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 "npshannon.h"
19 #include "jackknife.h"
23 #include "bergerparker.h"
25 #include "goodscoverage.h"
33 //**********************************************************************************************************************
34 CollectCommand::CollectCommand(string option){
36 globaldata = GlobalData::getInstance();
42 //allow user to run help
43 if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
46 //valid paramters for this command
47 string Array[] = {"freq","label","calc","abund","size"};
48 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
50 OptionParser parser(option);
51 map<string,string> parameters = parser.getParameters();
53 ValidParameters validParameter;
55 //check to make sure all parameters are valid for command
56 for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
57 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
60 //make sure the user has already run the read.otu command
61 if ((globaldata->getListFile() == "") && (globaldata->getRabundFile() == "") && (globaldata->getSabundFile() == "")) { mothurOut("You must read a list, sabund or rabund before you can use the collect.single command."); mothurOutEndLine(); abort = true; }
63 //check for optional parameter and set defaults
64 // ...at some point should added some additional type checking...
65 label = validParameter.validFile(parameters, "label", false);
66 if (label == "not found") { label = ""; }
68 if(label != "all") { splitAtDash(label, labels); allLines = 0; }
69 else { allLines = 1; }
72 //if the user has not specified any labels use the ones from read.otu
74 allLines = globaldata->allLines;
75 labels = globaldata->labels;
78 calc = validParameter.validFile(parameters, "calc", false);
79 if (calc == "not found") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
81 if (calc == "default") { calc = "sobs-chao-ace-jack-shannon-npshannon-simpson"; }
83 splitAtDash(calc, Estimators);
86 temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
89 temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
92 temp = validParameter.validFile(parameters, "size", false); if (temp == "not found") { temp = "0"; }
96 string fileNameRoot = getRootName(globaldata->inputFileName);
98 validCalculator = new ValidCalculators();
100 for (i=0; i<Estimators.size(); i++) {
101 if (validCalculator->isValidCalculator("single", Estimators[i]) == true) {
102 if (Estimators[i] == "sobs") {
103 cDisplays.push_back(new CollectDisplay(new Sobs(), new OneColumnFile(fileNameRoot+"sobs")));
104 }else if (Estimators[i] == "chao") {
105 cDisplays.push_back(new CollectDisplay(new Chao1(), new ThreeColumnFile(fileNameRoot+"chao")));
106 }else if (Estimators[i] == "nseqs") {
107 cDisplays.push_back(new CollectDisplay(new NSeqs(), new OneColumnFile(fileNameRoot+"nseqs")));
108 }else if (Estimators[i] == "coverage") {
109 cDisplays.push_back(new CollectDisplay(new Coverage(), new OneColumnFile(fileNameRoot+"coverage")));
110 }else if (Estimators[i] == "ace") {
111 cDisplays.push_back(new CollectDisplay(new Ace(abund), new ThreeColumnFile(fileNameRoot+"ace")));
112 }else if (Estimators[i] == "jack") {
113 cDisplays.push_back(new CollectDisplay(new Jackknife(), new ThreeColumnFile(fileNameRoot+"jack")));
114 }else if (Estimators[i] == "shannon") {
115 cDisplays.push_back(new CollectDisplay(new Shannon(), new ThreeColumnFile(fileNameRoot+"shannon")));
116 }else if (Estimators[i] == "npshannon") {
117 cDisplays.push_back(new CollectDisplay(new NPShannon(), new OneColumnFile(fileNameRoot+"np_shannon")));
118 }else if (Estimators[i] == "simpson") {
119 cDisplays.push_back(new CollectDisplay(new Simpson(), new ThreeColumnFile(fileNameRoot+"simpson")));
120 }else if (Estimators[i] == "bootstrap") {
121 cDisplays.push_back(new CollectDisplay(new Bootstrap(), new OneColumnFile(fileNameRoot+"bootstrap")));
122 }else if (Estimators[i] == "geometric") {
123 cDisplays.push_back(new CollectDisplay(new Geom(), new OneColumnFile(fileNameRoot+"geometric")));
124 }else if (Estimators[i] == "qstat") {
125 cDisplays.push_back(new CollectDisplay(new QStat(), new OneColumnFile(fileNameRoot+"qstat")));
126 }else if (Estimators[i] == "logseries") {
127 cDisplays.push_back(new CollectDisplay(new LogSD(), new OneColumnFile(fileNameRoot+"logseries")));
128 }else if (Estimators[i] == "bergerparker") {
129 cDisplays.push_back(new CollectDisplay(new BergerParker(), new OneColumnFile(fileNameRoot+"bergerparker")));
130 }else if (Estimators[i] == "bstick") {
131 cDisplays.push_back(new CollectDisplay(new BStick(), new ThreeColumnFile(fileNameRoot+"bstick")));
132 }else if (Estimators[i] == "goodscoverage") {
133 cDisplays.push_back(new CollectDisplay(new GoodsCoverage(), new OneColumnFile(fileNameRoot+"goodscoverage")));
134 }else if (Estimators[i] == "efron") {
135 cDisplays.push_back(new CollectDisplay(new Efron(size), new OneColumnFile(fileNameRoot+"efron")));
136 }else if (Estimators[i] == "boneh") {
137 cDisplays.push_back(new CollectDisplay(new Boneh(size), new OneColumnFile(fileNameRoot+"boneh")));
138 }else if (Estimators[i] == "solow") {
139 cDisplays.push_back(new CollectDisplay(new Solow(size), new OneColumnFile(fileNameRoot+"solow")));
140 }else if (Estimators[i] == "shen") {
141 cDisplays.push_back(new CollectDisplay(new Shen(size, abund), new OneColumnFile(fileNameRoot+"shen")));
149 catch(exception& e) {
150 errorOut(e, "CollectCommand", "CollectCommand");
154 //**********************************************************************************************************************
156 void CollectCommand::help(){
158 mothurOut("The collect.single command can only be executed after a successful read.otu command. WITH ONE EXECEPTION. \n");
159 mothurOut("The collect.single command can be executed after a successful cluster command. It will use the .list file from the output of the cluster.\n");
160 mothurOut("The collect.single command parameters are label, freq, calc and abund. No parameters are required. \n");
161 mothurOut("The collect.single command should be in the following format: \n");
162 mothurOut("collect.single(label=yourLabel, iters=yourIters, freq=yourFreq, calc=yourEstimators).\n");
163 mothurOut("Example collect(label=unique-.01-.03, iters=10000, freq=10, calc=sobs-chao-ace-jack).\n");
164 mothurOut("The default values for freq is 100, and calc are sobs-chao-ace-jack-shannon-npshannon-simpson.\n");
165 validCalculator->printCalc("single", cout);
166 mothurOut("The label parameter is used to analyze specific labels in your input.\n");
167 mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n");
169 catch(exception& e) {
170 errorOut(e, "CollectCommand", "help");
175 //**********************************************************************************************************************
177 CollectCommand::~CollectCommand(){
178 if (abort == false) {
180 delete input; globaldata->ginput = NULL;
182 delete validCalculator;
183 globaldata->gorder = NULL;
187 //**********************************************************************************************************************
189 int CollectCommand::execute(){
192 if (abort == true) { return 0; }
194 //if the users entered no valid calculators don't execute command
195 if (cDisplays.size() == 0) { return 0; }
197 read = new ReadOTUFile(globaldata->inputFileName);
198 read->read(&*globaldata);
200 order = globaldata->gorder;
201 string lastLabel = order->getLabel();
202 input = globaldata->ginput;
204 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
205 set<string> processedLabels;
206 set<string> userLabels = labels;
208 while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
210 if(allLines == 1 || labels.count(order->getLabel()) == 1){
212 cCurve = new Collect(order, cDisplays);
213 cCurve->getCurve(freq);
216 mothurOut(order->getLabel()); mothurOutEndLine();
217 processedLabels.insert(order->getLabel());
218 userLabels.erase(order->getLabel());
222 //you have a label the user want that is smaller than this label and the last label has not already been processed
223 if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
224 string saveLabel = order->getLabel();
227 order = (input->getOrderVector(lastLabel));
229 cCurve = new Collect(order, cDisplays);
230 cCurve->getCurve(freq);
233 mothurOut(order->getLabel()); mothurOutEndLine();
234 processedLabels.insert(order->getLabel());
235 userLabels.erase(order->getLabel());
237 //restore real lastlabel to save below
238 order->setLabel(saveLabel);
241 lastLabel = order->getLabel();
244 order = (input->getOrderVector());
247 //output error messages about any remaining user labels
248 set<string>::iterator it;
249 bool needToRun = false;
250 for (it = userLabels.begin(); it != userLabels.end(); it++) {
251 mothurOut("Your file does not include the label " + *it);
252 if (processedLabels.count(lastLabel) != 1) {
253 mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
256 mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
260 //run last label if you need to
261 if (needToRun == true) {
262 if (order != NULL) { delete order; }
263 order = (input->getOrderVector(lastLabel));
265 mothurOut(order->getLabel()); mothurOutEndLine();
267 cCurve = new Collect(order, cDisplays);
268 cCurve->getCurve(freq);
274 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
277 catch(exception& e) {
278 errorOut(e, "CollectCommand", "execute");
283 //**********************************************************************************************************************