: bootstrap.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels, iters=yourIters).\n");
+ mothurOut("Example bootstrap.shared(groups=A-B-C, calc=jabund-sorabund, iters=100).\n");
mothurOut("The default value for groups is all the groups in your groupfile.\n");
mothurOut("The default value for calc is jclass-thetayc. The default for iters is 1000.\n");
}
if (abort == true) { return 0; }
- int count = 1;
util = new SharedUtil();
//read first line
//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;
//set users groups
util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "treegroup");
tmap->makeSim(globaldata->gGroupmap);
globaldata->gTreemap = tmap;
- while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
+ while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
- if(allLines == 1 || lines.count(count) == 1 || labels.count(order->getLabel()) == 1){
+ if(allLines == 1 || labels.count(order->getLabel()) == 1){
- mothurOut(order->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ mothurOut(order->getLabel()); mothurOutEndLine();
process(order);
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
- userLines.erase(count);
}
- //you have a label the user want that is smaller than this line and the last line has not already been processed
+ //you have a label the user want that is smaller than this label and the last label has not already been processed
if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
+ string saveLabel = order->getLabel();
delete order;
order = input->getSharedOrderVector(lastLabel);
- mothurOut(order->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ mothurOut(order->getLabel()); mothurOutEndLine();
process(order);
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
+
+ //restore real lastlabel to save below
+ order->setLabel(saveLabel);
}
//get next line to process
delete order;
order = input->getSharedOrderVector();
- count++;
}
//output error messages about any remaining user labels
//run last line if you need to
if (needToRun == true) {
- delete order;
+ if (order != NULL) { delete order; }
order = input->getSharedOrderVector(lastLabel);
- mothurOut(order->getLabel() + "\t" + toString(count)); mothurOutEndLine();
+ mothurOut(order->getLabel()); mothurOutEndLine();
process(order);
delete order;
}
-
-
//reset groups parameter
globaldata->Groups.clear();
try{
EstOutput data;
vector<SharedRAbundVector*> subset;
-
-
+
//open an ostream for each calc to print to
for (int z = 0; z < treeCalculators.size(); z++) {
//create a new filename
- outputFile = getRootName(globaldata->inputFileName) + treeCalculators[z]->getName() + ".boot" + order->getLabel() + ".tre";
+ outputFile = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + treeCalculators[z]->getName() + ".boot" + order->getLabel() + ".tre";
openOutputFile(outputFile, *(out[z]));
}
//set global data to calc trees
globaldata->gTree = trees[k];
- string filename = getRootName(globaldata->inputFileName) + treeCalculators[k]->getName() + ".boot" + order->getLabel();
+ string filename = getRootName(getSimpleName(globaldata->inputFileName)) + treeCalculators[k]->getName() + ".boot" + order->getLabel();
consensus = new ConcensusCommand(filename);
consensus->execute();
delete consensus;