X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bootstrapsharedcommand.cpp;h=b7d6c45e6e0179704a0e902c7960810e65df7eca;hb=64b2b8d59acac0332e61b6622e7d16a300bdce3e;hp=b44ce4b15d8f4121db33d12285616da1c8fde8f7;hpb=74844a60d80c6dd06e3fb02ee9b928424f9019b0;p=mothur.git diff --git a/bootstrapsharedcommand.cpp b/bootstrapsharedcommand.cpp index b44ce4b..b7d6c45 100644 --- a/bootstrapsharedcommand.cpp +++ b/bootstrapsharedcommand.cpp @@ -19,9 +19,55 @@ #include "sharedmorisitahorn.h" #include "sharedbraycurtis.h" - //********************************************************************************************************************** - +vector BootSharedCommand::getValidParameters(){ + try { + string AlignArray[] = {"label","calc","groups","iters","outputdir","inputdir"}; + vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "BootSharedCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +BootSharedCommand::BootSharedCommand(){ + try { + abort = true; + //initialize outputTypes + vector tempOutNames; + outputTypes["tree"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "BootSharedCommand", "BootSharedCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector BootSharedCommand::getRequiredParameters(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "BootSharedCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector BootSharedCommand::getRequiredFiles(){ + try { + string AlignArray[] = {"shared"}; + vector myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "BootSharedCommand", "getRequiredFiles"); + exit(1); + } +} +//********************************************************************************************************************** BootSharedCommand::BootSharedCommand(string option) { try { globaldata = GlobalData::getInstance(); @@ -49,10 +95,14 @@ BootSharedCommand::BootSharedCommand(string option) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + //initialize outputTypes + vector tempOutNames; + outputTypes["tree"] = tempOutNames; + //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 + outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it } @@ -67,7 +117,7 @@ BootSharedCommand::BootSharedCommand(string option) { label = validParameter.validFile(parameters, "label", false); if (label == "not found") { label = ""; } else { - if(label != "all") { splitAtDash(label, labels); allLines = 0; } + if(label != "all") { m->splitAtDash(label, labels); allLines = 0; } else { allLines = 1; } } @@ -80,7 +130,7 @@ BootSharedCommand::BootSharedCommand(string option) { groups = validParameter.validFile(parameters, "groups", false); if (groups == "not found") { groups = ""; } else { - splitAtDash(groups, Groups); + m->splitAtDash(groups, Groups); globaldata->Groups = Groups; } @@ -89,7 +139,7 @@ BootSharedCommand::BootSharedCommand(string option) { else { if (calc == "default") { calc = "jclass-thetayc"; } } - splitAtDash(calc, Estimators); + m->splitAtDash(calc, Estimators); string temp; temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; } @@ -219,24 +269,27 @@ int BootSharedCommand::execute(){ 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){ m->mothurOut(order->getLabel()); m->mothurOutEndLine(); - process(order); + 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()); } //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)) { + if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { string saveLabel = order->getLabel(); delete order; order = input->getSharedOrderVector(lastLabel); m->mothurOut(order->getLabel()); m->mothurOutEndLine(); - process(order); + 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()); @@ -253,6 +306,9 @@ int BootSharedCommand::execute(){ 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::iterator it; bool needToRun = false; @@ -266,16 +322,22 @@ int BootSharedCommand::execute(){ } } + 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); m->mothurOut(order->getLabel()); m->mothurOutEndLine(); - process(order); + 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(); @@ -294,13 +356,15 @@ int BootSharedCommand::execute(){ } //********************************************************************************************************************** -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 @@ -354,9 +418,13 @@ void BootSharedCommand::createTree(ostream* out, Tree* t){ //assemble tree t->assembleTree(); + + if (m->control_pressed) { return 1; } //print newick file t->print(*out); + + return 0; } catch(exception& e) { @@ -382,7 +450,7 @@ void BootSharedCommand::printSims() { } } /***********************************************************/ -void BootSharedCommand::process(SharedOrderVector* order) { +int BootSharedCommand::process(SharedOrderVector* order) { try{ EstOutput data; vector subset; @@ -390,9 +458,9 @@ void BootSharedCommand::process(SharedOrderVector* order) { //open an ostream for each calc to print to for (int z = 0; z < treeCalculators.size(); z++) { //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); + outputFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + treeCalculators[z]->getName() + ".boot" + order->getLabel() + ".tre"; + m->openOutputFile(outputFile, *(out[z])); + outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile); } m->mothurOut("Generating bootstrap trees..."); cout.flush(); @@ -400,18 +468,22 @@ void BootSharedCommand::process(SharedOrderVector* order) { //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); } } @@ -437,9 +509,13 @@ void BootSharedCommand::process(SharedOrderVector* order) { 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); } @@ -456,10 +532,12 @@ void BootSharedCommand::process(SharedOrderVector* order) { 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 = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + treeCalculators[k]->getName() + ".boot" + order->getLabel(); + string filename = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + treeCalculators[k]->getName() + ".boot" + order->getLabel(); consensus = new ConcensusCommand(filename); consensus->execute(); delete consensus; @@ -477,6 +555,8 @@ void BootSharedCommand::process(SharedOrderVector* order) { //close ostream for each calc for (int z = 0; z < treeCalculators.size(); z++) { out[z]->close(); } + + return 0; } catch(exception& e) {