2 * treegroupscommand.cpp
5 * Created by Sarah Westcott on 4/8/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "treegroupscommand.h"
11 #include "subsample.h"
12 #include "consensus.h"
14 //**********************************************************************************************************************
15 vector<string> TreeGroupCommand::setParameters(){
17 CommandParameter pshared("shared", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pshared);
18 CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "none",false,false); parameters.push_back(pphylip);
19 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "ColumnName",false,false); parameters.push_back(pname);
20 CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnShared", "PhylipColumnShared", "ColumnName",false,false); parameters.push_back(pcolumn);
21 CommandParameter piters("iters", "Number", "", "1000", "", "", "",false,false); parameters.push_back(piters);
22 CommandParameter psubsample("subsample", "String", "", "", "", "", "",false,false); parameters.push_back(psubsample);
23 CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
24 CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
25 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
26 CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
27 CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "",true,false); parameters.push_back(pcalc);
29 CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
30 //CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "",false,false); parameters.push_back(poutput);
31 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
32 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
34 vector<string> myArray;
35 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
39 m->errorOut(e, "TreeGroupCommand", "setParameters");
43 //**********************************************************************************************************************
44 string TreeGroupCommand::getHelpString(){
46 string helpString = "";
47 ValidCalculators validCalculator;
48 helpString += "The tree.shared command creates a .tre to represent the similiarity between groups or sequences.\n";
49 helpString += "The tree.shared command parameters are shared, groups, calc, phylip, column, name, cutoff, precision, processors, subsample, iters and label.\n";
50 helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n";
51 helpString += "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";
52 helpString += "The phylip or column parameter are required if you do not provide a sharedfile, and only one may be used. If you use a column file the name filename is required. \n";
53 helpString += "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";
54 helpString += "The tree.shared command should be in the following format: tree.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n";
55 helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample.\n";
56 helpString += "The subsample parameter allows you to enter the size pergroup of the sample or you can set subsample=T and mothur will use the size of your smallest group. The subsample parameter may only be used with a shared file.\n";
57 helpString += "Example tree.shared(groups=A-B-C, calc=jabund-sorabund).\n";
58 helpString += "The default value for groups is all the groups in your groupfile.\n";
59 helpString += "The default value for calc is jclass-thetayc.\n";
60 helpString += "The tree.shared command outputs a .tre file for each calculator you specify at each distance you choose.\n";
61 helpString += validCalculator.printCalc("treegroup");
62 helpString += "Or the tree.shared command can be in the following format: tree.shared(phylip=yourPhylipFile).\n";
63 helpString += "Example tree.shared(phylip=abrecovery.dist).\n";
64 helpString += "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n";
68 m->errorOut(e, "TreeGroupCommand", "getHelpString");
72 //**********************************************************************************************************************
73 string TreeGroupCommand::getOutputFileNameTag(string type, string inputName=""){
75 string outputFileName = "";
76 map<string, vector<string> >::iterator it;
78 //is this a type this command creates
79 it = outputTypes.find(type);
80 if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
82 if (type == "tree") { outputFileName = "tre"; }
83 else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; }
85 return outputFileName;
88 m->errorOut(e, "TreeGroupCommand", "getOutputFileNameTag");
92 //**********************************************************************************************************************
93 TreeGroupCommand::TreeGroupCommand(){
95 abort = true; calledHelp = true;
97 //initialize outputTypes
98 vector<string> tempOutNames;
99 outputTypes["tree"] = tempOutNames;
101 catch(exception& e) {
102 m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
106 //**********************************************************************************************************************
108 TreeGroupCommand::TreeGroupCommand(string option) {
110 abort = false; calledHelp = false;
113 //allow user to run help
114 if(option == "help") { help(); abort = true; calledHelp = true; }
115 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
118 vector<string> myArray = setParameters();
120 OptionParser parser(option);
121 map<string, string> parameters = parser. getParameters();
123 ValidParameters validParameter;
124 map<string, string>::iterator it;
126 //check to make sure all parameters are valid for command
127 for (it = parameters.begin(); it != parameters.end(); it++) {
128 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
131 //initialize outputTypes
132 vector<string> tempOutNames;
133 outputTypes["tree"] = tempOutNames;
135 //if the user changes the input directory command factory will send this info to us in the output parameter
136 string inputDir = validParameter.validFile(parameters, "inputdir", false);
137 if (inputDir == "not found"){ inputDir = ""; }
140 it = parameters.find("phylip");
141 //user has given a template file
142 if(it != parameters.end()){
143 path = m->hasPath(it->second);
144 //if the user has not given a path then, add inputdir. else leave path alone.
145 if (path == "") { parameters["phylip"] = inputDir + it->second; }
148 it = parameters.find("column");
149 //user has given a template file
150 if(it != parameters.end()){
151 path = m->hasPath(it->second);
152 //if the user has not given a path then, add inputdir. else leave path alone.
153 if (path == "") { parameters["column"] = inputDir + it->second; }
156 it = parameters.find("name");
157 //user has given a template file
158 if(it != parameters.end()){
159 path = m->hasPath(it->second);
160 //if the user has not given a path then, add inputdir. else leave path alone.
161 if (path == "") { parameters["name"] = inputDir + it->second; }
165 //check for required parameters
166 phylipfile = validParameter.validFile(parameters, "phylip", true);
167 if (phylipfile == "not open") { phylipfile = ""; abort = true; }
168 else if (phylipfile == "not found") { phylipfile = ""; }
169 else { inputfile = phylipfile; format = "phylip"; m->setPhylipFile(phylipfile); }
171 columnfile = validParameter.validFile(parameters, "column", true);
172 if (columnfile == "not open") { columnfile = ""; abort = true; }
173 else if (columnfile == "not found") { columnfile = ""; }
174 else { inputfile = columnfile; format = "column"; m->setColumnFile(columnfile); }
176 sharedfile = validParameter.validFile(parameters, "shared", true);
177 if (sharedfile == "not open") { sharedfile = ""; abort = true; }
178 else if (sharedfile == "not found") { sharedfile = ""; }
179 else { inputfile = sharedfile; format = "sharedfile"; m->setSharedFile(sharedfile); }
181 namefile = validParameter.validFile(parameters, "name", true);
182 if (namefile == "not open") { abort = true; }
183 else if (namefile == "not found") { namefile = ""; }
184 else { m->setNameFile(namefile); }
186 if ((phylipfile == "") && (columnfile == "") && (sharedfile == "")) {
187 //is there are current file available for either of these?
188 //give priority to shared, then column, then phylip
189 sharedfile = m->getSharedFile();
190 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
192 columnfile = m->getColumnFile();
193 if (columnfile != "") { inputfile = columnfile; format = "column"; m->mothurOut("Using " + columnfile + " as input file for the column parameter."); m->mothurOutEndLine(); }
195 phylipfile = m->getPhylipFile();
196 if (phylipfile != "") { inputfile = phylipfile; format = "phylip"; m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
198 m->mothurOut("No valid current files. You must provide a shared, phylip or column file."); m->mothurOutEndLine();
204 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; }
206 if (columnfile != "") {
207 if (namefile == "") {
208 namefile = m->getNameFile();
209 if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
211 m->mothurOut("You need to provide a namefile if you are going to use the column format."); m->mothurOutEndLine();
217 //check for optional parameter and set defaults
218 // ...at some point should added some additional type checking...
219 label = validParameter.validFile(parameters, "label", false);
220 if (label == "not found") { label = ""; }
222 if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
223 else { allLines = 1; }
226 groups = validParameter.validFile(parameters, "groups", false);
227 if (groups == "not found") { groups = ""; }
229 m->splitAtDash(groups, Groups);
230 m->setGroups(Groups);
233 calc = validParameter.validFile(parameters, "calc", false);
234 if (calc == "not found") { calc = "jclass-thetayc"; }
236 if (calc == "default") { calc = "jclass-thetayc"; }
238 m->splitAtDash(calc, Estimators);
239 if (m->inUsersGroups("citation", Estimators)) {
240 ValidCalculators validCalc; validCalc.printCitations(Estimators);
241 //remove citation from list of calcs
242 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } }
246 temp = validParameter.validFile(parameters, "precision", false); if (temp == "not found") { temp = "100"; }
247 m->mothurConvert(temp, precision);
249 temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "10"; }
250 m->mothurConvert(temp, cutoff);
251 cutoff += (5 / (precision * 10.0));
253 temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
254 m->setProcessors(temp);
255 m->mothurConvert(temp, processors);
257 temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
258 m->mothurConvert(temp, iters);
260 temp = validParameter.validFile(parameters, "subsample", false); if (temp == "not found") { temp = "F"; }
261 if (m->isNumeric1(temp)) { m->mothurConvert(temp, subsampleSize); subsample = true; }
263 if (m->isTrue(temp)) { subsample = true; subsampleSize = -1; } //we will set it to smallest group later
264 else { subsample = false; }
267 if (subsample == false) { iters = 1; }
269 if (subsample && (format != "sharedfile")) { m->mothurOut("[ERROR]: the subsample parameter can only be used with a shared file.\n"); abort=true; }
271 //if the user changes the output directory command factory will send this info to us in the output parameter
272 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
274 outputDir += m->hasPath(inputfile); //if user entered a file with a path then preserve it
279 catch(exception& e) {
280 m->errorOut(e, "TreeGroupCommand", "TreeGroupCommand");
284 //**********************************************************************************************************************
286 TreeGroupCommand::~TreeGroupCommand(){
287 if (abort == false) {
288 if (format == "sharedfile") { delete input; }
289 else { delete list; }
295 //**********************************************************************************************************************
297 int TreeGroupCommand::execute(){
300 if (abort == true) { if (calledHelp) { return 0; } return 2; }
302 if (format == "sharedfile") {
304 ValidCalculators validCalculator;
306 for (int i=0; i<Estimators.size(); i++) {
307 if (validCalculator.isValidCalculator("treegroup", Estimators[i]) == true) {
308 if (Estimators[i] == "sharedsobs") {
309 treeCalculators.push_back(new SharedSobsCS());
310 }else if (Estimators[i] == "sharedchao") {
311 treeCalculators.push_back(new SharedChao1());
312 }else if (Estimators[i] == "sharedace") {
313 treeCalculators.push_back(new SharedAce());
314 }else if (Estimators[i] == "jabund") {
315 treeCalculators.push_back(new JAbund());
316 }else if (Estimators[i] == "sorabund") {
317 treeCalculators.push_back(new SorAbund());
318 }else if (Estimators[i] == "jclass") {
319 treeCalculators.push_back(new Jclass());
320 }else if (Estimators[i] == "sorclass") {
321 treeCalculators.push_back(new SorClass());
322 }else if (Estimators[i] == "jest") {
323 treeCalculators.push_back(new Jest());
324 }else if (Estimators[i] == "sorest") {
325 treeCalculators.push_back(new SorEst());
326 }else if (Estimators[i] == "thetayc") {
327 treeCalculators.push_back(new ThetaYC());
328 }else if (Estimators[i] == "thetan") {
329 treeCalculators.push_back(new ThetaN());
330 }else if (Estimators[i] == "kstest") {
331 treeCalculators.push_back(new KSTest());
332 }else if (Estimators[i] == "sharednseqs") {
333 treeCalculators.push_back(new SharedNSeqs());
334 }else if (Estimators[i] == "ochiai") {
335 treeCalculators.push_back(new Ochiai());
336 }else if (Estimators[i] == "anderberg") {
337 treeCalculators.push_back(new Anderberg());
338 }else if (Estimators[i] == "kulczynski") {
339 treeCalculators.push_back(new Kulczynski());
340 }else if (Estimators[i] == "kulczynskicody") {
341 treeCalculators.push_back(new KulczynskiCody());
342 }else if (Estimators[i] == "lennon") {
343 treeCalculators.push_back(new Lennon());
344 }else if (Estimators[i] == "morisitahorn") {
345 treeCalculators.push_back(new MorHorn());
346 }else if (Estimators[i] == "braycurtis") {
347 treeCalculators.push_back(new BrayCurtis());
348 }else if (Estimators[i] == "whittaker") {
349 treeCalculators.push_back(new Whittaker());
350 }else if (Estimators[i] == "odum") {
351 treeCalculators.push_back(new Odum());
352 }else if (Estimators[i] == "canberra") {
353 treeCalculators.push_back(new Canberra());
354 }else if (Estimators[i] == "structeuclidean") {
355 treeCalculators.push_back(new StructEuclidean());
356 }else if (Estimators[i] == "structchord") {
357 treeCalculators.push_back(new StructChord());
358 }else if (Estimators[i] == "hellinger") {
359 treeCalculators.push_back(new Hellinger());
360 }else if (Estimators[i] == "manhattan") {
361 treeCalculators.push_back(new Manhattan());
362 }else if (Estimators[i] == "structpearson") {
363 treeCalculators.push_back(new StructPearson());
364 }else if (Estimators[i] == "soergel") {
365 treeCalculators.push_back(new Soergel());
366 }else if (Estimators[i] == "spearman") {
367 treeCalculators.push_back(new Spearman());
368 }else if (Estimators[i] == "structkulczynski") {
369 treeCalculators.push_back(new StructKulczynski());
370 }else if (Estimators[i] == "speciesprofile") {
371 treeCalculators.push_back(new SpeciesProfile());
372 }else if (Estimators[i] == "hamming") {
373 treeCalculators.push_back(new Hamming());
374 }else if (Estimators[i] == "structchi2") {
375 treeCalculators.push_back(new StructChi2());
376 }else if (Estimators[i] == "gower") {
377 treeCalculators.push_back(new Gower());
378 }else if (Estimators[i] == "memchi2") {
379 treeCalculators.push_back(new MemChi2());
380 }else if (Estimators[i] == "memchord") {
381 treeCalculators.push_back(new MemChord());
382 }else if (Estimators[i] == "memeuclidean") {
383 treeCalculators.push_back(new MemEuclidean());
384 }else if (Estimators[i] == "mempearson") {
385 treeCalculators.push_back(new MemPearson());
390 //if the users entered no valid calculators don't execute command
391 if (treeCalculators.size() == 0) { m->mothurOut("You have given no valid calculators."); m->mothurOutEndLine(); return 0; }
393 input = new InputData(sharedfile, "sharedfile");
394 lookup = input->getSharedRAbundVectors();
395 lastLabel = lookup[0]->getLabel();
397 if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); return 0; }
399 //used in tree constructor
402 //create treemap class from groupmap for tree class to use
403 tmap = new TreeMap();
404 tmap->makeSim(m->getAllGroups());
406 //clear globaldatas old tree names if any
407 m->Treenames.clear();
409 //fills globaldatas tree names
410 m->Treenames = m->getGroups();
412 if (m->control_pressed) { return 0; }
417 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
420 filename = inputfile;
422 ReadMatrix* readMatrix;
423 if (format == "column") { readMatrix = new ReadColumnMatrix(filename); }
424 else if (format == "phylip") { readMatrix = new ReadPhylipMatrix(filename); }
426 readMatrix->setCutoff(cutoff);
429 nameMap = new NameAssignment(namefile);
436 readMatrix->read(nameMap);
437 list = readMatrix->getListVector();
438 SparseDistanceMatrix* dMatrix = readMatrix->getDMatrix();
441 tmap = new TreeMap();
443 if (m->control_pressed) { return 0; }
447 vector<string> namesGroups = tmap->getNamesOfGroups();
448 m->setGroups(namesGroups);
450 //clear globaldatas old tree names if any
451 m->Treenames.clear();
453 //fills globaldatas tree names
454 m->Treenames = m->getGroups();
456 //used in tree constructor
459 if (m->control_pressed) { return 0; }
461 vector< vector<double> > matrix = makeSimsDist(dMatrix);
465 if (m->control_pressed) { return 0; }
467 //create a new filename
468 string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + getOutputFileNameTag("tree");
469 outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
471 Tree* newTree = createTree(matrix);
473 if (newTree != NULL) { writeTree(outputFile, newTree); delete newTree; }
475 if (m->control_pressed) { return 0; }
477 m->mothurOut("Tree complete. "); m->mothurOutEndLine();
481 //reset groups parameter
484 //set tree file as new current treefile
486 itTypes = outputTypes.find("tree");
487 if (itTypes != outputTypes.end()) {
488 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTreeFile(current); }
491 m->mothurOutEndLine();
492 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
493 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
494 m->mothurOutEndLine();
498 catch(exception& e) {
499 m->errorOut(e, "TreeGroupCommand", "execute");
503 //**********************************************************************************************************************
505 Tree* TreeGroupCommand::createTree(vector< vector<double> >& simMatrix){
508 t = new Tree(tmap, simMatrix);
510 if (m->control_pressed) { delete t; t = NULL; return t; }
513 map<string, string> empty;
514 t->assembleTree(empty);
518 catch(exception& e) {
519 m->errorOut(e, "TreeGroupCommand", "createTree");
523 /***********************************************************/
524 int TreeGroupCommand::writeTree(string out, Tree* T) {
528 t->createNewickFile(out);
530 if (m->control_pressed) { m->mothurRemove(out); outputNames.pop_back(); return 1; }
535 catch(exception& e) {
536 m->errorOut(e, "TreeGroupCommand", "printSims");
541 /***********************************************************/
542 void TreeGroupCommand::printSims(ostream& out, vector< vector<double> >& simMatrix) {
545 for (int m = 0; m < simMatrix.size(); m++) {
546 //out << lookup[m]->getGroup() << '\t';
547 for (int n = 0; n < simMatrix.size(); n++) {
548 out << simMatrix[m][n] << '\t';
554 catch(exception& e) {
555 m->errorOut(e, "TreeGroupCommand", "printSims");
559 /***********************************************************/
560 vector< vector<double> > TreeGroupCommand::makeSimsDist(SparseDistanceMatrix* matrix) {
562 numGroups = list->size();
564 //initialize simMatrix
565 vector< vector<double> > simMatrix;
566 simMatrix.resize(numGroups);
567 for (int k = 0; k < simMatrix.size(); k++) {
568 for (int j = 0; j < simMatrix.size(); j++) {
569 simMatrix[k].push_back(0.0);
573 //go through sparse matrix and fill sims
574 //go through each cell in the sparsematrix
575 for (int i = 0; i < matrix->seqVec.size(); i++) {
576 for (int j = 0; j < matrix->seqVec[i].size(); j++) {
578 //already checked everyone else in row
579 if (i < matrix->seqVec[i][j].index) {
580 simMatrix[i][matrix->seqVec[i][j].index] = -(matrix->seqVec[i][j].dist -1.0);
581 simMatrix[matrix->seqVec[i][j].index][i] = -(matrix->seqVec[i][j].dist -1.0);
583 if (m->control_pressed) { return simMatrix; }
590 catch(exception& e) {
591 m->errorOut(e, "TreeGroupCommand", "makeSimsDist");
596 /***********************************************************/
597 int TreeGroupCommand::makeSimsShared() {
601 if (subsampleSize == -1) { //user has not set size, set size = smallest samples size
602 subsampleSize = lookup[0]->getNumSeqs();
603 for (int i = 1; i < lookup.size(); i++) {
604 int thisSize = lookup[i]->getNumSeqs();
606 if (thisSize < subsampleSize) { subsampleSize = thisSize; }
611 vector<SharedRAbundVector*> temp;
612 for (int i = 0; i < lookup.size(); i++) {
613 if (lookup[i]->getNumSeqs() < subsampleSize) {
614 m->mothurOut(lookup[i]->getGroup() + " contains " + toString(lookup[i]->getNumSeqs()) + ". Eliminating."); m->mothurOutEndLine();
617 Groups.push_back(lookup[i]->getGroup());
618 temp.push_back(lookup[i]);
622 m->setGroups(Groups);
625 if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups. I cannot run the command."); m->mothurOutEndLine(); m->control_pressed = true; return 0; }
628 numGroups = lookup.size();
629 lines.resize(processors);
630 for (int i = 0; i < processors; i++) {
631 lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
632 lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups);
635 set<string> processedLabels;
636 set<string> userLabels = labels;
638 //as long as you are not at the end of the file or done wih the lines you want
639 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
640 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; }
642 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
643 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
646 processedLabels.insert(lookup[0]->getLabel());
647 userLabels.erase(lookup[0]->getLabel());
650 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
651 string saveLabel = lookup[0]->getLabel();
653 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
654 lookup = input->getSharedRAbundVectors(lastLabel);
656 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
659 processedLabels.insert(lookup[0]->getLabel());
660 userLabels.erase(lookup[0]->getLabel());
662 //restore real lastlabel to save below
663 lookup[0]->setLabel(saveLabel);
666 lastLabel = lookup[0]->getLabel();
668 //get next line to process
669 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
670 lookup = input->getSharedRAbundVectors();
673 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; }
675 //output error messages about any remaining user labels
676 set<string>::iterator it;
677 bool needToRun = false;
678 for (it = userLabels.begin(); it != userLabels.end(); it++) {
679 m->mothurOut("Your file does not include the label " + *it);
680 if (processedLabels.count(lastLabel) != 1) {
681 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
684 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
688 //run last label if you need to
689 if (needToRun == true) {
690 for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
691 lookup = input->getSharedRAbundVectors(lastLabel);
693 m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
695 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
698 for(int i = 0 ; i < treeCalculators.size(); i++) { delete treeCalculators[i]; }
702 catch(exception& e) {
703 m->errorOut(e, "TreeGroupCommand", "makeSimsShared");
708 /***********************************************************/
709 int TreeGroupCommand::process(vector<SharedRAbundVector*> thisLookup) {
711 vector< vector< vector<seqDist> > > calcDistsTotals; //each iter, one for each calc, then each groupCombos dists. this will be used to make .dist files
712 vector< vector<seqDist> > calcDists; calcDists.resize(treeCalculators.size());
714 for (int thisIter = 0; thisIter < iters; thisIter++) {
716 vector<SharedRAbundVector*> thisItersLookup = thisLookup;
720 vector<string> tempLabels; //dont need since we arent printing the sampled sharedRabunds
722 //make copy of lookup so we don't get access violations
723 vector<SharedRAbundVector*> newLookup;
724 for (int k = 0; k < thisItersLookup.size(); k++) {
725 SharedRAbundVector* temp = new SharedRAbundVector();
726 temp->setLabel(thisItersLookup[k]->getLabel());
727 temp->setGroup(thisItersLookup[k]->getGroup());
728 newLookup.push_back(temp);
732 for (int k = 0; k < thisItersLookup[0]->getNumBins(); k++) {
733 if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
734 for (int j = 0; j < thisItersLookup.size(); j++) { newLookup[j]->push_back(thisItersLookup[j]->getAbundance(k), thisItersLookup[j]->getGroup()); }
737 tempLabels = sample.getSample(newLookup, subsampleSize);
738 thisItersLookup = newLookup;
742 driver(thisItersLookup, 0, numGroups, calcDists);
745 vector<int> processIDS;
747 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
748 //loop through and create all the processes you want
749 while (process != processors) {
753 processIDS.push_back(pid);
757 driver(thisItersLookup, lines[process].start, lines[process].end, calcDists);
759 string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(getpid()) + ".dist";
761 m->openOutputFile(tempdistFileName, outtemp);
763 for (int i = 0; i < calcDists.size(); i++) {
764 outtemp << calcDists[i].size() << endl;
766 for (int j = 0; j < calcDists[i].size(); j++) {
767 outtemp << calcDists[i][j].seq1 << '\t' << calcDists[i][j].seq2 << '\t' << calcDists[i][j].dist << endl;
774 m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
775 for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
780 //parent do your part
781 driver(thisItersLookup, lines[0].start, lines[0].end, calcDists);
783 //force parent to wait until all the processes are done
784 for (int i = 0; i < processIDS.size(); i++) {
785 int temp = processIDS[i];
789 for (int i = 0; i < processIDS.size(); i++) {
790 string tempdistFileName = m->getRootName(m->getSimpleName(sharedfile)) + toString(processIDS[i]) + ".dist";
792 m->openInputFile(tempdistFileName, intemp);
794 for (int k = 0; k < calcDists.size(); k++) {
796 intemp >> size; m->gobble(intemp);
798 for (int j = 0; j < size; j++) {
803 intemp >> seq1 >> seq2 >> dist; m->gobble(intemp);
805 seqDist tempDist(seq1, seq2, dist);
806 calcDists[k].push_back(tempDist);
810 m->mothurRemove(tempdistFileName);
813 //////////////////////////////////////////////////////////////////////////////////////////////////////
814 //Windows version shared memory, so be careful when passing variables through the treeSharedData struct.
815 //Above fork() will clone, so memory is separate, but that's not the case with windows,
816 //Taking advantage of shared memory to pass results vectors.
817 //////////////////////////////////////////////////////////////////////////////////////////////////////
819 vector<treeSharedData*> pDataArray;
820 DWORD dwThreadIdArray[processors-1];
821 HANDLE hThreadArray[processors-1];
823 //Create processor worker threads.
824 for( int i=1; i<processors; i++ ){
826 //make copy of lookup so we don't get access violations
827 vector<SharedRAbundVector*> newLookup;
828 for (int k = 0; k < thisItersLookup.size(); k++) {
829 SharedRAbundVector* temp = new SharedRAbundVector();
830 temp->setLabel(thisItersLookup[k]->getLabel());
831 temp->setGroup(thisItersLookup[k]->getGroup());
832 newLookup.push_back(temp);
836 for (int k = 0; k < thisItersLookup[0]->getNumBins(); k++) {
837 if (m->control_pressed) { for (int j = 0; j < newLookup.size(); j++) { delete newLookup[j]; } return 0; }
838 for (int j = 0; j < thisItersLookup.size(); j++) { newLookup[j]->push_back(thisItersLookup[j]->getAbundance(k), thisItersLookup[j]->getGroup()); }
841 // Allocate memory for thread data.
842 treeSharedData* tempSum = new treeSharedData(m, lines[i].start, lines[i].end, Estimators, newLookup);
843 pDataArray.push_back(tempSum);
844 processIDS.push_back(i);
846 hThreadArray[i-1] = CreateThread(NULL, 0, MyTreeSharedThreadFunction, pDataArray[i-1], 0, &dwThreadIdArray[i-1]);
849 //parent do your part
850 driver(thisItersLookup, lines[0].start, lines[0].end, calcDists);
852 //Wait until all threads have terminated.
853 WaitForMultipleObjects(processors-1, hThreadArray, TRUE, INFINITE);
855 //Close all thread handles and free memory allocations.
856 for(int i=0; i < pDataArray.size(); i++){
857 for (int j = 0; j < pDataArray[i]->thisLookup.size(); j++) { delete pDataArray[i]->thisLookup[j]; }
859 for (int k = 0; k < calcDists.size(); k++) {
860 int size = pDataArray[i]->calcDists[k].size();
861 for (int j = 0; j < size; j++) { calcDists[k].push_back(pDataArray[i]->calcDists[k][j]); }
864 CloseHandle(hThreadArray[i]);
865 delete pDataArray[i];
871 calcDistsTotals.push_back(calcDists);
876 for (int i = 0; i < thisItersLookup.size(); i++) { delete thisItersLookup[i]; }
877 thisItersLookup.clear();
878 for (int i = 0; i < calcDists.size(); i++) { calcDists[i].clear(); }
883 //we need to find the average distance and standard deviation for each groups distance
885 vector< vector<seqDist> > calcAverages; calcAverages.resize(treeCalculators.size());
886 for (int i = 0; i < calcAverages.size(); i++) { //initialize sums to zero.
887 calcAverages[i].resize(calcDistsTotals[0][i].size());
889 for (int j = 0; j < calcAverages[i].size(); j++) {
890 calcAverages[i][j].seq1 = calcDists[i][j].seq1;
891 calcAverages[i][j].seq2 = calcDists[i][j].seq2;
892 calcAverages[i][j].dist = 0.0;
896 for (int thisIter = 0; thisIter < iters; thisIter++) { //sum all groups dists for each calculator
897 for (int i = 0; i < calcAverages.size(); i++) { //initialize sums to zero.
898 for (int j = 0; j < calcAverages[i].size(); j++) {
899 calcAverages[i][j].dist += calcDistsTotals[thisIter][i][j].dist;
904 for (int i = 0; i < calcAverages.size(); i++) { //finds average.
905 for (int j = 0; j < calcAverages[i].size(); j++) {
906 calcAverages[i][j].dist /= (float) iters;
910 //create average tree for each calc
911 for (int i = 0; i < calcDists.size(); i++) {
912 vector< vector<double> > matrix; //square matrix to represent the distance
913 matrix.resize(thisLookup.size());
914 for (int k = 0; k < thisLookup.size(); k++) { matrix[k].resize(thisLookup.size(), 0.0); }
916 for (int j = 0; j < calcAverages[i].size(); j++) {
917 int row = calcAverages[i][j].seq1;
918 int column = calcAverages[i][j].seq2;
919 float dist = calcAverages[i][j].dist;
921 matrix[row][column] = dist;
922 matrix[column][row] = dist;
925 //create a new filename
926 string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".ave." + getOutputFileNameTag("tree");
927 outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
929 //creates tree from similarity matrix and write out file
930 Tree* newTree = createTree(matrix);
931 if (newTree != NULL) { writeTree(outputFile, newTree); }
934 //create all trees for each calc and find their consensus tree
935 for (int i = 0; i < calcDists.size(); i++) {
936 if (m->control_pressed) { break; }
938 //create a new filename
939 string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".all." + getOutputFileNameTag("tree");
940 outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
943 m->openOutputFile(outputFile, outAll);
946 for (int myIter = 0; myIter < iters; myIter++) {
948 if(m->control_pressed) { break; }
951 vector< vector<double> > matrix; //square matrix to represent the distance
952 matrix.resize(thisLookup.size());
953 for (int k = 0; k < thisLookup.size(); k++) { matrix[k].resize(thisLookup.size(), 0.0); }
955 for (int j = 0; j < calcDistsTotals[myIter][i].size(); j++) {
956 int row = calcDistsTotals[myIter][i][j].seq1;
957 int column = calcDistsTotals[myIter][i][j].seq2;
958 double dist = calcDistsTotals[myIter][i][j].dist;
960 matrix[row][column] = dist;
961 matrix[column][row] = dist;
964 //creates tree from similarity matrix and write out file
965 Tree* newTree = createTree(matrix);
966 if (newTree != NULL) {
967 newTree->print(outAll);
968 trees.push_back(newTree);
972 if (m->control_pressed) { for (int k = 0; k < trees.size(); k++) { delete trees[k]; } }
975 //clear old tree names if any
976 m->Treenames.clear(); m->Treenames = m->getGroups(); //may have changed if subsample eliminated groups
977 Tree* conTree = consensus.getTree(trees);
979 //create a new filename
980 string conFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".cons." + getOutputFileNameTag("tree");
981 outputNames.push_back(conFile); outputTypes["tree"].push_back(conFile);
983 m->openOutputFile(conFile, outTree);
985 if (conTree != NULL) { conTree->print(outTree, "boot"); delete conTree; }
990 for (int i = 0; i < calcDists.size(); i++) {
991 if (m->control_pressed) { break; }
994 vector< vector<double> > matrix; //square matrix to represent the distance
995 matrix.resize(thisLookup.size());
996 for (int k = 0; k < thisLookup.size(); k++) { matrix[k].resize(thisLookup.size(), 0.0); }
998 for (int j = 0; j < calcDists[i].size(); j++) {
999 int row = calcDists[i][j].seq1;
1000 int column = calcDists[i][j].seq2;
1001 double dist = calcDists[i][j].dist;
1003 matrix[row][column] = dist;
1004 matrix[column][row] = dist;
1007 //create a new filename
1008 string outputFile = outputDir + m->getRootName(m->getSimpleName(inputfile)) + treeCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + getOutputFileNameTag("tree");
1009 outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
1011 //creates tree from similarity matrix and write out file
1012 Tree* newTree = createTree(matrix);
1013 if (newTree != NULL) { writeTree(outputFile, newTree); delete newTree; }
1019 catch(exception& e) {
1020 m->errorOut(e, "TreeGroupCommand", "process");
1024 /**************************************************************************************************/
1025 int TreeGroupCommand::driver(vector<SharedRAbundVector*> thisLookup, int start, int end, vector< vector<seqDist> >& calcDists) {
1027 vector<SharedRAbundVector*> subset;
1028 for (int k = start; k < end; k++) { // pass cdd each set of groups to compare
1030 for (int l = 0; l < k; l++) {
1032 if (k != l) { //we dont need to similiarity of a groups to itself
1033 subset.clear(); //clear out old pair of sharedrabunds
1034 //add new pair of sharedrabunds
1035 subset.push_back(thisLookup[k]); subset.push_back(thisLookup[l]);
1037 for(int i=0;i<treeCalculators.size();i++) {
1039 //if this calc needs all groups to calculate the pair load all groups
1040 if (treeCalculators[i]->getNeedsAll()) {
1041 //load subset with rest of lookup for those calcs that need everyone to calc for a pair
1042 for (int w = 0; w < thisLookup.size(); w++) {
1043 if ((w != k) && (w != l)) { subset.push_back(thisLookup[w]); }
1047 vector<double> tempdata = treeCalculators[i]->getValues(subset); //saves the calculator outputs
1049 if (m->control_pressed) { return 1; }
1051 seqDist temp(l, k, -(tempdata[0]-1.0));
1052 calcDists[i].push_back(temp);
1060 catch(exception& e) {
1061 m->errorOut(e, "TreeGroupCommand", "driver");
1065 /***********************************************************/