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-np_shannon-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["np_shannon"] = 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["np_shannon"] = 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; }
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; }
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; }
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; }
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);
277 temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
280 temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
281 convert(temp, abund);
283 temp = validParameter.validFile(parameters, "size", false); if (temp == "not found") { temp = "0"; }
288 catch(exception& e) {
289 m->errorOut(e, "CollectCommand", "CollectCommand");
293 //**********************************************************************************************************************
295 int CollectCommand::execute(){
298 if (abort == true) { if (calledHelp) { return 0; } return 2; }
300 if ((format != "sharedfile")) { inputFileNames.push_back(inputfile); }
301 else { inputFileNames = parseSharedFile(sharedfile); format = "rabund"; }
303 for (int p = 0; p < inputFileNames.size(); p++) {
305 if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } m->Groups.clear(); return 0; }
307 if (outputDir == "") { outputDir += m->hasPath(inputFileNames[p]); }
308 string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
309 //globaldata->inputFileName = inputFileNames[p];
311 if (inputFileNames.size() > 1) {
312 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
315 ValidCalculators validCalculator;
317 for (int i=0; i<Estimators.size(); i++) {
318 if (validCalculator.isValidCalculator("single", Estimators[i]) == true) {
319 if (Estimators[i] == "sobs") {
320 cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
321 outputNames.push_back(fileNameRoot+"sobs"); outputTypes["sobs"].push_back(fileNameRoot+"sobs");
322 }else if (Estimators[i] == "chao") {
323 cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
324 outputNames.push_back(fileNameRoot+"chao"); outputTypes["chao"].push_back(fileNameRoot+"chao");
325 }else if (Estimators[i] == "nseqs") {
326 cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs")));
327 outputNames.push_back(fileNameRoot+"nseqs"); outputTypes["nseqs"].push_back(fileNameRoot+"nseqs");
328 }else if (Estimators[i] == "coverage") {
329 cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage")));
330 outputNames.push_back(fileNameRoot+"coverage"); outputTypes["coverage"].push_back(fileNameRoot+"coverage");
331 }else if (Estimators[i] == "ace") {
332 cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
333 outputNames.push_back(fileNameRoot+"ace"); outputTypes["ace"].push_back(fileNameRoot+"ace");
334 }else if (Estimators[i] == "jack") {
335 cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
336 outputNames.push_back(fileNameRoot+"jack"); outputTypes["jack"].push_back(fileNameRoot+"jack");
337 }else if (Estimators[i] == "shannon") {
338 cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
339 outputNames.push_back(fileNameRoot+"shannon"); outputTypes["shannon"].push_back(fileNameRoot+"shannon");
340 }else if (Estimators[i] == "shannoneven") {
341 cDisplays.push_back(new CollectDisplay(new ShannonEven(), new OneColumnFile(fileNameRoot+"shannoneven")));
342 outputNames.push_back(fileNameRoot+"shannoneven"); outputTypes["shannoneven"].push_back(fileNameRoot+"shannoneven");
343 }else if (Estimators[i] == "npshannon") {
344 cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
345 outputNames.push_back(fileNameRoot+"np_shannon"); outputTypes["np_shannon"].push_back(fileNameRoot+"np_shannon");
346 }else if (Estimators[i] == "heip") {
347 cDisplays.push_back(new CollectDisplay(new Heip(), new OneColumnFile(fileNameRoot+"heip")));
348 outputNames.push_back(fileNameRoot+"heip"); outputTypes["heip"].push_back(fileNameRoot+"heip");
349 }else if (Estimators[i] == "smithwilson") {
350 cDisplays.push_back(new CollectDisplay(new SmithWilson(), new OneColumnFile(fileNameRoot+"smithwilson")));
351 outputNames.push_back(fileNameRoot+"smithwilson"); outputTypes["smithwilson"].push_back(fileNameRoot+"smithwilson");
352 }else if (Estimators[i] == "simpson") {
353 cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
354 outputNames.push_back(fileNameRoot+"simpson"); outputTypes["simpson"].push_back(fileNameRoot+"simpson");
355 }else if (Estimators[i] == "simpsoneven") {
356 cDisplays.push_back(new CollectDisplay(new SimpsonEven(), new OneColumnFile(fileNameRoot+"simpsoneven")));
357 outputNames.push_back(fileNameRoot+"simpsoneven"); outputTypes["simpsoneven"].push_back(fileNameRoot+"simpsoneven");
358 }else if (Estimators[i] == "invsimpson") {
359 cDisplays.push_back(new CollectDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+"invsimpson")));
360 outputNames.push_back(fileNameRoot+"invsimpson"); outputTypes["invsimpson"].push_back(fileNameRoot+"invsimpson");
361 }else if (Estimators[i] == "bootstrap") {
362 cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
363 outputNames.push_back(fileNameRoot+"bootstrap"); outputTypes["bootstrap"].push_back(fileNameRoot+"bootstrap");
364 }else if (Estimators[i] == "geometric") {
365 cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric")));
366 outputNames.push_back(fileNameRoot+"geometric"); outputTypes["geometric"].push_back(fileNameRoot+"geometric");
367 }else if (Estimators[i] == "qstat") {
368 cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
369 outputNames.push_back(fileNameRoot+"qstat"); outputTypes["qstat"].push_back(fileNameRoot+"qstat");
370 }else if (Estimators[i] == "logseries") {
371 cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries")));
372 outputNames.push_back(fileNameRoot+"logseries"); outputTypes["logseries"].push_back(fileNameRoot+"logseries");
373 }else if (Estimators[i] == "bergerparker") {
374 cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
375 outputNames.push_back(fileNameRoot+"bergerparker"); outputTypes["bergerparker"].push_back(fileNameRoot+"bergerparker");
376 }else if (Estimators[i] == "bstick") {
377 cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick")));
378 outputNames.push_back(fileNameRoot+"bstick"); outputTypes["bstick"].push_back(fileNameRoot+"bstick");
379 }else if (Estimators[i] == "goodscoverage") {
380 cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage")));
381 outputNames.push_back(fileNameRoot+"goodscoverage"); outputTypes["goodscoverage"].push_back(fileNameRoot+"goodscoverage");
382 }else if (Estimators[i] == "efron") {
383 cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+"efron")));
384 outputNames.push_back(fileNameRoot+"efron"); outputTypes["efron"].push_back(fileNameRoot+"efron");
385 }else if (Estimators[i] == "boneh") {
386 cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+"boneh")));
387 outputNames.push_back(fileNameRoot+"boneh"); outputTypes["boneh"].push_back(fileNameRoot+"boneh");
388 }else if (Estimators[i] == "solow") {
389 cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+"solow")));
390 outputNames.push_back(fileNameRoot+"solow"); outputTypes["solow"].push_back(fileNameRoot+"solow");
391 }else if (Estimators[i] == "shen") {
392 cDisplays.push_back(new CollectDisplay(new Shen(size, abund), new OneColumnFile(fileNameRoot+"shen")));
393 outputNames.push_back(fileNameRoot+"shen"); outputTypes["shen"].push_back(fileNameRoot+"shen");
398 //if the users entered no valid calculators don't execute command
399 if (cDisplays.size() == 0) { return 0; }
401 input = new InputData(inputFileNames[p], format);
402 order = input->getOrderVector();
403 string lastLabel = order->getLabel();
405 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
406 set<string> processedLabels;
407 set<string> userLabels = labels;
409 if (m->control_pressed) {
410 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
411 for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
419 while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
421 if (m->control_pressed) {
422 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
423 for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
431 if(allLines == 1 || labels.count(order->getLabel()) == 1){
433 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
434 cCurve = new Collect(order, cDisplays);
435 cCurve->getCurve(freq);
438 processedLabels.insert(order->getLabel());
439 userLabels.erase(order->getLabel());
443 //you have a label the user want that is smaller than this label and the last label has not already been processed
444 if ((m->anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
445 string saveLabel = order->getLabel();
448 order = (input->getOrderVector(lastLabel));
450 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
451 cCurve = new Collect(order, cDisplays);
452 cCurve->getCurve(freq);
456 processedLabels.insert(order->getLabel());
457 userLabels.erase(order->getLabel());
459 //restore real lastlabel to save below
460 order->setLabel(saveLabel);
463 lastLabel = order->getLabel();
466 order = (input->getOrderVector());
470 if (m->control_pressed) {
471 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
472 for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
478 //output error messages about any remaining user labels
479 set<string>::iterator it;
480 bool needToRun = false;
481 for (it = userLabels.begin(); it != userLabels.end(); it++) {
482 m->mothurOut("Your file does not include the label " + *it);
483 if (processedLabels.count(lastLabel) != 1) {
484 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
487 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
491 //run last label if you need to
492 if (needToRun == true) {
493 if (order != NULL) { delete order; }
494 order = (input->getOrderVector(lastLabel));
496 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
498 cCurve = new Collect(order, cDisplays);
499 cCurve->getCurve(freq);
502 if (m->control_pressed) {
503 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
504 for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
513 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
518 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
520 m->mothurOutEndLine();
521 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
522 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
523 m->mothurOutEndLine();
528 catch(exception& e) {
529 m->errorOut(e, "CollectCommand", "execute");
534 //**********************************************************************************************************************
535 vector<string> CollectCommand::parseSharedFile(string filename) {
537 vector<string> filenames;
539 map<string, ofstream*> filehandles;
540 map<string, ofstream*>::iterator it3;
542 input = new InputData(filename, "sharedfile");
543 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
545 string sharedFileRoot = m->getRootName(filename);
547 //clears file before we start to write to it below
548 for (int i=0; i<lookup.size(); i++) {
549 remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
550 filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
554 for (int i=0; i<lookup.size(); i++) {
556 filehandles[lookup[i]->getGroup()] = temp;
557 groups.push_back(lookup[i]->getGroup());
560 while(lookup[0] != NULL) {
562 for (int i = 0; i < lookup.size(); i++) {
563 RAbundVector rav = lookup[i]->getRAbundVector();
564 m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
565 rav.print(*(filehandles[lookup[i]->getGroup()]));
566 (*(filehandles[lookup[i]->getGroup()])).close();
569 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
570 lookup = input->getSharedRAbundVectors();
574 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
582 catch(exception& e) {
583 m->errorOut(e, "CollectCommand", "parseSharedFile");
587 //**********************************************************************************************************************