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();
49 //allow user to run help
50 if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
53 //valid paramters for this command
54 string Array[] = {"freq","line","label","calc","groups"};
55 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
57 OptionParser parser(option);
58 map<string,string> parameters=parser.getParameters();
60 ValidParameters validParameter;
62 //check to make sure all parameters are valid for command
63 for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
64 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
67 //make sure the user has already run the read.otu command
68 if (globaldata->getSharedFile() == "") {
69 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; }
70 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; }
74 //check for optional parameter and set defaults
75 // ...at some point should added some additional type checking...
76 line = validParameter.validFile(parameters, "line", false);
77 if (line == "not found") { line = ""; }
79 if(line != "all") { splitAtDash(line, lines); allLines = 0; }
80 else { allLines = 1; }
83 label = validParameter.validFile(parameters, "label", false);
84 if (label == "not found") { label = ""; }
86 if(label != "all") { splitAtDash(label, labels); allLines = 0; }
87 else { allLines = 1; }
90 //make sure user did not use both the line and label parameters
91 if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; }
92 //if the user has not specified any line or labels use the ones from read.otu
93 else if((line == "") && (label == "")) {
94 allLines = globaldata->allLines;
95 labels = globaldata->labels;
96 lines = globaldata->lines;
99 calc = validParameter.validFile(parameters, "calc", false);
100 if (calc == "not found") { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
102 if (calc == "default") { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan"; }
104 splitAtDash(calc, Estimators);
106 groups = validParameter.validFile(parameters, "groups", false);
107 if (groups == "not found") { groups = ""; }
109 splitAtDash(groups, Groups);
111 globaldata->Groups = Groups;
114 temp = validParameter.validFile(parameters, "freq", false); if (temp == "not found") { temp = "100"; }
117 if (abort == false) {
119 string fileNameRoot = getRootName(globaldata->inputFileName);
120 format = globaldata->getFormat();
123 validCalculator = new ValidCalculators();
124 util = new SharedUtil();
126 for (i=0; i<Estimators.size(); i++) {
127 if (validCalculator->isValidCalculator("shared", Estimators[i]) == true) {
128 if (Estimators[i] == "sharedchao") {
129 cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+"shared.chao")));
130 }else if (Estimators[i] == "sharedsobs") {
131 cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(fileNameRoot+"shared.sobs")));
132 }else if (Estimators[i] == "sharedace") {
133 cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace")));
134 }else if (Estimators[i] == "jabund") {
135 cDisplays.push_back(new CollectDisplay(new JAbund(), new SharedOneColumnFile(fileNameRoot+"jabund")));
136 }else if (Estimators[i] == "sorabund") {
137 cDisplays.push_back(new CollectDisplay(new SorAbund(), new SharedOneColumnFile(fileNameRoot+"sorabund")));
138 }else if (Estimators[i] == "jclass") {
139 cDisplays.push_back(new CollectDisplay(new Jclass(), new SharedOneColumnFile(fileNameRoot+"jclass")));
140 }else if (Estimators[i] == "sorclass") {
141 cDisplays.push_back(new CollectDisplay(new SorClass(), new SharedOneColumnFile(fileNameRoot+"sorclass")));
142 }else if (Estimators[i] == "jest") {
143 cDisplays.push_back(new CollectDisplay(new Jest(), new SharedOneColumnFile(fileNameRoot+"jest")));
144 }else if (Estimators[i] == "sorest") {
145 cDisplays.push_back(new CollectDisplay(new SorEst(), new SharedOneColumnFile(fileNameRoot+"sorest")));
146 }else if (Estimators[i] == "thetayc") {
147 cDisplays.push_back(new CollectDisplay(new ThetaYC(), new SharedOneColumnFile(fileNameRoot+"thetayc")));
148 }else if (Estimators[i] == "thetan") {
149 cDisplays.push_back(new CollectDisplay(new ThetaN(), new SharedOneColumnFile(fileNameRoot+"thetan")));
150 }else if (Estimators[i] == "kstest") {
151 cDisplays.push_back(new CollectDisplay(new KSTest(), new SharedOneColumnFile(fileNameRoot+"kstest")));
152 }else if (Estimators[i] == "whittaker") {
153 cDisplays.push_back(new CollectDisplay(new Whittaker(), new SharedOneColumnFile(fileNameRoot+"whittaker")));
154 }else if (Estimators[i] == "sharednseqs") {
155 cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+"shared.nseqs")));
156 }else if (Estimators[i] == "ochiai") {
157 cDisplays.push_back(new CollectDisplay(new Ochiai(), new SharedOneColumnFile(fileNameRoot+"ochiai")));
158 }else if (Estimators[i] == "anderberg") {
159 cDisplays.push_back(new CollectDisplay(new Anderberg(), new SharedOneColumnFile(fileNameRoot+"anderberg")));
160 }else if (Estimators[i] == "skulczynski") {
161 cDisplays.push_back(new CollectDisplay(new Kulczynski(), new SharedOneColumnFile(fileNameRoot+"kulczynski")));
162 }else if (Estimators[i] == "kulczynskicody") {
163 cDisplays.push_back(new CollectDisplay(new KulczynskiCody(), new SharedOneColumnFile(fileNameRoot+"kulczynskicody")));
164 }else if (Estimators[i] == "lennon") {
165 cDisplays.push_back(new CollectDisplay(new Lennon(), new SharedOneColumnFile(fileNameRoot+"lennon")));
166 }else if (Estimators[i] == "morisitahorn") {
167 cDisplays.push_back(new CollectDisplay(new MorHorn(), new SharedOneColumnFile(fileNameRoot+"morisitahorn")));
168 }else if (Estimators[i] == "braycurtis") {
169 cDisplays.push_back(new CollectDisplay(new BrayCurtis(), new SharedOneColumnFile(fileNameRoot+"braycurtis")));
177 catch(exception& e) {
178 errorOut(e, "CollectSharedCommand", "CollectSharedCommand");
182 //**********************************************************************************************************************
184 void CollectSharedCommand::help(){
186 mothurOut("The collect.shared command can only be executed after a successful read.otu command.\n");
187 mothurOut("The collect.shared command parameters are label, line, freq, calc and groups. No parameters are required, but you may not use \n");
188 mothurOut("both the line and label parameters at the same time. The collect.shared command should be in the following format: \n");
189 mothurOut("collect.shared(label=yourLabel, line=yourLines, freq=yourFreq, calc=yourEstimators, groups=yourGroups).\n");
190 mothurOut("Example collect.shared(label=unique-.01-.03, line=0-5-10, freq=10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n");
191 mothurOut("The default values for freq is 100 and calc are sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan.\n");
192 mothurOut("The default value for groups is all the groups in your groupfile.\n");
193 validCalculator->printCalc("shared", cout);
194 mothurOut("The label and line parameters are used to analyze specific lines in your input.\n");
195 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");
196 mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
199 catch(exception& e) {
200 errorOut(e, "CollectSharedCommand", "help");
205 //**********************************************************************************************************************
207 CollectSharedCommand::~CollectSharedCommand(){
208 if (abort == false) {
209 delete input; globaldata->ginput = NULL;
212 delete validCalculator;
213 globaldata->gorder = NULL;
217 //**********************************************************************************************************************
219 int CollectSharedCommand::execute(){
222 if (abort == true) { return 0; }
226 //if the users entered no valid calculators don't execute command
227 if (cDisplays.size() == 0) { return 0; }
229 read = new ReadOTUFile(globaldata->inputFileName);
230 read->read(&*globaldata);
232 input = globaldata->ginput;
233 order = input->getSharedOrderVector();
234 string lastLabel = order->getLabel();
236 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
237 set<string> processedLabels;
238 set<string> userLabels = labels;
239 set<int> userLines = lines;
242 util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "collect");
243 util->updateGroupIndex(globaldata->Groups, globaldata->gGroupmap->groupIndex);
245 while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
247 if(allLines == 1 || lines.count(count) == 1 || labels.count(order->getLabel()) == 1){
249 //create collectors curve
250 cCurve = new Collect(order, cDisplays);
251 cCurve->getSharedCurve(freq);
254 mothurOut(order->getLabel() + "\t" + toString(count)); mothurOutEndLine();
255 processedLabels.insert(order->getLabel());
256 userLabels.erase(order->getLabel());
257 userLines.erase(count);
259 //you have a label the user want that is smaller than this line and the last line has not already been processed
262 if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
264 order = input->getSharedOrderVector(lastLabel);
266 //create collectors curve
267 cCurve = new Collect(order, cDisplays);
268 cCurve->getSharedCurve(freq);
271 mothurOut(order->getLabel() + "\t" + toString(count)); mothurOutEndLine();
272 processedLabels.insert(order->getLabel());
273 userLabels.erase(order->getLabel());
277 lastLabel = order->getLabel();
279 //get next line to process
281 order = input->getSharedOrderVector();
285 //output error messages about any remaining user labels
286 set<string>::iterator it;
287 bool needToRun = false;
288 for (it = userLabels.begin(); it != userLabels.end(); it++) {
289 mothurOut("Your file does not include the label " + *it);
290 if (processedLabels.count(lastLabel) != 1) {
291 mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
294 mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
298 //run last line if you need to
299 if (needToRun == true) {
301 order = input->getSharedOrderVector(lastLabel);
303 cCurve = new Collect(order, cDisplays);
304 cCurve->getCurve(freq);
307 mothurOut(order->getLabel() + "\t" + toString(count)); mothurOutEndLine();
311 for(int i=0;i<cDisplays.size();i++){ delete cDisplays[i]; }
313 //reset groups parameter
314 globaldata->Groups.clear();
318 catch(exception& e) {
319 errorOut(e, "CollectSharedCommand", "execute");
324 /***********************************************************/