X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=treegroupscommand.cpp;h=a31c15192f1f27dcc1b84ddf114d0dcf485d41a3;hb=0bcfddf7bc721a334bdae42d86a580019303537d;hp=dae04f556490260903f99b4f349d6faea249e26e;hpb=0bb069a445785a88a95e3f1427afba7df056a0b3;p=mothur.git diff --git a/treegroupscommand.cpp b/treegroupscommand.cpp index dae04f5..a31c151 100644 --- a/treegroupscommand.cpp +++ b/treegroupscommand.cpp @@ -8,6 +8,10 @@ */ #include "treegroupscommand.h" +#include "sharedsobscollectsummary.h" +#include "sharedchao1.h" +#include "sharedace.h" +#include "sharednseqs.h" #include "sharedjabund.h" #include "sharedsorabund.h" #include "sharedjclass.h" @@ -16,95 +20,194 @@ #include "sharedsorest.h" #include "sharedthetayc.h" #include "sharedthetan.h" +#include "sharedkstest.h" +#include "whittaker.h" +#include "sharedochiai.h" +#include "sharedanderbergs.h" +#include "sharedkulczynski.h" +#include "sharedkulczynskicody.h" +#include "sharedlennon.h" #include "sharedmorisitahorn.h" #include "sharedbraycurtis.h" +#include "sharedjackknife.h" +#include "whittaker.h" +#include "odum.h" +#include "canberra.h" +#include "structeuclidean.h" +#include "structchord.h" +#include "hellinger.h" +#include "manhattan.h" +#include "structpearson.h" +#include "soergel.h" +#include "spearman.h" +#include "structkulczynski.h" +#include "structchi2.h" +#include "speciesprofile.h" +#include "hamming.h" +#include "gower.h" +#include "memchi2.h" +#include "memchord.h" +#include "memeuclidean.h" +#include "mempearson.h" - +//********************************************************************************************************************** +vector TreeGroupCommand::getValidParameters(){ + try { + string Array[] = {"label","calc","groups", "phylip", "column", "name", "precision","cutoff","outputdir","inputdir"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "TreeGroupCommand", "getValidParameters"); + exit(1); + } +} +//********************************************************************************************************************** +TreeGroupCommand::TreeGroupCommand(){ + try { + abort = true; calledHelp = true; + globaldata = GlobalData::getInstance(); + //initialize outputTypes + vector tempOutNames; + outputTypes["tree"] = tempOutNames; + } + catch(exception& e) { + m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand"); + exit(1); + } +} +//********************************************************************************************************************** +vector TreeGroupCommand::getRequiredParameters(){ + try { + vector myArray; + return myArray; + } + catch(exception& e) { + m->errorOut(e, "TreeGroupCommand", "getRequiredParameters"); + exit(1); + } +} +//********************************************************************************************************************** +vector TreeGroupCommand::getRequiredFiles(){ + try { + string Array[] = {"phylip","column","shared","or"}; + vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + return myArray; + } + catch(exception& e) { + m->errorOut(e, "TreeGroupCommand", "getRequiredFiles"); + exit(1); + } +} //********************************************************************************************************************** -TreeGroupCommand::TreeGroupCommand(string option){ +TreeGroupCommand::TreeGroupCommand(string option) { try { globaldata = GlobalData::getInstance(); - abort = false; + abort = false; calledHelp = false; allLines = 1; - lines.clear(); labels.clear(); Groups.clear(); Estimators.clear(); //allow user to run help - if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; } + if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; calledHelp = true; } else { //valid paramters for this command - string Array[] = {"line","label","calc","groups", "phylip", "column", "name", "precision","cutoff"}; + string Array[] = {"label","calc","groups", "phylip", "column", "name", "precision","cutoff","outputdir","inputdir"}; vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); OptionParser parser(option); map parameters = parser. getParameters(); ValidParameters validParameter; + map::iterator it; //check to make sure all parameters are valid for command - for (map::iterator it = parameters.begin(); it != parameters.end(); it++) { + for (it = parameters.begin(); it != parameters.end(); it++) { if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; } } + //initialize outputTypes + vector tempOutNames; + outputTypes["tree"] = tempOutNames; + + //if the user changes the input directory command factory will send this info to us in the output parameter + string inputDir = validParameter.validFile(parameters, "inputdir", false); + if (inputDir == "not found"){ inputDir = ""; } + else { + string path; + it = parameters.find("phylip"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["phylip"] = inputDir + it->second; } + } + + it = parameters.find("column"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["column"] = inputDir + it->second; } + } + + it = parameters.find("name"); + //user has given a template file + if(it != parameters.end()){ + path = m->hasPath(it->second); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { parameters["name"] = inputDir + it->second; } + } + } + + format = globaldata->getFormat(); + //required parameters phylipfile = validParameter.validFile(parameters, "phylip", true); if (phylipfile == "not open") { abort = true; } else if (phylipfile == "not found") { phylipfile = ""; } - else { format = "phylip"; } + else { globaldata->newRead(); format = "phylip"; globaldata->setPhylipFile(phylipfile); } columnfile = validParameter.validFile(parameters, "column", true); if (columnfile == "not open") { abort = true; } else if (columnfile == "not found") { columnfile = ""; } - else { format = "column"; } + else { globaldata->newRead(); format = "column"; globaldata->setColumnFile(columnfile); } namefile = validParameter.validFile(parameters, "name", true); if (namefile == "not open") { abort = true; } else if (namefile == "not found") { namefile = ""; } else { globaldata->setNameFile(namefile); } - format = globaldata->getFormat(); - //error checking on files - if ((globaldata->getSharedFile() == "") && ((phylipfile == "") && (columnfile == ""))) { mothurOut("You must run the read.otu command or provide a distance file before running the tree.shared command."); mothurOutEndLine(); abort = true; } - else if ((phylipfile != "") && (columnfile != "")) { mothurOut("When running the tree.shared command with a distance file you may not use both the column and the phylip parameters."); mothurOutEndLine(); abort = true; } + if ((globaldata->getSharedFile() == "") && ((phylipfile == "") && (columnfile == ""))) { m->mothurOut("You must run the read.otu command or provide a distance file before running the tree.shared command."); m->mothurOutEndLine(); abort = true; } + else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When running the tree.shared command with a distance file you may not use both the column and the phylip parameters."); m->mothurOutEndLine(); abort = true; } if (columnfile != "") { - if (namefile == "") { mothurOut("You need to provide a namefile if you are going to use the column format."); mothurOutEndLine(); abort = true; } + if (namefile == "") { m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine(); abort = true; } } //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 { - if(label != "all") { splitAtDash(label, labels); allLines = 0; } + if(label != "all") { m->splitAtDash(label, labels); allLines = 0; } 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 (groups == "not found") { groups = ""; } else { - splitAtDash(groups, Groups); + m->splitAtDash(groups, Groups); globaldata->Groups = Groups; } @@ -113,7 +216,7 @@ TreeGroupCommand::TreeGroupCommand(string option){ else { if (calc == "default") { calc = "jclass-thetayc"; } } - splitAtDash(calc, Estimators); + m->splitAtDash(calc, Estimators); string temp; temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; } @@ -122,6 +225,12 @@ TreeGroupCommand::TreeGroupCommand(string option){ temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "10"; } convert(temp, cutoff); cutoff += (5 / (precision * 10.0)); + + //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 += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it + } if (abort == false) { @@ -132,7 +241,13 @@ TreeGroupCommand::TreeGroupCommand(string option){ int i; for (i=0; iisValidCalculator("treegroup", Estimators[i]) == true) { - if (Estimators[i] == "jabund") { + if (Estimators[i] == "sharedsobs") { + treeCalculators.push_back(new SharedSobsCS()); + }else if (Estimators[i] == "sharedchao") { + treeCalculators.push_back(new SharedChao1()); + }else if (Estimators[i] == "sharedace") { + treeCalculators.push_back(new SharedAce()); + }else if (Estimators[i] == "jabund") { treeCalculators.push_back(new JAbund()); }else if (Estimators[i] == "sorabund") { treeCalculators.push_back(new SorAbund()); @@ -148,10 +263,62 @@ TreeGroupCommand::TreeGroupCommand(string option){ treeCalculators.push_back(new ThetaYC()); }else if (Estimators[i] == "thetan") { treeCalculators.push_back(new ThetaN()); + }else if (Estimators[i] == "kstest") { + treeCalculators.push_back(new KSTest()); + }else if (Estimators[i] == "sharednseqs") { + treeCalculators.push_back(new SharedNSeqs()); + }else if (Estimators[i] == "ochiai") { + treeCalculators.push_back(new Ochiai()); + }else if (Estimators[i] == "anderberg") { + treeCalculators.push_back(new Anderberg()); + }else if (Estimators[i] == "kulczynski") { + treeCalculators.push_back(new Kulczynski()); + }else if (Estimators[i] == "kulczynskicody") { + treeCalculators.push_back(new KulczynskiCody()); + }else if (Estimators[i] == "lennon") { + treeCalculators.push_back(new Lennon()); }else if (Estimators[i] == "morisitahorn") { treeCalculators.push_back(new MorHorn()); }else if (Estimators[i] == "braycurtis") { treeCalculators.push_back(new BrayCurtis()); + }else if (Estimators[i] == "whittaker") { + treeCalculators.push_back(new Whittaker()); + }else if (Estimators[i] == "odum") { + treeCalculators.push_back(new Odum()); + }else if (Estimators[i] == "canberra") { + treeCalculators.push_back(new Canberra()); + }else if (Estimators[i] == "structeuclidean") { + treeCalculators.push_back(new StructEuclidean()); + }else if (Estimators[i] == "structchord") { + treeCalculators.push_back(new StructChord()); + }else if (Estimators[i] == "hellinger") { + treeCalculators.push_back(new Hellinger()); + }else if (Estimators[i] == "manhattan") { + treeCalculators.push_back(new Manhattan()); + }else if (Estimators[i] == "structpearson") { + treeCalculators.push_back(new StructPearson()); + }else if (Estimators[i] == "soergel") { + treeCalculators.push_back(new Soergel()); + }else if (Estimators[i] == "spearman") { + treeCalculators.push_back(new Spearman()); + }else if (Estimators[i] == "structkulczynski") { + treeCalculators.push_back(new StructKulczynski()); + }else if (Estimators[i] == "speciesprofile") { + treeCalculators.push_back(new SpeciesProfile()); + }else if (Estimators[i] == "hamming") { + treeCalculators.push_back(new Hamming()); + }else if (Estimators[i] == "structchi2") { + treeCalculators.push_back(new StructChi2()); + }else if (Estimators[i] == "gower") { + treeCalculators.push_back(new Gower()); + }else if (Estimators[i] == "memchi2") { + treeCalculators.push_back(new MemChi2()); + }else if (Estimators[i] == "memchord") { + treeCalculators.push_back(new MemChord()); + }else if (Estimators[i] == "memeuclidean") { + treeCalculators.push_back(new MemEuclidean()); + }else if (Estimators[i] == "mempearson") { + treeCalculators.push_back(new MemPearson()); } } } @@ -161,7 +328,7 @@ TreeGroupCommand::TreeGroupCommand(string option){ } catch(exception& e) { - errorOut(e, "TreeGroupCommand", "TreeGroupCommand"); + m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand"); exit(1); } } @@ -170,25 +337,25 @@ TreeGroupCommand::TreeGroupCommand(string option){ void TreeGroupCommand::help(){ try { - mothurOut("The tree.shared command creates a .tre to represent the similiarity between groups or sequences.\n"); - mothurOut("The tree.shared command can only be executed after a successful read.otu command or by providing a distance file.\n"); - mothurOut("The tree.shared command parameters are groups, calc, phylip, column, name, cutoff, precision, 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 phylip or column parameter are required if you do not run the read.otu command first, and only one may be used. If you use a column file the name filename is required. \n"); - mothurOut("If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n"); - mothurOut("The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels).\n"); - mothurOut("Example tree.shared(groups=A-B-C, line=1-3-5, calc=jabund-sorabund).\n"); - mothurOut("The default value for groups is all the groups in your groupfile.\n"); - mothurOut("The default value for calc is jclass-thetayc.\n"); - mothurOut("The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose.\n"); + m->mothurOut("The tree.shared command creates a .tre to represent the similiarity between groups or sequences.\n"); + m->mothurOut("The tree.shared command can only be executed after a successful read.otu command or by providing a distance file.\n"); + m->mothurOut("The tree.shared command parameters are groups, calc, phylip, column, name, cutoff, precision 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 allow you to select what distance levels you would like trees created for, and are also separated by dashes.\n"); + m->mothurOut("The phylip or column parameter are required if you do not run the read.otu command first, and only one may be used. If you use a column file the name filename is required. \n"); + m->mothurOut("If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed.\n"); + m->mothurOut("The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n"); + m->mothurOut("Example tree.shared(groups=A-B-C, calc=jabund-sorabund).\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.\n"); + m->mothurOut("The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose.\n"); validCalculator->printCalc("treegroup", cout); - mothurOut("Or the tree.shared command can be in the following format: tree.shared(phylip=yourPhylipFile).\n"); - mothurOut("Example tree.shared(phylip=abrecovery.dist).\n"); - mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n"); + m->mothurOut("Or the tree.shared command can be in the following format: tree.shared(phylip=yourPhylipFile).\n"); + m->mothurOut("Example tree.shared(phylip=abrecovery.dist).\n"); + m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n"); } catch(exception& e) { - errorOut(e, "TreeGroupCommand", "help"); + m->errorOut(e, "TreeGroupCommand", "help"); exit(1); } } @@ -197,11 +364,12 @@ void TreeGroupCommand::help(){ //********************************************************************************************************************** TreeGroupCommand::~TreeGroupCommand(){ + globaldata->Groups.clear(); if (abort == false) { - if (format == "sharedfile") { delete read; delete input; globaldata->ginput = NULL;} + if (format == "sharedfile") { delete read; delete input; globaldata->ginput = NULL; } else { delete readMatrix; delete matrix; delete list; } - delete tmap; + delete tmap; globaldata->gTreemap = NULL; delete validCalculator; } @@ -212,12 +380,13 @@ TreeGroupCommand::~TreeGroupCommand(){ int TreeGroupCommand::execute(){ try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } if (format == "sharedfile") { //if the users entered no valid calculators don't execute command - if (treeCalculators.size() == 0) { mothurOut("You have given no valid calculators."); mothurOutEndLine(); return 0; } - + if (treeCalculators.size() == 0) { m->mothurOut("You have given no valid calculators."); m->mothurOutEndLine(); return 0; } + + if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap; globaldata->gGroupmap = NULL; } //you have groups read = new ReadOTUFile(globaldata->inputFileName); read->read(&*globaldata); @@ -226,13 +395,28 @@ int TreeGroupCommand::execute(){ lookup = input->getSharedRAbundVectors(); lastLabel = lookup[0]->getLabel(); - if (lookup.size() < 2) { mothurOut("You have not provided enough valid groups. I cannot run the command."); mothurOutEndLine(); return 0; } + if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); return 0; } //used in tree constructor globaldata->runParse = false; + //create treemap class from groupmap for tree class to use + tmap = new TreeMap(); + tmap->makeSim(globaldata->gGroupmap); + globaldata->gTreemap = tmap; + + //clear globaldatas old tree names if any + globaldata->Treenames.clear(); + + //fills globaldatas tree names + globaldata->Treenames = globaldata->Groups; + + if (m->control_pressed) { return 0; } + //create tree file makeSimsShared(); + + if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; } }else{ //read in dist file filename = globaldata->inputFileName; @@ -256,6 +440,9 @@ int TreeGroupCommand::execute(){ //make treemap tmap = new TreeMap(); + + if (m->control_pressed) { return 0; } + tmap->makeSim(list); globaldata->gTreemap = tmap; @@ -270,28 +457,42 @@ int TreeGroupCommand::execute(){ //used in tree constructor globaldata->runParse = false; + if (m->control_pressed) { return 0; } + makeSimsDist(); + + if (m->control_pressed) { return 0; } //create a new filename - outputFile = getRootName(globaldata->inputFileName) + "tre"; + outputFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + "tre"; + outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile); createTree(); - mothurOut("Tree complete. "); mothurOutEndLine(); + + if (m->control_pressed) { return 0; } + + m->mothurOut("Tree complete. "); m->mothurOutEndLine(); + } //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, "TreeGroupCommand", "execute"); + m->errorOut(e, "TreeGroupCommand", "execute"); exit(1); } } //********************************************************************************************************************** -void TreeGroupCommand::createTree(){ +int TreeGroupCommand::createTree(){ try { //create tree t = new Tree(); @@ -300,7 +501,9 @@ void TreeGroupCommand::createTree(){ //there are numGroups - 1 merges to do for (int i = 0; i < (numGroups - 1); i++) { float largest = -1000.0; - + + if (m->control_pressed) { delete t; return 1; } + int row, column; //find largest value in sims matrix by searching lower triangle for (int j = 1; j < simMatrix.size(); j++) { @@ -354,15 +557,21 @@ void TreeGroupCommand::createTree(){ //assemble tree t->assembleTree(); + if (m->control_pressed) { delete t; return 1; } + //print newick file t->createNewickFile(outputFile); //delete tree delete t; + + if (m->control_pressed) { remove(outputFile.c_str()); outputNames.pop_back(); return 1; } + + return 0; } catch(exception& e) { - errorOut(e, "TreeGroupCommand", "createTree"); + m->errorOut(e, "TreeGroupCommand", "createTree"); exit(1); } } @@ -386,12 +595,12 @@ void TreeGroupCommand::printSims(ostream& out) { } catch(exception& e) { - errorOut(e, "TreeGroupCommand", "printSims"); + m->errorOut(e, "TreeGroupCommand", "printSims"); exit(1); } } /***********************************************************/ -void TreeGroupCommand::makeSimsDist() { +int TreeGroupCommand::makeSimsDist() { try { numGroups = list->size(); @@ -402,9 +611,9 @@ void TreeGroupCommand::makeSimsDist() { //initialize simMatrix simMatrix.clear(); simMatrix.resize(numGroups); - for (int m = 0; m < simMatrix.size(); m++) { + for (int k = 0; k < simMatrix.size(); k++) { for (int j = 0; j < simMatrix.size(); j++) { - simMatrix[m].push_back(0.0); + simMatrix[k].push_back(0.0); } } @@ -413,58 +622,52 @@ void TreeGroupCommand::makeSimsDist() { for(MatData currentCell = matrix->begin(); currentCell != matrix->end(); currentCell++){ //similairity = -(distance-1) simMatrix[currentCell->row][currentCell->column] = -(currentCell->dist -1.0); - simMatrix[currentCell->column][currentCell->row] = -(currentCell->dist -1.0); + simMatrix[currentCell->column][currentCell->row] = -(currentCell->dist -1.0); + + if (m->control_pressed) { return 1; } + } - + return 0; } catch(exception& e) { - errorOut(e, "TreeGroupCommand", "makeSimsDist"); + m->errorOut(e, "TreeGroupCommand", "makeSimsDist"); exit(1); } } /***********************************************************/ -void TreeGroupCommand::makeSimsShared() { +int TreeGroupCommand::makeSimsShared() { try { - int count = 1; - - //clear globaldatas old tree names if any - globaldata->Treenames.clear(); - - //fills globaldatas tree names - globaldata->Treenames = globaldata->Groups; - - //create treemap class from groupmap for tree class to use - tmap = new TreeMap(); - tmap->makeSim(globaldata->gGroupmap); - globaldata->gTreemap = tmap; - set processedLabels; set userLabels = labels; - set userLines = lines; - + //as long as you are not at the end of the file or done wih the lines you want - while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) { + while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) { + if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for(int i = 0 ; i < treeCalculators.size(); i++) { delete treeCalculators[i]; } return 1; } - if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){ - mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine(); + if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){ + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); process(lookup); processedLabels.insert(lookup[0]->getLabel()); userLabels.erase(lookup[0]->getLabel()); - userLines.erase(count); } - if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) { + string saveLabel = lookup[0]->getLabel(); + for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } lookup = input->getSharedRAbundVectors(lastLabel); - mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine(); + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); process(lookup); processedLabels.insert(lookup[0]->getLabel()); userLabels.erase(lookup[0]->getLabel()); + + //restore real lastlabel to save below + lookup[0]->setLabel(saveLabel); } lastLabel = lookup[0]->getLabel(); @@ -472,42 +675,45 @@ void TreeGroupCommand::makeSimsShared() { //get next line to process for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } lookup = input->getSharedRAbundVectors(); - count++; } + if (m->control_pressed) { for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } for(int i = 0 ; i < treeCalculators.size(); i++) { delete treeCalculators[i]; } return 1; } + //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(); } } - //run last line if you need to + //run last label if you need to if (needToRun == true) { - for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } + for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } } lookup = input->getSharedRAbundVectors(lastLabel); - mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine(); + m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine(); process(lookup); for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; } } for(int i = 0 ; i < treeCalculators.size(); i++) { delete treeCalculators[i]; } + + return 0; } catch(exception& e) { - errorOut(e, "TreeGroupCommand", "makeSimsShared"); + m->errorOut(e, "TreeGroupCommand", "makeSimsShared"); exit(1); } } /***********************************************************/ -void TreeGroupCommand::process(vector thisLookup) { +int TreeGroupCommand::process(vector thisLookup) { try{ EstOutput data; vector subset; @@ -518,9 +724,9 @@ void TreeGroupCommand::process(vector thisLookup) { //initialize simMatrix simMatrix.clear(); simMatrix.resize(numGroups); - for (int m = 0; m < simMatrix.size(); m++) { + for (int k = 0; k < simMatrix.size(); k++) { for (int j = 0; j < simMatrix.size(); j++) { - simMatrix[m].push_back(0.0); + simMatrix[k].push_back(0.0); } } @@ -529,7 +735,8 @@ void TreeGroupCommand::process(vector thisLookup) { for (int g = 0; g < numGroups; g++) { index[g] = g; } //create a new filename - outputFile = getRootName(globaldata->inputFileName) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre"; + outputFile = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".tre"; + outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile); for (int k = 0; k < thisLookup.size(); k++) { for (int l = k; l < thisLookup.size(); l++) { @@ -540,21 +747,52 @@ void TreeGroupCommand::process(vector thisLookup) { //add new pair of sharedrabunds subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]); + //if this calc needs all groups to calculate the pair load all groups + if (treeCalculators[i]->getNeedsAll()) { + //load subset with rest of lookup for those calcs that need everyone to calc for a pair + for (int w = 0; w < thisLookup.size(); w++) { + if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); } + } + } + data = treeCalculators[i]->getValues(subset); //saves the calculator outputs + //cout << thisLookup[k]->getGroup() << '\t' << thisLookup[l]->getGroup() << '\t' << (1.0 - data[0]) << endl; + if (m->control_pressed) { return 1; } + //save values in similarity matrix simMatrix[k][l] = data[0]; simMatrix[l][k] = data[0]; } } } - + + //createdistance file from simMatrix + /*string o = outputDir + m->getRootName(m->getSimpleName(globaldata->inputFileName)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".dist"; + ofstream outDist; + m->openOutputFile(o, outDist); + outDist << simMatrix.size() << endl; + for (int k = 0; k < simMatrix.size(); k++) { + outDist << thisLookup[k]->getGroup() << '\t'; + for (int l = 0; l < k; l++) { + outDist << (1.0-simMatrix[k][l]) << '\t'; + } + outDist << endl; + } + outDist.close();*/ + + + if (m->control_pressed) { return 1; } //creates tree from similarity matrix and write out file createTree(); + + if (m->control_pressed) { return 1; } } + + return 0; } catch(exception& e) { - errorOut(e, "TreeGroupCommand", "process"); + m->errorOut(e, "TreeGroupCommand", "process"); exit(1); } }