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();
29 //allow user to run help
30 if(option == "help") { help(); abort = true; }
33 //valid paramters for this command
34 string AlignArray[] = {"groups","label","calc", "abund"};
35 vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
37 OptionParser parser(option);
38 map<string,string> parameters = parser.getParameters();
40 ValidParameters validParameter;
42 //check to make sure all parameters are valid for command
43 for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
44 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
47 //make sure the user has already run the read.otu command
48 if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
49 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;
52 //check for optional parameter and set defaults
53 // ...at some point should added some additional type checking...
54 label = validParameter.validFile(parameters, "label", false);
55 if (label == "not found") { label = ""; }
57 if(label != "all") { splitAtDash(label, labels); allLines = 0; }
58 else { allLines = 1; }
61 //if the user has not specified any labels use the ones from read.otu
63 allLines = globaldata->allLines;
64 labels = globaldata->labels;
67 groups = validParameter.validFile(parameters, "groups", false);
68 if (groups == "not found") { groups = ""; }
70 splitAtDash(groups, Groups);
71 globaldata->Groups = Groups;
74 format = globaldata->getFormat();
75 calc = validParameter.validFile(parameters, "calc", false);
76 if (calc == "not found") {
77 if(format == "list") { calc = "sobs"; }
78 else { calc = "sharedsobs"; }
81 if (calc == "default") {
82 if(format == "list") { calc = "sobs"; }
83 else { calc = "sharedsobs"; }
86 splitAtDash(calc, Estimators);
89 temp = validParameter.validFile(parameters, "abund", false); if (temp == "not found") { temp = "10"; }
93 validCalculator = new ValidCalculators();
97 if (format == "list") {
98 for (i=0; i<Estimators.size(); i++) {
99 if (validCalculator->isValidCalculator("vennsingle", Estimators[i]) == true) {
100 if (Estimators[i] == "sobs") {
101 vennCalculators.push_back(new Sobs());
102 }else if (Estimators[i] == "chao") {
103 vennCalculators.push_back(new Chao1());
104 }else if (Estimators[i] == "ace") {
107 vennCalculators.push_back(new Ace(abund));
112 for (i=0; i<Estimators.size(); i++) {
113 if (validCalculator->isValidCalculator("vennshared", Estimators[i]) == true) {
114 if (Estimators[i] == "sharedsobs") {
115 vennCalculators.push_back(new SharedSobsCS());
116 }else if (Estimators[i] == "sharedchao") {
117 vennCalculators.push_back(new SharedChao1());
118 }else if (Estimators[i] == "sharedace") {
119 vennCalculators.push_back(new SharedAce());
132 catch(exception& e) {
133 errorOut(e, "VennCommand", "VennCommand");
138 //**********************************************************************************************************************
140 void VennCommand::help(){
142 mothurOut("The venn command can only be executed after a successful read.otu command.\n");
143 mothurOut("The venn command parameters are groups, calc, abund and label. No parameters are required.\n");
144 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");
145 mothurOut("The group names are separated by dashes. The label allows you to select what distance levels you would like a venn diagram created for, and are also separated by dashes.\n");
146 mothurOut("The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, label=yourLabels, abund=yourAbund).\n");
147 mothurOut("Example venn(groups=A-B-C, calc=sharedsobs-sharedchao, abund=20).\n");
148 mothurOut("The default value for groups is all the groups in your groupfile up to 4, and all labels in your inputfile will be used.\n");
149 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");
150 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");
151 mothurOut("The only estmiator available four 4 groups is sharedsobs.\n");
152 mothurOut("The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n");
153 mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
155 catch(exception& e) {
156 errorOut(e, "VennCommand", "help");
162 //**********************************************************************************************************************
164 VennCommand::~VennCommand(){
165 if (abort == false) {
166 delete input; globaldata->ginput = NULL;
169 globaldata->sabund = NULL;
174 //**********************************************************************************************************************
176 int VennCommand::execute(){
179 if (abort == true) { return 0; }
183 //if the users entered no valid calculators don't execute command
184 if (vennCalculators.size() == 0) { return 0; }
186 if (format == "sharedfile") {
188 read = new ReadOTUFile(globaldata->inputFileName);
189 read->read(&*globaldata);
191 input = globaldata->ginput;
192 lookup = input->getSharedRAbundVectors();
193 lastLabel = lookup[0]->getLabel();
194 }else if (format == "list") {
195 //you are using just a list file and have only one group
196 read = new ReadOTUFile(globaldata->inputFileName);
197 read->read(&*globaldata);
199 sabund = globaldata->sabund;
200 lastLabel = sabund->getLabel();
201 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 if (format != "list") {
210 //as long as you are not at the end of the file or done wih the lines you want
211 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
213 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
214 mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
215 processedLabels.insert(lookup[0]->getLabel());
216 userLabels.erase(lookup[0]->getLabel());
218 if (lookup.size() > 4) {
219 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();
220 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
222 venn->getPic(lookup, vennCalculators);
225 if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
226 string saveLabel = lookup[0]->getLabel();
228 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
229 lookup = input->getSharedRAbundVectors(lastLabel);
231 mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
232 processedLabels.insert(lookup[0]->getLabel());
233 userLabels.erase(lookup[0]->getLabel());
235 if (lookup.size() > 4) {
236 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();
237 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
239 venn->getPic(lookup, vennCalculators);
241 //restore real lastlabel to save below
242 lookup[0]->setLabel(saveLabel);
246 lastLabel = lookup[0]->getLabel();
248 //get next line to process
249 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
250 lookup = input->getSharedRAbundVectors();
253 //output error messages about any remaining user labels
254 set<string>::iterator it;
255 bool needToRun = false;
256 for (it = userLabels.begin(); it != userLabels.end(); it++) {
257 mothurOut("Your file does not include the label " + *it);
258 if (processedLabels.count(lastLabel) != 1) {
259 mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
262 mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
266 //run last label if you need to
267 if (needToRun == true) {
268 for (int i = 0; i < lookup.size(); i++) { if (lookup[i] != NULL) { delete lookup[i]; } }
269 lookup = input->getSharedRAbundVectors(lastLabel);
271 mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
272 processedLabels.insert(lookup[0]->getLabel());
273 userLabels.erase(lookup[0]->getLabel());
275 if (lookup.size() > 4) {
276 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();
277 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
279 venn->getPic(lookup, vennCalculators);
280 for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
284 //reset groups parameter
285 globaldata->Groups.clear();
289 while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
291 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
293 mothurOut(sabund->getLabel()); mothurOutEndLine();
294 venn->getPic(sabund, vennCalculators);
296 processedLabels.insert(sabund->getLabel());
297 userLabels.erase(sabund->getLabel());
300 if ((anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
301 string saveLabel = sabund->getLabel();
304 sabund = input->getSAbundVector(lastLabel);
306 mothurOut(sabund->getLabel()); mothurOutEndLine();
307 venn->getPic(sabund, vennCalculators);
309 processedLabels.insert(sabund->getLabel());
310 userLabels.erase(sabund->getLabel());
312 //restore real lastlabel to save below
313 sabund->setLabel(saveLabel);
316 lastLabel = sabund->getLabel();
319 sabund = input->getSAbundVector();
322 //output error messages about any remaining user labels
323 set<string>::iterator it;
324 bool needToRun = false;
325 for (it = userLabels.begin(); it != userLabels.end(); it++) {
326 mothurOut("Your file does not include the label " + *it);
327 if (processedLabels.count(lastLabel) != 1) {
328 mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
331 mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
335 //run last label if you need to
336 if (needToRun == true) {
337 if (sabund != NULL) { delete sabund; }
338 sabund = input->getSAbundVector(lastLabel);
340 mothurOut(sabund->getLabel()); mothurOutEndLine();
341 venn->getPic(sabund, vennCalculators);
348 for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
351 catch(exception& e) {
352 errorOut(e, "VennCommand", "execute");
357 //**********************************************************************************************************************