//**********************************************************************************************************************
-BootSharedCommand::BootSharedCommand(string option){
+BootSharedCommand::BootSharedCommand(string option) {
try {
globaldata = GlobalData::getInstance();
abort = false;
//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);
}
}
if(allLines == 1 || labels.count(order->getLabel()) == 1){
- mothurOut(order->getLabel()); mothurOutEndLine();
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
process(order);
processedLabels.insert(order->getLabel());
delete order;
order = input->getSharedOrderVector(lastLabel);
- mothurOut(order->getLabel()); mothurOutEndLine();
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
process(order);
processedLabels.insert(order->getLabel());
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 (needToRun == true) {
if (order != NULL) { delete order; }
order = input->getSharedOrderVector(lastLabel);
- mothurOut(order->getLabel()); mothurOutEndLine();
+ m->mothurOut(order->getLabel()); m->mothurOutEndLine();
process(order);
delete order;
//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);
}
}
}
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);
}
}
//create a new filename
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++) {
}
}
- 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();
//set global data to calc trees
globaldata->gTree = trees[k];
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();
}
catch(exception& e) {
- errorOut(e, "BootSharedCommand", "process");
+ m->errorOut(e, "BootSharedCommand", "process");
exit(1);
}
}
projects / mothur.git / blobdiff