5 * Created by Sarah Westcott on 3/30/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "venncommand.h"
14 //#include "jackknife.h"
15 #include "sharedsobscollectsummary.h"
16 #include "sharedchao1.h"
17 #include "sharedace.h"
20 //**********************************************************************************************************************
22 VennCommand::VennCommand(string option){
24 globaldata = GlobalData::getInstance();
30 //allow user to run help
31 if(option == "help") { help(); abort = true; }
34 //valid paramters for this command
35 string AlignArray[] = {"groups","line","label","calc", "abund"};
36 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
38 OptionParser parser(option);
39 map<string,string> parameters = parser.getParameters();
41 ValidParameters validParameter;
43 //check to make sure all parameters are valid for command
44 for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
45 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
48 //make sure the user has already run the read.otu command
49 if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
50 mothurOut("You must read a list, or a list and a group, or a shared before you can use the venn command."); mothurOutEndLine(); abort = true;
53 //check for optional parameter and set defaults
54 // ...at some point should added some additional type checking...
55 line = validParameter.validFile(parameters, "line", false);
56 if (line == "not found") { line = ""; }
58 if(line != "all") { splitAtDash(line, lines); allLines = 0; }
59 else { allLines = 1; }
62 label = validParameter.validFile(parameters, "label", false);
63 if (label == "not found") { label = ""; }
65 if(label != "all") { splitAtDash(label, labels); allLines = 0; }
66 else { allLines = 1; }
69 //make sure user did not use both the line and label parameters
70 if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; }
71 //if the user has not specified any line or labels use the ones from read.otu
72 else if ((line == "") && (label == "")) {
73 allLines = globaldata->allLines;
74 labels = globaldata->labels;
75 lines = globaldata->lines;
78 groups = validParameter.validFile(parameters, "groups", false);
79 if (groups == "not found") { groups = ""; }
81 splitAtDash(groups, Groups);
82 globaldata->Groups = Groups;
85 format = globaldata->getFormat();
86 calc = validParameter.validFile(parameters, "calc", false);
87 if (calc == "not found") {
88 if(format == "list") { calc = "sobs"; }
89 else { calc = "sharedsobs"; }
92 if (calc == "default") {
93 if(format == "list") { calc = "sobs"; }
94 else { calc = "sharedsobs"; }
97 splitAtDash(calc, Estimators);
100 temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
101 convert(temp, abund);
103 if (abort == false) {
104 validCalculator = new ValidCalculators();
108 if (format == "list") {
109 for (i=0; i<Estimators.size(); i++) {
110 if (validCalculator->isValidCalculator("vennsingle", Estimators[i]) == true) {
111 if (Estimators[i] == "sobs") {
112 vennCalculators.push_back(new Sobs());
113 }else if (Estimators[i] == "chao") {
114 vennCalculators.push_back(new Chao1());
115 }else if (Estimators[i] == "ace") {
118 vennCalculators.push_back(new Ace(abund));
123 for (i=0; i<Estimators.size(); i++) {
124 if (validCalculator->isValidCalculator("vennshared", Estimators[i]) == true) {
125 if (Estimators[i] == "sharedsobs") {
126 vennCalculators.push_back(new SharedSobsCS());
127 }else if (Estimators[i] == "sharedchao") {
128 vennCalculators.push_back(new SharedChao1());
129 }else if (Estimators[i] == "sharedace") {
130 vennCalculators.push_back(new SharedAce());
143 catch(exception& e) {
144 errorOut(e, "VennCommand", "VennCommand");
149 //**********************************************************************************************************************
151 void VennCommand::help(){
153 mothurOut("The venn command can only be executed after a successful read.otu command.\n");
154 mothurOut("The venn command parameters are groups, calc, abund, line and label. No parameters are required, but you may not use line and label at the same time.\n");
155 mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included in your venn diagram, you may only use a maximum of 4 groups.\n");
156 mothurOut("The group names are separated by dashes. The line and label allow you to select what distance levels you would like a venn diagram created for, and are also separated by dashes.\n");
157 mothurOut("The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels, abund=yourAbund).\n");
158 mothurOut("Example venn(groups=A-B-C, line=1-3-5, calc=sharedsobs-sharedchao, abund=20).\n");
159 mothurOut("The default value for groups is all the groups in your groupfile up to 4, and all lines in your inputfile will be used.\n");
160 mothurOut("The default value for calc is sobs if you have only read a list file or if you have selected only one group, and sharedsobs if you have multiple groups.\n");
161 mothurOut("The default available estimators for calc are sobs, chao and ace if you have only read a list file, and sharedsobs, sharedchao and sharedace if you have read a list and group file or a shared file.\n");
162 mothurOut("The only estmiator available four 4 groups is sharedsobs.\n");
163 mothurOut("The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n");
164 mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
166 catch(exception& e) {
167 errorOut(e, "VennCommand", "help");
173 //**********************************************************************************************************************
175 VennCommand::~VennCommand(){
176 if (abort == false) {
177 delete input; globaldata->ginput = NULL;
180 globaldata->sabund = NULL;
185 //**********************************************************************************************************************
187 int VennCommand::execute(){
190 if (abort == true) { return 0; }
195 //if the users entered no valid calculators don't execute command
196 if (vennCalculators.size() == 0) { return 0; }
198 if (format == "sharedfile") {
200 read = new ReadOTUFile(globaldata->inputFileName);
201 read->read(&*globaldata);
203 input = globaldata->ginput;
204 lookup = input->getSharedRAbundVectors();
205 lastLabel = lookup[0]->getLabel();
206 }else if (format == "list") {
207 //you are using just a list file and have only one group
208 read = new ReadOTUFile(globaldata->inputFileName);
209 read->read(&*globaldata);
211 sabund = globaldata->sabund;
212 lastLabel = sabund->getLabel();
213 input = globaldata->ginput;
216 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
217 set<string> processedLabels;
218 set<string> userLabels = labels;
219 set<int> userLines = lines;
221 if (format != "list") {
223 //as long as you are not at the end of the file or done wih the lines you want
224 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
226 if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
227 mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
228 processedLabels.insert(lookup[0]->getLabel());
229 userLabels.erase(lookup[0]->getLabel());
230 userLines.erase(count);
232 if (lookup.size() > 4) {
233 mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile."); mothurOutEndLine();
234 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
236 venn->getPic(lookup, vennCalculators);
239 if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
240 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
241 lookup = input->getSharedRAbundVectors(lastLabel);
243 mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
244 processedLabels.insert(lookup[0]->getLabel());
245 userLabels.erase(lookup[0]->getLabel());
247 if (lookup.size() > 4) {
248 mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile."); mothurOutEndLine();
249 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
251 venn->getPic(lookup, vennCalculators);
255 lastLabel = lookup[0]->getLabel();
257 //get next line to process
258 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
259 lookup = input->getSharedRAbundVectors();
263 //output error messages about any remaining user labels
264 set<string>::iterator it;
265 bool needToRun = false;
266 for (it = userLabels.begin(); it != userLabels.end(); it++) {
267 mothurOut("Your file does not include the label " + *it);
268 if (processedLabels.count(lastLabel) != 1) {
269 mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
272 mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
276 //run last line if you need to
277 if (needToRun == true) {
278 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
279 lookup = input->getSharedRAbundVectors(lastLabel);
281 mothurOut(lookup[0]->getLabel() + "\t" + toString(count)); mothurOutEndLine();
282 processedLabels.insert(lookup[0]->getLabel());
283 userLabels.erase(lookup[0]->getLabel());
285 if (lookup.size() > 4) {
286 mothurOut("Error: Too many groups chosen. You may use up to 4 groups with the venn command. I will use the first four groups in your groupfile."); mothurOutEndLine();
287 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
289 venn->getPic(lookup, vennCalculators);
290 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
294 //reset groups parameter
295 globaldata->Groups.clear();
299 while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
301 if(allLines == 1 || lines.count(count) == 1 || labels.count(sabund->getLabel()) == 1){
303 mothurOut(sabund->getLabel() + "\t" + toString(count)); mothurOutEndLine();
304 venn->getPic(sabund, vennCalculators);
306 processedLabels.insert(sabund->getLabel());
307 userLabels.erase(sabund->getLabel());
308 userLines.erase(count);
311 if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
313 sabund = input->getSAbundVector(lastLabel);
315 mothurOut(sabund->getLabel() + "\t" + toString(count)); mothurOutEndLine();
316 venn->getPic(sabund, vennCalculators);
318 processedLabels.insert(sabund->getLabel());
319 userLabels.erase(sabund->getLabel());
322 lastLabel = sabund->getLabel();
325 sabund = input->getSAbundVector();
329 //output error messages about any remaining user labels
330 set<string>::iterator it;
331 bool needToRun = false;
332 for (it = userLabels.begin(); it != userLabels.end(); it++) {
333 mothurOut("Your file does not include the label " + *it);
334 if (processedLabels.count(lastLabel) != 1) {
335 mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
338 mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
342 //run last line if you need to
343 if (needToRun == true) {
345 sabund = input->getSAbundVector(lastLabel);
347 mothurOut(sabund->getLabel() + "\t" + toString(count)); mothurOutEndLine();
348 venn->getPic(sabund, vennCalculators);
355 for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
358 catch(exception& e) {
359 errorOut(e, "VennCommand", "execute");
364 //**********************************************************************************************************************