2 * rarefactsharedcommand.cpp
5 * Created by Sarah Westcott on 1/6/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "rarefactsharedcommand.h"
11 #include "sharedsobs.h"
12 #include "sharednseqs.h"
14 //**********************************************************************************************************************
16 RareFactSharedCommand::RareFactSharedCommand(string option){
18 globaldata = GlobalData::getInstance();
27 //allow user to run help
28 if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
31 //valid paramters for this command
32 string Array[] = {"iters","line","label","calc","groups", "jumble"};
33 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
35 OptionParser parser(option);
36 map<string,string> parameters = parser.getParameters();
38 ValidParameters validParameter;
40 //check to make sure all parameters are valid for command
41 for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
42 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
45 //make sure the user has already run the read.otu command
46 if (globaldata->getSharedFile() == "") {
47 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; }
48 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; }
52 //check for optional parameter and set defaults
53 // ...at some point should added some additional type checking...
54 line = validParameter.validFile(parameters, "line", false);
55 if (line == "not found") { line = ""; }
57 if(line != "all") { splitAtDash(line, lines); allLines = 0; }
58 else { allLines = 1; }
61 label = validParameter.validFile(parameters, "label", false);
62 if (label == "not found") { label = ""; }
64 if(label != "all") { splitAtDash(label, labels); allLines = 0; }
65 else { allLines = 1; }
68 //make sure user did not use both the line and label parameters
69 if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; }
70 //if the user has not specified any line or labels use the ones from read.otu
71 else if((line == "") && (label == "")) {
72 allLines = globaldata->allLines;
73 labels = globaldata->labels;
74 lines = globaldata->lines;
77 calc = validParameter.validFile(parameters, "calc", false);
78 if (calc == "not found") { calc = "sharedobserved"; }
80 if (calc == "default") { calc = "sharedobserved"; }
82 splitAtDash(calc, Estimators);
84 groups = validParameter.validFile(parameters, "groups", false);
85 if (groups == "not found") { groups = ""; }
87 splitAtDash(groups, Groups);
89 globaldata->Groups = Groups;
92 temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
93 convert(temp, nIters);
95 temp = validParameter.validFile(parameters, "jumble", false); if (temp == "not found") { temp = "T"; }
96 if (isTrue(temp)) { jumble = true; }
97 else { jumble = false; }
98 globaldata->jumble = jumble;
100 if (abort == false) {
102 string fileNameRoot = getRootName(globaldata->inputFileName);
103 // format = globaldata->getFormat();
106 validCalculator = new ValidCalculators();
108 for (int i=0; i<Estimators.size(); i++) {
109 if (validCalculator->isValidCalculator("sharedrarefaction", Estimators[i]) == true) {
110 if (Estimators[i] == "sharedobserved") {
111 rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
112 }else if (Estimators[i] == "sharednseqs") {
113 rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.r_nseqs", "")));
122 catch(exception& e) {
123 errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand");
128 //**********************************************************************************************************************
130 void RareFactSharedCommand::help(){
132 mothurOut("The rarefaction.shared command can only be executed after a successful read.otu command.\n");
133 mothurOut("The rarefaction.shared command parameters are label, line, iters, groups, jumble and calc. No parameters are required, but you may not use \n");
134 mothurOut("both the line and label parameters at the same time. The rarefaction command should be in the following format: \n");
135 mothurOut("rarefaction.shared(label=yourLabel, line=yourLines, iters=yourIters, calc=yourEstimators, jumble=yourJumble, groups=yourGroups).\n");
136 mothurOut("Example rarefaction.shared(label=unique-.01-.03, line=0-5-10, iters=10000, groups=B-C, jumble=T, calc=sharedobserved).\n");
137 mothurOut("The default values for iters is 1000, freq is 100, and calc is sharedobserved which calculates the shared rarefaction curve for the observed richness.\n");
138 mothurOut("The default value for groups is all the groups in your groupfile, and jumble is true.\n");
139 validCalculator->printCalc("sharedrarefaction", cout);
140 mothurOut("The label and line parameters are used to analyze specific lines in your input.\n");
141 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");
142 mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n");
144 catch(exception& e) {
145 errorOut(e, "RareFactSharedCommand", "help");
150 //**********************************************************************************************************************
152 RareFactSharedCommand::~RareFactSharedCommand(){
153 if (abort == false) {
154 delete input; globaldata->ginput = NULL;
156 delete validCalculator;
160 //**********************************************************************************************************************
162 int RareFactSharedCommand::execute(){
165 if (abort == true) { return 0; }
169 //if the users entered no valid calculators don't execute command
170 if (rDisplays.size() == 0) { return 0; }
172 read = new ReadOTUFile(globaldata->inputFileName);
173 read->read(&*globaldata);
175 input = globaldata->ginput;
176 lookup = input->getSharedRAbundVectors();
177 string lastLabel = lookup[0]->getLabel();
179 if (lookup.size() < 2) {
180 mothurOut("I cannot run the command without at least 2 valid groups.");
181 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
185 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
186 set<string> processedLabels;
187 set<string> userLabels = labels;
188 set<int> userLines = lines;
190 //as long as you are not at the end of the file or done wih the lines you want
191 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
193 if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
195 rCurve = new Rarefact(lookup, rDisplays);
196 rCurve->getSharedCurve(freq, nIters);
199 mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
200 processedLabels.insert(lookup[0]->getLabel());
201 userLabels.erase(lookup[0]->getLabel());
202 userLines.erase(count);
205 if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
206 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
207 lookup = input->getSharedRAbundVectors(lastLabel);
209 mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
210 rCurve = new Rarefact(lookup, rDisplays);
211 rCurve->getSharedCurve(freq, nIters);
214 processedLabels.insert(lookup[0]->getLabel());
215 userLabels.erase(lookup[0]->getLabel());
219 lastLabel = lookup[0]->getLabel();
221 //get next line to process
222 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
223 lookup = input->getSharedRAbundVectors();
227 //output error messages about any remaining user labels
228 set<string>::iterator it;
229 bool needToRun = false;
230 for (it = userLabels.begin(); it != userLabels.end(); it++) {
231 mothurOut("Your file does not include the label " + *it);
232 if (processedLabels.count(lastLabel) != 1) {
233 mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
236 mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
240 //run last line if you need to
241 if (needToRun == true) {
242 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
243 lookup = input->getSharedRAbundVectors(lastLabel);
245 mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
246 rCurve = new Rarefact(lookup, rDisplays);
247 rCurve->getSharedCurve(freq, nIters);
249 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
252 for(int i=0;i<rDisplays.size();i++){ delete rDisplays[i]; }
254 //reset groups parameter
255 globaldata->Groups.clear();
259 catch(exception& e) {
260 errorOut(e, "RareFactSharedCommand", "execute");
266 //**********************************************************************************************************************