X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bootstrapsharedcommand.cpp;h=9424347180c7713c6b498fd16cada4e7e86accd4;hb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;hp=bfd3e984f28208d37e49f22403ad59647af38e7f;hpb=6777912b79eb6d011163da47f3ada09d1a9293c1;p=mothur.git diff --git a/bootstrapsharedcommand.cpp b/bootstrapsharedcommand.cpp index bfd3e98..9424347 100644 --- a/bootstrapsharedcommand.cpp +++ b/bootstrapsharedcommand.cpp @@ -22,7 +22,7 @@ //********************************************************************************************************************** -BootSharedCommand::BootSharedCommand(string option){ +BootSharedCommand::BootSharedCommand(string option) { try { globaldata = GlobalData::getInstance(); abort = false; @@ -52,14 +52,14 @@ BootSharedCommand::BootSharedCommand(string option){ //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 } //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 @@ -67,7 +67,7 @@ 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 +80,7 @@ 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 +89,7 @@ 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"; } @@ -144,7 +144,7 @@ BootSharedCommand::BootSharedCommand(string option){ } catch(exception& e) { - errorOut(e, "BootSharedCommand", "BootSharedCommand"); + m->errorOut(e, "BootSharedCommand", "BootSharedCommand"); exit(1); } } @@ -153,17 +153,17 @@ BootSharedCommand::BootSharedCommand(string option){ 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); } } @@ -219,24 +219,27 @@ 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){ - 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()); } //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); - 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()); @@ -253,48 +256,65 @@ 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; 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 @@ -348,35 +368,39 @@ 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) { - 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 subset; @@ -384,27 +408,32 @@ 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])); + outputFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + treeCalculators[z]->getName() + ".boot" + order->getLabel() + ".tre"; + m->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); } } @@ -430,15 +459,19 @@ 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); } } - 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(); @@ -447,16 +480,21 @@ void BootSharedCommand::process(SharedOrderVector* order) { //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 = 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; + 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(); @@ -467,10 +505,12 @@ 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) { - errorOut(e, "BootSharedCommand", "process"); + m->errorOut(e, "BootSharedCommand", "process"); exit(1); } }