2 * collectsharedcommand.cpp
5 * Created by Sarah Westcott on 1/2/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "collectsharedcommand.h"
11 #include "sharedsobscollectsummary.h"
12 #include "sharedchao1.h"
13 #include "sharedace.h"
14 #include "sharedjabund.h"
15 #include "sharedsorabund.h"
16 #include "sharedjclass.h"
17 #include "sharedsorclass.h"
18 #include "sharedjest.h"
19 #include "sharedsorest.h"
20 #include "sharedthetayc.h"
21 #include "sharedthetan.h"
22 #include "sharedkstest.h"
23 #include "whittaker.h"
24 #include "sharednseqs.h"
25 #include "sharedochiai.h"
26 #include "sharedanderbergs.h"
27 #include "sharedkulczynski.h"
28 #include "sharedkulczynskicody.h"
29 #include "sharedlennon.h"
30 #include "sharedmorisitahorn.h"
31 #include "sharedbraycurtis.h"
32 #include "sharedjackknife.h"
33 #include "whittaker.h"
37 //**********************************************************************************************************************
39 CollectSharedCommand::CollectSharedCommand(string option){
41 globaldata = GlobalData::getInstance();
48 //allow user to run help
49 if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
52 //valid paramters for this command
53 string Array[] = {"freq","label","calc","groups"};
54 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
56 OptionParser parser(option);
57 map<string,string> parameters=parser.getParameters();
59 ValidParameters validParameter;
61 //check to make sure all parameters are valid for command
62 for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
63 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
66 //make sure the user has already run the read.otu command
67 if (globaldata->getSharedFile() == "") {
68 if (globaldata->getListFile() == "") { mothurOut("You must read a list and a group, or a shared before you can use the collect.shared command."); mothurOutEndLine(); abort = true; }
69 else if (globaldata->getGroupFile() == "") { mothurOut("You must read a list and a group, or a shared before you can use the collect.shared command."); mothurOutEndLine(); abort = true; }
73 //check for optional parameter and set defaults
74 // ...at some point should added some additional type checking..
75 label = validParameter.validFile(parameters, "label", false);
76 if (label == "not found") { label = ""; }
78 if(label != "all") { splitAtDash(label, labels); allLines = 0; }
79 else { allLines = 1; }
82 //if the user has not specified any labels use the ones from read.otu
84 allLines = globaldata->allLines;
85 labels = globaldata->labels;
88 calc = validParameter.validFile(parameters, "calc", false);
89 if (calc == "not found") { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
91 if (calc == "default") { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
93 splitAtDash(calc, Estimators);
95 groups = validParameter.validFile(parameters, "groups", false);
96 if (groups == "not found") { groups = ""; }
98 splitAtDash(groups, Groups);
100 globaldata->Groups = Groups;
103 temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
106 if (abort == false) {
108 string fileNameRoot = getRootName(globaldata->inputFileName);
109 format = globaldata->getFormat();
112 validCalculator = new ValidCalculators();
113 util = new SharedUtil();
115 for (i=0; i<Estimators.size(); i++) {
116 if (validCalculator->isValidCalculator("shared", Estimators[i]) == true) {
117 if (Estimators[i] == "sharedchao") {
118 cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+"shared.chao")));
119 }else if (Estimators[i] == "sharedsobs") {
120 cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(fileNameRoot+"shared.sobs")));
121 }else if (Estimators[i] == "sharedace") {
122 cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace")));
123 }else if (Estimators[i] == "jabund") {
124 cDisplays.push_back(new CollectDisplay(new JAbund(), new SharedOneColumnFile(fileNameRoot+"jabund")));
125 }else if (Estimators[i] == "sorabund") {
126 cDisplays.push_back(new CollectDisplay(new SorAbund(), new SharedOneColumnFile(fileNameRoot+"sorabund")));
127 }else if (Estimators[i] == "jclass") {
128 cDisplays.push_back(new CollectDisplay(new Jclass(), new SharedOneColumnFile(fileNameRoot+"jclass")));
129 }else if (Estimators[i] == "sorclass") {
130 cDisplays.push_back(new CollectDisplay(new SorClass(), new SharedOneColumnFile(fileNameRoot+"sorclass")));
131 }else if (Estimators[i] == "jest") {
132 cDisplays.push_back(new CollectDisplay(new Jest(), new SharedOneColumnFile(fileNameRoot+"jest")));
133 }else if (Estimators[i] == "sorest") {
134 cDisplays.push_back(new CollectDisplay(new SorEst(), new SharedOneColumnFile(fileNameRoot+"sorest")));
135 }else if (Estimators[i] == "thetayc") {
136 cDisplays.push_back(new CollectDisplay(new ThetaYC(), new SharedOneColumnFile(fileNameRoot+"thetayc")));
137 }else if (Estimators[i] == "thetan") {
138 cDisplays.push_back(new CollectDisplay(new ThetaN(), new SharedOneColumnFile(fileNameRoot+"thetan")));
139 }else if (Estimators[i] == "kstest") {
140 cDisplays.push_back(new CollectDisplay(new KSTest(), new SharedOneColumnFile(fileNameRoot+"kstest")));
141 }else if (Estimators[i] == "whittaker") {
142 cDisplays.push_back(new CollectDisplay(new Whittaker(), new SharedOneColumnFile(fileNameRoot+"whittaker")));
143 }else if (Estimators[i] == "sharednseqs") {
144 cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+"shared.nseqs")));
145 }else if (Estimators[i] == "ochiai") {
146 cDisplays.push_back(new CollectDisplay(new Ochiai(), new SharedOneColumnFile(fileNameRoot+"ochiai")));
147 }else if (Estimators[i] == "anderberg") {
148 cDisplays.push_back(new CollectDisplay(new Anderberg(), new SharedOneColumnFile(fileNameRoot+"anderberg")));
149 }else if (Estimators[i] == "skulczynski") {
150 cDisplays.push_back(new CollectDisplay(new Kulczynski(), new SharedOneColumnFile(fileNameRoot+"kulczynski")));
151 }else if (Estimators[i] == "kulczynskicody") {
152 cDisplays.push_back(new CollectDisplay(new KulczynskiCody(), new SharedOneColumnFile(fileNameRoot+"kulczynskicody")));
153 }else if (Estimators[i] == "lennon") {
154 cDisplays.push_back(new CollectDisplay(new Lennon(), new SharedOneColumnFile(fileNameRoot+"lennon")));
155 }else if (Estimators[i] == "morisitahorn") {
156 cDisplays.push_back(new CollectDisplay(new MorHorn(), new SharedOneColumnFile(fileNameRoot+"morisitahorn")));
157 }else if (Estimators[i] == "braycurtis") {
158 cDisplays.push_back(new CollectDisplay(new BrayCurtis(), new SharedOneColumnFile(fileNameRoot+"braycurtis")));
166 catch(exception& e) {
167 errorOut(e, "CollectSharedCommand", "CollectSharedCommand");
171 //**********************************************************************************************************************
173 void CollectSharedCommand::help(){
175 mothurOut("The collect.shared command can only be executed after a successful read.otu command.\n");
176 mothurOut("The collect.shared command parameters are label, freq, calc and groups. No parameters are required \n");
177 mothurOut("The collect.shared command should be in the following format: \n");
178 mothurOut("collect.shared(label=yourLabel, freq=yourFreq, calc=yourEstimators, groups=yourGroups).\n");
179 mothurOut("Example collect.shared(label=unique-.01-.03, freq=10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n");
180 mothurOut("The default values for freq is 100 and calc are sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan.\n");
181 mothurOut("The default value for groups is all the groups in your groupfile.\n");
182 validCalculator->printCalc("shared", cout);
183 mothurOut("The label parameter is used to analyze specific labels in your input.\n");
184 mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed. You must enter at least 2 valid groups.\n");
185 mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
188 catch(exception& e) {
189 errorOut(e, "CollectSharedCommand", "help");
194 //**********************************************************************************************************************
196 CollectSharedCommand::~CollectSharedCommand(){
197 if (abort == false) {
198 delete input; globaldata->ginput = NULL;
201 delete validCalculator;
202 globaldata->gorder = NULL;
206 //**********************************************************************************************************************
208 int CollectSharedCommand::execute(){
211 if (abort == true) { return 0; }
213 //if the users entered no valid calculators don't execute command
214 if (cDisplays.size() == 0) { return 0; }
216 read = new ReadOTUFile(globaldata->inputFileName);
217 read->read(&*globaldata);
219 input = globaldata->ginput;
220 order = input->getSharedOrderVector();
221 string lastLabel = order->getLabel();
223 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
224 set<string> processedLabels;
225 set<string> userLabels = labels;
228 util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "collect");
229 util->updateGroupIndex(globaldata->Groups, globaldata->gGroupmap->groupIndex);
231 while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
233 if(allLines == 1 || labels.count(order->getLabel()) == 1){
235 //create collectors curve
236 cCurve = new Collect(order, cDisplays);
237 cCurve->getSharedCurve(freq);
240 mothurOut(order->getLabel()); mothurOutEndLine();
241 processedLabels.insert(order->getLabel());
242 userLabels.erase(order->getLabel());
245 //you have a label the user want that is smaller than this label and the last label has not already been processed
246 if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
248 order = input->getSharedOrderVector(lastLabel);
250 //create collectors curve
251 cCurve = new Collect(order, cDisplays);
252 cCurve->getSharedCurve(freq);
255 mothurOut(order->getLabel()); mothurOutEndLine();
256 processedLabels.insert(order->getLabel());
257 userLabels.erase(order->getLabel());
261 lastLabel = order->getLabel();
263 //get next line to process
265 order = input->getSharedOrderVector();
268 //output error messages about any remaining user labels
269 set<string>::iterator it;
270 bool needToRun = false;
271 for (it = userLabels.begin(); it != userLabels.end(); it++) {
272 mothurOut("Your file does not include the label " + *it);
273 if (processedLabels.count(lastLabel) != 1) {
274 mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
277 mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
281 //run last label if you need to
282 if (needToRun == true) {
283 if (order != NULL) { delete order; }
284 order = input->getSharedOrderVector(lastLabel);
286 cCurve = new Collect(order, cDisplays);
287 cCurve->getSharedCurve(freq);
290 mothurOut(order->getLabel()); mothurOutEndLine();
294 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
296 //reset groups parameter
297 globaldata->Groups.clear();
301 catch(exception& e) {
302 errorOut(e, "CollectSharedCommand", "execute");
307 /***********************************************************/