//**********************************************************************************************************************
-BootSharedCommand::BootSharedCommand(string option){
+BootSharedCommand::BootSharedCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
else {
//valid paramters for this command
- string Array[] = {"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; }
- else if (globaldata->getGroupFile() == "") { mothurOut("You must read a list and a group, or a shared before you can use the bootstrap.shared command."); mothurOutEndLine(); abort = true; }
+ if (globaldata->getListFile() == "") { m->mothurOut("You must read a list and a group, or a shared before you can use the bootstrap.shared command."); m->mothurOutEndLine(); abort = true; }
+ else if (globaldata->getGroupFile() == "") { m->mothurOut("You must read a list and a group, or a shared before you can use the bootstrap.shared command."); m->mothurOutEndLine(); abort = true; }
}
//check for optional parameter and set defaults
}
catch(exception& e) {
- errorOut(e, "BootSharedCommand", "BootSharedCommand");
+ m->errorOut(e, "BootSharedCommand", "BootSharedCommand");
exit(1);
}
}
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 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 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");
+ m->mothurOut("The bootstrap.shared command can only be executed after a successful read.otu command.\n");
+ m->mothurOut("The bootstrap.shared command parameters are groups, calc, iters and label.\n");
+ m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n");
+ m->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");
+ m->mothurOut("The bootstrap.shared command should be in the following format: bootstrap.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels, iters=yourIters).\n");
+ m->mothurOut("Example bootstrap.shared(groups=A-B-C, calc=jabund-sorabund, iters=100).\n");
+ m->mothurOut("The default value for groups is all the groups in your groupfile.\n");
+ m->mothurOut("The default value for calc is jclass-thetayc. The default for iters is 1000.\n");
}
catch(exception& e) {
- errorOut(e, "BootSharedCommand", "help");
+ m->errorOut(e, "BootSharedCommand", "help");
exit(1);
}
}
globaldata->gTreemap = tmap;
while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
-
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; }
+
if(allLines == 1 || labels.count(order->getLabel()) == 1){
- mothurOut(order->getLabel()); mothurOutEndLine();
- process(order);
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
+ int error = process(order);
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; }
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
delete order;
order = input->getSharedOrderVector(lastLabel);
- mothurOut(order->getLabel()); mothurOutEndLine();
- process(order);
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
+ int error = process(order);
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; }
processedLabels.insert(order->getLabel());
userLabels.erase(order->getLabel());
order = input->getSharedOrderVector();
}
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); 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 (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; }
+
//run last line if you need to
if (needToRun == true) {
if (order != NULL) { delete order; }
order = input->getSharedOrderVector(lastLabel);
- mothurOut(order->getLabel()); mothurOutEndLine();
- process(order);
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
+ int error = process(order);
+ if (error == 1) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; }
+
delete order;
}
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } globaldata->Groups.clear(); return 0; }
+
//reset groups parameter
globaldata->Groups.clear();
+
+ 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, "BootSharedCommand", "execute");
+ m->errorOut(e, "BootSharedCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
-void BootSharedCommand::createTree(ostream* out, Tree* t){
+int BootSharedCommand::createTree(ostream* out, Tree* t){
try {
//do merges and create tree structure by setting parents and children
//there are numGroups - 1 merges to do
for (int i = 0; i < (numGroups - 1); i++) {
+ if (m->control_pressed) { return 1; }
+
float largest = -1000.0;
int row, column;
//find largest value in sims matrix by searching lower triangle
//assemble tree
t->assembleTree();
+
+ if (m->control_pressed) { return 1; }
//print newick file
t->print(*out);
+
+ return 0;
}
catch(exception& e) {
- errorOut(e, "BootSharedCommand", "createTree");
+ m->errorOut(e, "BootSharedCommand", "createTree");
exit(1);
}
}
/***********************************************************/
void BootSharedCommand::printSims() {
try {
- mothurOut("simsMatrix"); mothurOutEndLine();
- for (int m = 0; m < simMatrix.size(); m++) {
+ m->mothurOut("simsMatrix"); m->mothurOutEndLine();
+ for (int k = 0; k < simMatrix.size(); k++) {
for (int n = 0; n < simMatrix.size(); n++) {
- mothurOut(simMatrix[m][n]); mothurOut("\t");
+ m->mothurOut(toString(simMatrix[k][n])); m->mothurOut("\t");
}
- mothurOutEndLine();
+ m->mothurOutEndLine();
}
}
catch(exception& e) {
- errorOut(e, "BootSharedCommand", "printSims");
+ m->errorOut(e, "BootSharedCommand", "printSims");
exit(1);
}
}
/***********************************************************/
-void BootSharedCommand::process(SharedOrderVector* order) {
+int BootSharedCommand::process(SharedOrderVector* order) {
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]));
+ outputNames.push_back(outputFile);
}
- mothurOut("Generating bootstrap trees..."); cout.flush();
+ m->mothurOut("Generating bootstrap trees..."); cout.flush();
//create a file for each calculator with the 1000 trees in it.
for (int p = 0; p < iters; p++) {
+ if (m->control_pressed) { return 1; }
+
util->getSharedVectorswithReplacement(globaldata->Groups, lookup, order); //fills group vectors from order vector.
//for each calculator
for(int i = 0 ; i < treeCalculators.size(); i++) {
-
+
+ if (m->control_pressed) { return 1; }
+
//initialize simMatrix
simMatrix.clear();
simMatrix.resize(numGroups);
- for (int m = 0; m < simMatrix.size(); m++) {
+ for (int o = 0; o < simMatrix.size(); o++) {
for (int j = 0; j < simMatrix.size(); j++) {
- simMatrix[m].push_back(0.0);
+ simMatrix[o].push_back(0.0);
}
}
tempTree = new Tree();
+ if (m->control_pressed) { delete tempTree; return 1; }
+
//creates tree from similarity matrix and write out file
createTree(out[i], tempTree);
+ if (m->control_pressed) { delete tempTree; return 1; }
+
//save trees for consensus command.
trees[i].push_back(tempTree);
}
}
- mothurOut("\tDone."); mothurOutEndLine();
+ m->mothurOut("\tDone."); m->mothurOutEndLine();
//delete globaldata's tree
//for (int m = 0; m < globaldata->gTree.size(); m++) { delete globaldata->gTree[m]; }
//globaldata->gTree.clear();
//create consensus trees for each bootstrapped tree set
for (int k = 0; k < trees.size(); k++) {
- mothurOut("Generating consensus tree for " + treeCalculators[k]->getName()); mothurOutEndLine();
+ m->mothurOut("Generating consensus tree for " + treeCalculators[k]->getName()); m->mothurOutEndLine();
+
+ if (m->control_pressed) { return 1; }
//set global data to calc trees
globaldata->gTree = trees[k];
- string filename = getRootName(globaldata->inputFileName) + treeCalculators[k]->getName() + ".boot" + order->getLabel();
+ string filename = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + treeCalculators[k]->getName() + ".boot" + order->getLabel();
consensus = new ConcensusCommand(filename);
consensus->execute();
delete consensus;
+ outputNames.push_back(filename + ".cons.pairs");
+ outputNames.push_back(filename + ".cons.tre");
+
//delete globaldata's tree
//for (int m = 0; m < globaldata->gTree.size(); m++) { delete globaldata->gTree[m]; }
//globaldata->gTree.clear();
//close ostream for each calc
for (int z = 0; z < treeCalculators.size(); z++) { out[z]->close(); }
+
+ return 0;
}
catch(exception& e) {
- errorOut(e, "BootSharedCommand", "process");
+ m->errorOut(e, "BootSharedCommand", "process");
exit(1);
}
}
projects / mothur.git / blobdiff