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 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";
67 helpString += "The collect.single command should be in the following format: \n";
68 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";
69 helpString += "collect.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n";
70 helpString += "Example collect(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-chao-ace-jack).\n";
71 helpString += "The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson.\n";
72 helpString += validCalculator->printCalc("single");
73 helpString += "The label parameter is used to analyze specific labels in your input.\n";
74 helpString += "Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n";
78 m->errorOut(e, "CollectCommand", "getHelpString");
82 //**********************************************************************************************************************
83 CollectCommand::CollectCommand(){
85 abort = true; calledHelp = true;
87 vector<string> tempOutNames;
88 outputTypes["sobs"] = tempOutNames;
89 outputTypes["chao"] = tempOutNames;
90 outputTypes["nseqs"] = tempOutNames;
91 outputTypes["coverage"] = tempOutNames;
92 outputTypes["ace"] = tempOutNames;
93 outputTypes["jack"] = tempOutNames;
94 outputTypes["shannon"] = tempOutNames;
95 outputTypes["shannoneven"] = tempOutNames;
96 outputTypes["np_shannon"] = tempOutNames;
97 outputTypes["heip"] = tempOutNames;
98 outputTypes["smithwilson"] = tempOutNames;
99 outputTypes["simpson"] = tempOutNames;
100 outputTypes["simpsoneven"] = tempOutNames;
101 outputTypes["invsimpson"] = tempOutNames;
102 outputTypes["bootstrap"] = tempOutNames;
103 outputTypes["geometric"] = tempOutNames;
104 outputTypes["qstat"] = tempOutNames;
105 outputTypes["logseries"] = tempOutNames;
106 outputTypes["bergerparker"] = tempOutNames;
107 outputTypes["bstick"] = tempOutNames;
108 outputTypes["goodscoverage"] = tempOutNames;
109 outputTypes["efron"] = tempOutNames;
110 outputTypes["boneh"] = tempOutNames;
111 outputTypes["solow"] = tempOutNames;
112 outputTypes["shen"] = tempOutNames;
114 catch(exception& e) {
115 m->errorOut(e, "CollectCommand", "CollectCommand");
119 //**********************************************************************************************************************
120 CollectCommand::CollectCommand(string option) {
122 abort = false; calledHelp = false;
125 //allow user to run help
126 if(option == "help") { validCalculator = new ValidCalculators(); help(); delete validCalculator; abort = true; }
129 vector<string> myArray = setParameters();
131 OptionParser parser(option);
132 map<string,string> parameters = parser.getParameters();
133 map<string,string>::iterator it;
135 ValidParameters validParameter;
137 //check to make sure all parameters are valid for command
138 for (it = parameters.begin(); it != parameters.end(); it++) {
139 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
142 //initialize outputTypes
143 vector<string> tempOutNames;
144 outputTypes["sobs"] = tempOutNames;
145 outputTypes["chao"] = tempOutNames;
146 outputTypes["nseqs"] = tempOutNames;
147 outputTypes["coverage"] = tempOutNames;
148 outputTypes["ace"] = tempOutNames;
149 outputTypes["jack"] = tempOutNames;
150 outputTypes["shannon"] = tempOutNames;
151 outputTypes["shannoneven"] = tempOutNames;
152 outputTypes["np_shannon"] = tempOutNames;
153 outputTypes["heip"] = tempOutNames;
154 outputTypes["smithwilson"] = tempOutNames;
155 outputTypes["simpson"] = tempOutNames;
156 outputTypes["simpsoneven"] = tempOutNames;
157 outputTypes["invsimpson"] = tempOutNames;
158 outputTypes["bootstrap"] = tempOutNames;
159 outputTypes["geometric"] = tempOutNames;
160 outputTypes["qstat"] = tempOutNames;
161 outputTypes["logseries"] = tempOutNames;
162 outputTypes["bergerparker"] = tempOutNames;
163 outputTypes["bstick"] = tempOutNames;
164 outputTypes["goodscoverage"] = tempOutNames;
165 outputTypes["efron"] = tempOutNames;
166 outputTypes["boneh"] = tempOutNames;
167 outputTypes["solow"] = tempOutNames;
168 outputTypes["shen"] = tempOutNames;
170 //if the user changes the input directory command factory will send this info to us in the output parameter
171 string inputDir = validParameter.validFile(parameters, "inputdir", false);
172 if (inputDir == "not found"){ inputDir = ""; }
175 it = parameters.find("shared");
176 //user has given a template file
177 if(it != parameters.end()){
178 path = m->hasPath(it->second);
179 //if the user has not given a path then, add inputdir. else leave path alone.
180 if (path == "") { parameters["shared"] = inputDir + it->second; }
183 it = parameters.find("rabund");
184 //user has given a template file
185 if(it != parameters.end()){
186 path = m->hasPath(it->second);
187 //if the user has not given a path then, add inputdir. else leave path alone.
188 if (path == "") { parameters["rabund"] = inputDir + it->second; }
191 it = parameters.find("sabund");
192 //user has given a template file
193 if(it != parameters.end()){
194 path = m->hasPath(it->second);
195 //if the user has not given a path then, add inputdir. else leave path alone.
196 if (path == "") { parameters["sabund"] = inputDir + it->second; }
199 it = parameters.find("list");
200 //user has given a template file
201 if(it != parameters.end()){
202 path = m->hasPath(it->second);
203 //if the user has not given a path then, add inputdir. else leave path alone.
204 if (path == "") { parameters["list"] = inputDir + it->second; }
208 //check for required parameters
209 listfile = validParameter.validFile(parameters, "list", true);
210 if (listfile == "not open") { listfile = ""; abort = true; }
211 else if (listfile == "not found") { listfile = ""; }
212 else { format = "list"; inputfile = listfile; }
214 sabundfile = validParameter.validFile(parameters, "sabund", true);
215 if (sabundfile == "not open") { sabundfile = ""; abort = true; }
216 else if (sabundfile == "not found") { sabundfile = ""; }
217 else { format = "sabund"; inputfile = sabundfile; }
219 rabundfile = validParameter.validFile(parameters, "rabund", true);
220 if (rabundfile == "not open") { rabundfile = ""; abort = true; }
221 else if (rabundfile == "not found") { rabundfile = ""; }
222 else { format = "rabund"; inputfile = rabundfile; }
224 sharedfile = validParameter.validFile(parameters, "shared", true);
225 if (sharedfile == "not open") { sharedfile = ""; abort = true; }
226 else if (sharedfile == "not found") { sharedfile = ""; }
227 else { format = "sharedfile"; inputfile = sharedfile; }
230 //if the user changes the output directory command factory will send this info to us in the output parameter
231 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
233 if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) {
234 //is there are current file available for any of these?
235 //give priority to shared, then list, then rabund, then sabund
236 //if there is a current shared file, use it
237 sharedfile = m->getSharedFile();
238 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
240 listfile = m->getListFile();
241 if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
243 rabundfile = m->getRabundFile();
244 if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
246 sabundfile = m->getSabundFile();
247 if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
249 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();
257 //check for optional parameter and set defaults
258 // ...at some point should added some additional type checking...
259 label = validParameter.validFile(parameters, "label", false);
260 if (label == "not found") { label = ""; }
262 if(label != "all") { m->splitAtDash(label, labels); allLines = 0; }
263 else { allLines = 1; }
266 //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
267 calc = validParameter.validFile(parameters, "calc", false);
268 if (calc == "not found") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
270 if (calc == "default") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
272 m->splitAtDash(calc, Estimators);
275 temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
278 temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
279 convert(temp, abund);
281 temp = validParameter.validFile(parameters, "size", false); if (temp == "not found") { temp = "0"; }
286 catch(exception& e) {
287 m->errorOut(e, "CollectCommand", "CollectCommand");
291 //**********************************************************************************************************************
293 int CollectCommand::execute(){
296 if (abort == true) { if (calledHelp) { return 0; } return 2; }
298 if ((format != "sharedfile")) { inputFileNames.push_back(inputfile); }
299 else { inputFileNames = parseSharedFile(sharedfile); format = "rabund"; }
301 for (int p = 0; p < inputFileNames.size(); p++) {
303 if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } m->Groups.clear(); return 0; }
305 if (outputDir == "") { outputDir += m->hasPath(inputFileNames[p]); }
306 string fileNameRoot = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p]));
307 //globaldata->inputFileName = inputFileNames[p];
309 if (inputFileNames.size() > 1) {
310 m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[p]); m->mothurOutEndLine(); m->mothurOutEndLine();
313 validCalculator = new ValidCalculators();
315 for (int i=0; i<Estimators.size(); i++) {
316 if (validCalculator->isValidCalculator("single", Estimators[i]) == true) {
317 if (Estimators[i] == "sobs") {
318 cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
319 outputNames.push_back(fileNameRoot+"sobs"); outputTypes["sobs"].push_back(fileNameRoot+"sobs");
320 }else if (Estimators[i] == "chao") {
321 cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
322 outputNames.push_back(fileNameRoot+"chao"); outputTypes["chao"].push_back(fileNameRoot+"chao");
323 }else if (Estimators[i] == "nseqs") {
324 cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs")));
325 outputNames.push_back(fileNameRoot+"nseqs"); outputTypes["nseqs"].push_back(fileNameRoot+"nseqs");
326 }else if (Estimators[i] == "coverage") {
327 cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage")));
328 outputNames.push_back(fileNameRoot+"coverage"); outputTypes["coverage"].push_back(fileNameRoot+"coverage");
329 }else if (Estimators[i] == "ace") {
330 cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
331 outputNames.push_back(fileNameRoot+"ace"); outputTypes["ace"].push_back(fileNameRoot+"ace");
332 }else if (Estimators[i] == "jack") {
333 cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
334 outputNames.push_back(fileNameRoot+"jack"); outputTypes["jack"].push_back(fileNameRoot+"jack");
335 }else if (Estimators[i] == "shannon") {
336 cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
337 outputNames.push_back(fileNameRoot+"shannon"); outputTypes["shannon"].push_back(fileNameRoot+"shannon");
338 }else if (Estimators[i] == "shannoneven") {
339 cDisplays.push_back(new CollectDisplay(new ShannonEven(), new OneColumnFile(fileNameRoot+"shannoneven")));
340 outputNames.push_back(fileNameRoot+"shannoneven"); outputTypes["shannoneven"].push_back(fileNameRoot+"shannoneven");
341 }else if (Estimators[i] == "npshannon") {
342 cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
343 outputNames.push_back(fileNameRoot+"np_shannon"); outputTypes["np_shannon"].push_back(fileNameRoot+"np_shannon");
344 }else if (Estimators[i] == "heip") {
345 cDisplays.push_back(new CollectDisplay(new Heip(), new OneColumnFile(fileNameRoot+"heip")));
346 outputNames.push_back(fileNameRoot+"heip"); outputTypes["heip"].push_back(fileNameRoot+"heip");
347 }else if (Estimators[i] == "smithwilson") {
348 cDisplays.push_back(new CollectDisplay(new SmithWilson(), new OneColumnFile(fileNameRoot+"smithwilson")));
349 outputNames.push_back(fileNameRoot+"smithwilson"); outputTypes["smithwilson"].push_back(fileNameRoot+"smithwilson");
350 }else if (Estimators[i] == "simpson") {
351 cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
352 outputNames.push_back(fileNameRoot+"simpson"); outputTypes["simpson"].push_back(fileNameRoot+"simpson");
353 }else if (Estimators[i] == "simpsoneven") {
354 cDisplays.push_back(new CollectDisplay(new SimpsonEven(), new OneColumnFile(fileNameRoot+"simpsoneven")));
355 outputNames.push_back(fileNameRoot+"simpsoneven"); outputTypes["simpsoneven"].push_back(fileNameRoot+"simpsoneven");
356 }else if (Estimators[i] == "invsimpson") {
357 cDisplays.push_back(new CollectDisplay(new InvSimpson(), new ThreeColumnFile(fileNameRoot+"invsimpson")));
358 outputNames.push_back(fileNameRoot+"invsimpson"); outputTypes["invsimpson"].push_back(fileNameRoot+"invsimpson");
359 }else if (Estimators[i] == "bootstrap") {
360 cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
361 outputNames.push_back(fileNameRoot+"bootstrap"); outputTypes["bootstrap"].push_back(fileNameRoot+"bootstrap");
362 }else if (Estimators[i] == "geometric") {
363 cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric")));
364 outputNames.push_back(fileNameRoot+"geometric"); outputTypes["geometric"].push_back(fileNameRoot+"geometric");
365 }else if (Estimators[i] == "qstat") {
366 cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
367 outputNames.push_back(fileNameRoot+"qstat"); outputTypes["qstat"].push_back(fileNameRoot+"qstat");
368 }else if (Estimators[i] == "logseries") {
369 cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries")));
370 outputNames.push_back(fileNameRoot+"logseries"); outputTypes["logseries"].push_back(fileNameRoot+"logseries");
371 }else if (Estimators[i] == "bergerparker") {
372 cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
373 outputNames.push_back(fileNameRoot+"bergerparker"); outputTypes["bergerparker"].push_back(fileNameRoot+"bergerparker");
374 }else if (Estimators[i] == "bstick") {
375 cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick")));
376 outputNames.push_back(fileNameRoot+"bstick"); outputTypes["bstick"].push_back(fileNameRoot+"bstick");
377 }else if (Estimators[i] == "goodscoverage") {
378 cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage")));
379 outputNames.push_back(fileNameRoot+"goodscoverage"); outputTypes["goodscoverage"].push_back(fileNameRoot+"goodscoverage");
380 }else if (Estimators[i] == "efron") {
381 cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+"efron")));
382 outputNames.push_back(fileNameRoot+"efron"); outputTypes["efron"].push_back(fileNameRoot+"efron");
383 }else if (Estimators[i] == "boneh") {
384 cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+"boneh")));
385 outputNames.push_back(fileNameRoot+"boneh"); outputTypes["boneh"].push_back(fileNameRoot+"boneh");
386 }else if (Estimators[i] == "solow") {
387 cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+"solow")));
388 outputNames.push_back(fileNameRoot+"solow"); outputTypes["solow"].push_back(fileNameRoot+"solow");
389 }else if (Estimators[i] == "shen") {
390 cDisplays.push_back(new CollectDisplay(new Shen(size, abund), new OneColumnFile(fileNameRoot+"shen")));
391 outputNames.push_back(fileNameRoot+"shen"); outputTypes["shen"].push_back(fileNameRoot+"shen");
396 //if the users entered no valid calculators don't execute command
397 if (cDisplays.size() == 0) { return 0; }
399 input = new InputData(inputFileNames[p], format);
400 order = input->getOrderVector();
401 string lastLabel = order->getLabel();
403 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
404 set<string> processedLabels;
405 set<string> userLabels = labels;
407 if (m->control_pressed) {
408 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
409 for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
412 delete validCalculator;
418 while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
420 if (m->control_pressed) {
421 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
422 for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
425 delete validCalculator;
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();
474 delete validCalculator;
479 //output error messages about any remaining user labels
480 set<string>::iterator it;
481 bool needToRun = false;
482 for (it = userLabels.begin(); it != userLabels.end(); it++) {
483 m->mothurOut("Your file does not include the label " + *it);
484 if (processedLabels.count(lastLabel) != 1) {
485 m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
488 m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
492 //run last label if you need to
493 if (needToRun == true) {
494 if (order != NULL) { delete order; }
495 order = (input->getOrderVector(lastLabel));
497 m->mothurOut(order->getLabel()); m->mothurOutEndLine();
499 cCurve = new Collect(order, cDisplays);
500 cCurve->getCurve(freq);
503 if (m->control_pressed) {
504 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
505 for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } outputTypes.clear();
508 delete validCalculator;
515 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
518 delete validCalculator;
521 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
523 m->mothurOutEndLine();
524 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
525 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
526 m->mothurOutEndLine();
531 catch(exception& e) {
532 m->errorOut(e, "CollectCommand", "execute");
537 //**********************************************************************************************************************
538 vector<string> CollectCommand::parseSharedFile(string filename) {
540 vector<string> filenames;
542 map<string, ofstream*> filehandles;
543 map<string, ofstream*>::iterator it3;
545 input = new InputData(filename, "sharedfile");
546 vector<SharedRAbundVector*> lookup = input->getSharedRAbundVectors();
548 string sharedFileRoot = m->getRootName(filename);
550 //clears file before we start to write to it below
551 for (int i=0; i<lookup.size(); i++) {
552 remove((sharedFileRoot + lookup[i]->getGroup() + ".rabund").c_str());
553 filenames.push_back((sharedFileRoot + lookup[i]->getGroup() + ".rabund"));
557 for (int i=0; i<lookup.size(); i++) {
559 filehandles[lookup[i]->getGroup()] = temp;
560 groups.push_back(lookup[i]->getGroup());
563 while(lookup[0] != NULL) {
565 for (int i = 0; i < lookup.size(); i++) {
566 RAbundVector rav = lookup[i]->getRAbundVector();
567 m->openOutputFileAppend(sharedFileRoot + lookup[i]->getGroup() + ".rabund", *(filehandles[lookup[i]->getGroup()]));
568 rav.print(*(filehandles[lookup[i]->getGroup()]));
569 (*(filehandles[lookup[i]->getGroup()])).close();
572 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
573 lookup = input->getSharedRAbundVectors();
577 for (it3 = filehandles.begin(); it3 != filehandles.end(); it3++) {
585 catch(exception& e) {
586 m->errorOut(e, "CollectCommand", "parseSharedFile");
590 //**********************************************************************************************************************