//make sure the user has already run the read.otu command
if (globaldata->getSharedFile() == "") {
- if (globaldata->getListFile() == "") { cout << "You must read a list and a group, or a shared before you can use the bootstrap.shared command." << endl; abort = true; }
- else if (globaldata->getGroupFile() == "") { cout << "You must read a list and a group, or a shared before you can use the bootstrap.shared command." << endl; abort = true; }
+ 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; }
}
//check for optional parameter and set defaults
}
//make sure user did not use both the line and label parameters
- if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; }
+ 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 == "")) {
allLines = globaldata->allLines;
if (abort == false) {
+ //used in tree constructor
+ globaldata->runParse = false;
+
validCalculator = new ValidCalculators();
int i;
for (int i=0; i < treeCalculators.size(); i++) {
tempo = new ofstream;
out.push_back(tempo);
- }
+ }
+
+ //make a vector of tree* for each calculator
+ trees.resize(treeCalculators.size());
}
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function BootSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "BootSharedCommand", "BootSharedCommand");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the BootSharedCommand class function BootSharedCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
void BootSharedCommand::help(){
try {
- cout << "The bootstrap.shared command can only be executed after a successful read.otu command." << "\n";
- cout << "The bootstrap.shared command parameters are groups, calc, iters, line and label. You may not use line and label at the same time." << "\n";
- cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included used." << "\n";
- cout << "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";
- cout << "The bootstrap.shared command should be in the following format: bootstrap.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels, iters=yourIters)." << "\n";
- cout << "Example bootstrap.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund, iters=100)." << "\n";
- cout << "The default value for groups is all the groups in your groupfile." << "\n";
- cout << "The default value for calc is jclass-thetayc. The default for iters is 1000." << "\n";
+ 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 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 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");
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "BootSharedCommand", "help");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the BootSharedCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
if(allLines == 1 || lines.count(count) == 1 || labels.count(order->getLabel()) == 1){
- cout << order->getLabel() << '\t' << count << endl;
+ mothurOut(order->getLabel()); mothurOutEndLine();
process(order);
processedLabels.insert(order->getLabel());
delete order;
order = input->getSharedOrderVector(lastLabel);
- cout << order->getLabel() << '\t' << count << endl;
+ mothurOut(order->getLabel()); mothurOutEndLine();
process(order);
processedLabels.insert(order->getLabel());
set<string>::iterator it;
bool needToRun = false;
for (it = userLabels.begin(); it != userLabels.end(); it++) {
- cout << "Your file does not include the label "<< *it;
+ mothurOut("Your file does not include the label " + *it);
if (processedLabels.count(lastLabel) != 1) {
- cout << ". I will use " << lastLabel << "." << endl;
+ mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
needToRun = true;
}else {
- cout << ". Please refer to " << lastLabel << "." << endl;
+ mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
}
}
if (needToRun == true) {
delete order;
order = input->getSharedOrderVector(lastLabel);
- cout << order->getLabel() << '\t' << count << endl;
+ mothurOut(order->getLabel()); mothurOutEndLine();
process(order);
delete order;
}
-
+
+
+
//reset groups parameter
globaldata->Groups.clear();
return 0;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "BootSharedCommand", "execute");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the BootSharedCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
//**********************************************************************************************************************
-void BootSharedCommand::createTree(ostream* out){
+void BootSharedCommand::createTree(ostream* out, Tree* t){
try {
- //create tree
- t = new Tree();
//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++) {
- float largest = -1.0;
+ float largest = -1000.0;
int row, column;
//find largest value in sims matrix by searching lower triangle
for (int j = 1; j < simMatrix.size(); j++) {
index[column] = numGroups+i;
//zero out highest value that caused the merge.
- simMatrix[row][column] = -1.0;
- simMatrix[column][row] = -1.0;
+ simMatrix[row][column] = -1000.0;
+ simMatrix[column][row] = -1000.0;
//merge values in simsMatrix
for (int n = 0; n < simMatrix.size(); n++) {
simMatrix[row][n] = (simMatrix[row][n] + simMatrix[column][n]) / 2;
simMatrix[n][row] = simMatrix[row][n];
//delete column
- simMatrix[column][n] = -1.0;
- simMatrix[n][column] = -1.0;
+ simMatrix[column][n] = -1000.0;
+ simMatrix[n][column] = -1000.0;
}
}
+
+ //adjust tree to make sure root to tip length is .5
+ int root = t->findRoot();
+ t->tree[root].setBranchLength((0.5 - t->tree[root].getLengthToLeaves()));
//assemble tree
t->assembleTree();
//print newick file
t->print(*out);
- //delete tree
- delete t;
-
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
- catch(...) {
- cout << "An unknown error has occurred in the BootSharedCommand class function createTree. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "BootSharedCommand", "createTree");
exit(1);
}
}
/***********************************************************/
void BootSharedCommand::printSims() {
try {
- cout << "simsMatrix" << endl;
+ mothurOut("simsMatrix"); mothurOutEndLine();
for (int m = 0; m < simMatrix.size(); m++) {
for (int n = 0; n < simMatrix.size(); n++) {
- cout << simMatrix[m][n] << '\t';
+ mothurOut(simMatrix[m][n]); mothurOut("\t");
}
- cout << endl;
+ mothurOutEndLine();
}
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "BootSharedCommand", "printSims");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the BootSharedCommand class function printSims. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/***********************************************************/
void BootSharedCommand::process(SharedOrderVector* order) {
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
openOutputFile(outputFile, *(out[z]));
}
+ 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++) {
- util->getSharedVectorswithReplacement(Groups, lookup, order); //fills group vectors from order vector.
+ util->getSharedVectorswithReplacement(globaldata->Groups, lookup, order); //fills group vectors from order vector.
+
//for each calculator
for(int i = 0 ; i < treeCalculators.size(); i++) {
}
}
}
-
+
+ tempTree = new Tree();
+
//creates tree from similarity matrix and write out file
- createTree(out[i]);
+ createTree(out[i], tempTree);
+
+ //save trees for consensus command.
+ trees[i].push_back(tempTree);
}
}
+
+ mothurOut("\tDone."); 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();
+
+ //set global data to calc trees
+ globaldata->gTree = trees[k];
+
+ string filename = getRootName(globaldata->inputFileName) + treeCalculators[k]->getName() + ".boot" + order->getLabel();
+ consensus = new ConcensusCommand(filename);
+ consensus->execute();
+ delete consensus;
+
+ //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(); }
-
+
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the BootSharedCommand class Function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ errorOut(e, "BootSharedCommand", "process");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the BootSharedCommand class function process. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
- exit(1);
- }
}
/***********************************************************/
projects / mothur.git / blobdiff