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"};
vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
OptionParser parser(option);
//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);
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());
}
}
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();
}
//**********************************************************************************************************************
-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) {
errorOut(e, "BootSharedCommand", "createTree");
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) {
errorOut(e, "BootSharedCommand", "process");
projects / mothur.git / blobdiff