5 * Created by Sarah Westcott on 1/2/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "collectcommand.h"
15 #include "bootstrap.h"
17 #include "simpsoneven.h"
18 #include "invsimpson.h"
19 #include "npshannon.h"
21 #include "smithwilson.h"
23 #include "shannoneven.h"
24 #include "jackknife.h"
28 #include "bergerparker.h"
30 #include "goodscoverage.h"
38 //**********************************************************************************************************************
39 vector<string> CollectCommand::setParameters(){
41 CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
42 CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
43 CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
44 CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
45 CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
46 CommandParameter pfreq("freq", "Number", "", "100", "", "", "",false,false); parameters.push_back(pfreq);
47 CommandParameter pcalc("calc", "Multiple", "sobs-chao-nseqs-coverage-ace-jack-shannon-shannoneven-npshannon-heip-smithwilson-simpson-simpsoneven-invsimpson-bootstrap-geometric-qstat-logseries-bergerparker-bstick-goodscoverage-efron-boneh-solow-shen", "sobs-chao-ace-jack-shannon-npshannon-simpson", "", "", "",true,false); parameters.push_back(pcalc);
48 CommandParameter pabund("abund", "Number", "", "10", "", "", "",false,false); parameters.push_back(pabund);
49 CommandParameter psize("size", "Number", "", "0", "", "", "",false,false); parameters.push_back(psize);
50 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
51 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
53 vector<string> myArray;
54 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
58 m->errorOut(e, "CollectCommand", "setParameters");
62 //**********************************************************************************************************************
63 string CollectCommand::getHelpString(){
65 string helpString = "";
66 ValidCalculators validCalculator;
67 helpString += "The collect.single command parameters are list, sabund, rabund, shared, label, freq, calc and abund. list, sabund, rabund or shared is required unless you have a valid current file. \n";
68 helpString += "The collect.single command should be in the following format: \n";
69 helpString += "The freq parameter is used indicate when to output your data, by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%. \n";
70 helpString += "collect.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n";
71 helpString += "Example collect(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-chao-ace-jack).\n";
72 helpString += "The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson.\n";
73 helpString += validCalculator.printCalc("single");
74 helpString += "The label parameter is used to analyze specific labels in your input.\n";
75 helpString += "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n";
79 m->errorOut(e, "CollectCommand", "getHelpString");
83 //**********************************************************************************************************************
84 CollectCommand::CollectCommand(){
86 abort = true; calledHelp = true;
88 vector<string> tempOutNames;
89 outputTypes["sobs"] = tempOutNames;
90 outputTypes["chao"] = tempOutNames;
91 outputTypes["nseqs"] = tempOutNames;
92 outputTypes["coverage"] = tempOutNames;
93 outputTypes["ace"] = tempOutNames;
94 outputTypes["jack"] = tempOutNames;
95 outputTypes["shannon"] = tempOutNames;
96 outputTypes["shannoneven"] = tempOutNames;
97 outputTypes["npshannon"] = tempOutNames;
98 outputTypes["heip"] = tempOutNames;
99 outputTypes["smithwilson"] = tempOutNames;
100 outputTypes["simpson"] = tempOutNames;
101 outputTypes["simpsoneven"] = tempOutNames;
102 outputTypes["invsimpson"] = tempOutNames;
103 outputTypes["bootstrap"] = tempOutNames;
104 outputTypes["geometric"] = tempOutNames;
105 outputTypes["qstat"] = tempOutNames;
106 outputTypes["logseries"] = tempOutNames;
107 outputTypes["bergerparker"] = tempOutNames;
108 outputTypes["bstick"] = tempOutNames;
109 outputTypes["goodscoverage"] = tempOutNames;
110 outputTypes["efron"] = tempOutNames;
111 outputTypes["boneh"] = tempOutNames;
112 outputTypes["solow"] = tempOutNames;
113 outputTypes["shen"] = tempOutNames;
115 catch(exception& e) {
116 m->errorOut(e, "CollectCommand", "CollectCommand");
120 //**********************************************************************************************************************
121 CollectCommand::CollectCommand(string option) {
123 abort = false; calledHelp = false;
126 //allow user to run help
127 if(option == "help") { help(); calledHelp = true; abort = true; }
128 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
131 vector<string> myArray = setParameters();
133 OptionParser parser(option);
134 map<string,string> parameters = parser.getParameters();
135 map<string,string>::iterator it;
137 ValidParameters validParameter;
139 //check to make sure all parameters are valid for command
140 for (it = parameters.begin(); it != parameters.end(); it++) {
141 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
144 //initialize outputTypes
145 vector<string> tempOutNames;
146 outputTypes["sobs"] = tempOutNames;
147 outputTypes["chao"] = tempOutNames;
148 outputTypes["nseqs"] = tempOutNames;
149 outputTypes["coverage"] = tempOutNames;
150 outputTypes["ace"] = tempOutNames;
151 outputTypes["jack"] = tempOutNames;
152 outputTypes["shannon"] = tempOutNames;
153 outputTypes["shannoneven"] = tempOutNames;
154 outputTypes["npshannon"] = tempOutNames;
155 outputTypes["heip"] = tempOutNames;
156 outputTypes["smithwilson"] = tempOutNames;
157 outputTypes["simpson"] = tempOutNames;
158 outputTypes["simpsoneven"] = tempOutNames;
159 outputTypes["invsimpson"] = tempOutNames;
160 outputTypes["bootstrap"] = tempOutNames;
161 outputTypes["geometric"] = tempOutNames;
162 outputTypes["qstat"] = tempOutNames;
163 outputTypes["logseries"] = tempOutNames;
164 outputTypes["bergerparker"] = tempOutNames;
165 outputTypes["bstick"] = tempOutNames;
166 outputTypes["goodscoverage"] = tempOutNames;
167 outputTypes["efron"] = tempOutNames;
168 outputTypes["boneh"] = tempOutNames;
169 outputTypes["solow"] = tempOutNames;
170 outputTypes["shen"] = tempOutNames;
172 //if the user changes the input directory command factory will send this info to us in the output parameter
173 string inputDir = validParameter.validFile(parameters, "inputdir", false);
174 if (inputDir == "not found"){ inputDir = ""; }
177 it = parameters.find("shared");
178 //user has given a template file
179 if(it != parameters.end()){
180 path = m->hasPath(it->second);
181 //if the user has not given a path then, add inputdir. else leave path alone.
182 if (path == "") { parameters["shared"] = inputDir + it->second; }
185 it = parameters.find("rabund");
186 //user has given a template file
187 if(it != parameters.end()){
188 path = m->hasPath(it->second);
189 //if the user has not given a path then, add inputdir. else leave path alone.
190 if (path == "") { parameters["rabund"] = inputDir + it->second; }
193 it = parameters.find("sabund");
194 //user has given a template file
195 if(it != parameters.end()){
196 path = m->hasPath(it->second);
197 //if the user has not given a path then, add inputdir. else leave path alone.
198 if (path == "") { parameters["sabund"] = inputDir + it->second; }
201 it = parameters.find("list");
202 //user has given a template file
203 if(it != parameters.end()){
204 path = m->hasPath(it->second);
205 //if the user has not given a path then, add inputdir. else leave path alone.
206 if (path == "") { parameters["list"] = inputDir + it->second; }
210 //check for required parameters
211 listfile = validParameter.validFile(parameters, "list", true);
212 if (listfile == "not open") { listfile = ""; abort = true; }
213 else if (listfile == "not found") { listfile = ""; }
214 else { format = "list"; inputfile = listfile; m->setListFile(listfile); }
216 sabundfile = validParameter.validFile(parameters, "sabund", true);
217 if (sabundfile == "not open") { sabundfile = ""; abort = true; }
218 else if (sabundfile == "not found") { sabundfile = ""; }
219 else { format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
221 rabundfile = validParameter.validFile(parameters, "rabund", true);
222 if (rabundfile == "not open") { rabundfile = ""; abort = true; }
223 else if (rabundfile == "not found") { rabundfile = ""; }
224 else { format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
226 sharedfile = validParameter.validFile(parameters, "shared", true);
227 if (sharedfile == "not open") { sharedfile = ""; abort = true; }
228 else if (sharedfile == "not found") { sharedfile = ""; }
229 else { format = "sharedfile"; inputfile = sharedfile; m->setSharedFile(sharedfile); }
232 //if the user changes the output directory command factory will send this info to us in the output parameter
233 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
235 if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) {
236 //is there are current file available for any of these?
237 //give priority to shared, then list, then rabund, then sabund
238 //if there is a current shared file, use it
239 sharedfile = m->getSharedFile();
240 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
242 listfile = m->getListFile();
243 if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
245 rabundfile = m->getRabundFile();
246 if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
248 sabundfile = m->getSabundFile();
249 if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
251 m->mothurOut("No valid current files. You must provide a list, sabund, rabund or shared file before you can use the collect.single command."); m->mothurOutEndLine();
259 //check for optional parameter and set defaults
260 // ...at some point should added some additional type checking...
261 label = validParameter.validFile(parameters, "label", false);
262 if (label == "not found") { label = ""; }
264 if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
265 else { allLines = 1; }
268 //NOTE: if you add new calc options, don't forget to add them to the parameter initialize in setParameters or the gui won't be able to use them
269 calc = validParameter.validFile(parameters, "calc", false);
270 if (calc == "not found") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
272 if (calc == "default") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
274 m->splitAtDash(calc, Estimators);
275 if (m->inUsersGroups("citation", Estimators)) {
276 ValidCalculators validCalc; validCalc.printCitations(Estimators);
277 //remove citation from list of calcs
278 for (int i = 0; i < Estimators.size(); i++) { if (Estimators[i] == "citation") { Estimators.erase(Estimators.begin()+i); break; } }
282 temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
283 m->mothurConvert(temp, freq);
285 temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
286 m->mothurConvert(temp, abund);
288 temp = validParameter.validFile(parameters, "size", false); if (temp == "not found") { temp = "0"; }
289 m->mothurConvert(temp, size);
293 catch(exception& e) {
294 m->errorOut(e, "CollectCommand", "CollectCommand");
298 //**********************************************************************************************************************
300 int CollectCommand::execute(){
303 if (abort == true) { if (calledHelp) { return 0; } return 2; }
305 if ((format != "sharedfile")) { inputFileNames.push_back(inputfile); }
306 else { inputFileNames = parseSharedFile(sharedfile); format = "rabund"; }
308 for (int p = 0; p < inputFileNames.size(); p++) {
310 if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } m->clearGroups(); return 0; }
312 if (outputDir == "") { outputDir += m->hasPath(inputFileNames[p]); }
313 string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
314 //globaldata->inputFileName = inputFileNames[p];
316 if (inputFileNames.size() > 1) {
317 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
320 ValidCalculators validCalculator;
322 for (int i=0; i<Estimators.size(); i++) {
323 if (validCalculator.isValidCalculator("single", Estimators[i]) == true) {
324 if (Estimators[i] == "sobs") {
325 cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
326 outputNames.push_back(fileNameRoot+"sobs"); outputTypes["sobs"].push_back(fileNameRoot+"sobs");
327 }else if (Estimators[i] == "chao") {
328 cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
329 outputNames.push_back(fileNameRoot+"chao"); outputTypes["chao"].push_back(fileNameRoot+"chao");
330 }else if (Estimators[i] == "nseqs") {
331 cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs")));
332 outputNames.push_back(fileNameRoot+"nseqs"); outputTypes["nseqs"].push_back(fileNameRoot+"nseqs");
333 }else if (Estimators[i] == "coverage") {
334 cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage")));
335 outputNames.push_back(fileNameRoot+"coverage"); outputTypes["coverage"].push_back(fileNameRoot+"coverage");
336 }else if (Estimators[i] == "ace") {
337 cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
338 outputNames.push_back(fileNameRoot+"ace"); outputTypes["ace"].push_back(fileNameRoot+"ace");
339 }else if (Estimators[i] == "jack") {
340 cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
341 outputNames.push_back(fileNameRoot+"jack"); outputTypes["jack"].push_back(fileNameRoot+"jack");
342 }else if (Estimators[i] == "shannon") {
343 cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
344 outputNames.push_back(fileNameRoot+"shannon"); outputTypes["shannon"].push_back(fileNameRoot+"shannon");
345 }else if (Estimators[i] == "shannoneven") {
346 cDisplays.push_back(new CollectDisplay(new ShannonEven(), new OneColumnFile(fileNameRoot+"shannoneven")));
347 outputNames.push_back(fileNameRoot+"shannoneven"); outputTypes["shannoneven"].push_back(fileNameRoot+"shannoneven");
348 }else if (Estimators[i] == "npshannon") {
349 cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"npshannon")));
350 outputNames.push_back(fileNameRoot+"npshannon"); outputTypes["npshannon"].push_back(fileNameRoot+"npshannon");
351 }else if (Estimators[i] == "heip") {
352 cDisplays.push_back(new CollectDisplay(new Heip(), new OneColumnFile(fileNameRoot+"heip")));
353 outputNames.push_back(fileNameRoot+"heip"); outputTypes["heip"].push_back(fileNameRoot+"heip");
354 }else if (Estimators[i] == "smithwilson") {
355 cDisplays.push_back(new CollectDisplay(new SmithWilson(), new OneColumnFile(fileNameRoot+"smithwilson")));
356 outputNames.push_back(fileNameRoot+"smithwilson"); outputTypes["smithwilson"].push_back(fileNameRoot+"smithwilson");
357 }else if (Estimators[i] == "simpson") {
358 cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
359 outputNames.push_back(fileNameRoot+"simpson"); outputTypes["simpson"].push_back(fileNameRoot+"simpson");
360 }else if (Estimators[i] == "simpsoneven") {
361 cDisplays.push_back(new CollectDisplay(new SimpsonEven(), new OneColumnFile(fileNameRoot+"simpsoneven")));
362 outputNames.push_back(fileNameRoot+"simpsoneven"); outputTypes["simpsoneven"].push_back(fileNameRoot+"simpsoneven");
363 }else if (Estimators[i] == "invsimpson") {
364 cDisplays.push_back(new CollectDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+"invsimpson")));
365 outputNames.push_back(fileNameRoot+"invsimpson"); outputTypes["invsimpson"].push_back(fileNameRoot+"invsimpson");
366 }else if (Estimators[i] == "bootstrap") {
367 cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
368 outputNames.push_back(fileNameRoot+"bootstrap"); outputTypes["bootstrap"].push_back(fileNameRoot+"bootstrap");
369 }else if (Estimators[i] == "geometric") {
370 cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric")));
371 outputNames.push_back(fileNameRoot+"geometric"); outputTypes["geometric"].push_back(fileNameRoot+"geometric");
372 }else if (Estimators[i] == "qstat") {
373 cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
374 outputNames.push_back(fileNameRoot+"qstat"); outputTypes["qstat"].push_back(fileNameRoot+"qstat");
375 }else if (Estimators[i] == "logseries") {
376 cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries")));
377 outputNames.push_back(fileNameRoot+"logseries"); outputTypes["logseries"].push_back(fileNameRoot+"logseries");
378 }else if (Estimators[i] == "bergerparker") {
379 cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
380 outputNames.push_back(fileNameRoot+"bergerparker"); outputTypes["bergerparker"].push_back(fileNameRoot+"bergerparker");
381 }else if (Estimators[i] == "bstick") {
382 cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick")));
383 outputNames.push_back(fileNameRoot+"bstick"); outputTypes["bstick"].push_back(fileNameRoot+"bstick");
384 }else if (Estimators[i] == "goodscoverage") {
385 cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage")));
386 outputNames.push_back(fileNameRoot+"goodscoverage"); outputTypes["goodscoverage"].push_back(fileNameRoot+"goodscoverage");
387 }else if (Estimators[i] == "efron") {
388 cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+"efron")));
389 outputNames.push_back(fileNameRoot+"efron"); outputTypes["efron"].push_back(fileNameRoot+"efron");
390 }else if (Estimators[i] == "boneh") {
391 cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+"boneh")));
392 outputNames.push_back(fileNameRoot+"boneh"); outputTypes["boneh"].push_back(fileNameRoot+"boneh");
393 }else if (Estimators[i] == "solow") {
394 cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+"solow")));
395 outputNames.push_back(fileNameRoot+"solow"); outputTypes["solow"].push_back(fileNameRoot+"solow");
396 }else if (Estimators[i] == "shen") {
397 cDisplays.push_back(new CollectDisplay(new Shen(size, abund), new OneColumnFile(fileNameRoot+"shen")));
398 outputNames.push_back(fileNameRoot+"shen"); outputTypes["shen"].push_back(fileNameRoot+"shen");
403 //if the users entered no valid calculators don't execute command
404 if (cDisplays.size() == 0) { return 0; }
406 input = new InputData(inputFileNames[p], format);
407 order = input->getOrderVector();
408 string lastLabel = order->getLabel();
410 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
411 set<string> processedLabels;
412 set<string> userLabels = labels;
414 if (m->control_pressed) {
415 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
416 for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
424 while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
426 if (m->control_pressed) {
427 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
428 for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
436 if(allLines == 1 || labels.count(order->getLabel()) == 1){
438 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
439 cCurve = new Collect(order, cDisplays);
440 cCurve->getCurve(freq);
443 processedLabels.insert(order->getLabel());
444 userLabels.erase(order->getLabel());
448 //you have a label the user want that is smaller than this label and the last label has not already been processed
449 if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
450 string saveLabel = order->getLabel();
453 order = (input->getOrderVector(lastLabel));
455 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
456 cCurve = new Collect(order, cDisplays);
457 cCurve->getCurve(freq);
461 processedLabels.insert(order->getLabel());
462 userLabels.erase(order->getLabel());
464 //restore real lastlabel to save below
465 order->setLabel(saveLabel);
468 lastLabel = order->getLabel();
471 order = (input->getOrderVector());
475 if (m->control_pressed) {
476 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
477 for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
483 //output error messages about any remaining user labels
484 set<string>::iterator it;
485 bool needToRun = false;
486 for (it = userLabels.begin(); it != userLabels.end(); it++) {
487 m->mothurOut("Your file does not include the label " + *it);
488 if (processedLabels.count(lastLabel) != 1) {
489 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
492 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
496 //run last label if you need to
497 if (needToRun == true) {
498 if (order != NULL) { delete order; }
499 order = (input->getOrderVector(lastLabel));
501 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
503 cCurve = new Collect(order, cDisplays);
504 cCurve->getCurve(freq);
507 if (m->control_pressed) {
508 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
509 for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } outputTypes.clear();
518 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
523 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
525 m->mothurOutEndLine();
526 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
527 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
528 m->mothurOutEndLine();
533 catch(exception& e) {
534 m->errorOut(e, "CollectCommand", "execute");
539 //**********************************************************************************************************************
540 vector<string> CollectCommand::parseSharedFile(string filename) {
542 vector<string> filenames;
544 map<string, ofstream*> filehandles;
545 map<string, ofstream*>::iterator it3;
547 input = new InputData(filename, "sharedfile");
548 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
550 string sharedFileRoot = m->getRootName(filename);
552 //clears file before we start to write to it below
553 for (int i=0; i<lookup.size(); i++) {
554 m->mothurRemove((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
555 filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
559 for (int i=0; i<lookup.size(); i++) {
561 filehandles[lookup[i]->getGroup()] = temp;
562 groups.push_back(lookup[i]->getGroup());
565 while(lookup[0] != NULL) {
567 for (int i = 0; i < lookup.size(); i++) {
568 RAbundVector rav = lookup[i]->getRAbundVector();
569 m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
570 rav.print(*(filehandles[lookup[i]->getGroup()]));
571 (*(filehandles[lookup[i]->getGroup()])).close();
574 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
575 lookup = input->getSharedRAbundVectors();
579 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
587 catch(exception& e) {
588 m->errorOut(e, "CollectCommand", "parseSharedFile");
592 //**********************************************************************************************************************