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 cout << "You must read a list, or a list and a group, or a shared before you can use the venn command." << endl; 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 != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; 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 cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function VennCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
148 cout << "An unknown error has occurred in the VennCommand class function VennCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
153 //**********************************************************************************************************************
155 void VennCommand::help(){
157 cout << "The venn command can only be executed after a successful read.otu command." << "\n";
158 cout << "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";
159 cout << "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";
160 cout << "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";
161 cout << "The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, line=yourLines, label=yourLabels, abund=yourAbund)." << "\n";
162 cout << "Example venn(groups=A-B-C, line=1-3-5, calc=sharedsobs-sharedchao, abund=20)." << "\n";
163 cout << "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";
164 cout << "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";
165 cout << "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";
166 cout << "The only estmiator available four 4 groups is sharedsobs." << "\n";
167 cout << "The venn command outputs a .svg file for each calculator you specify at each distance you choose." << "\n";
168 cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
170 catch(exception& e) {
171 cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
175 cout << "An unknown error has occurred in the VennCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
181 //**********************************************************************************************************************
183 VennCommand::~VennCommand(){
184 if (abort == false) {
185 delete input; globaldata->ginput = NULL;
188 globaldata->sabund = NULL;
193 //**********************************************************************************************************************
195 int VennCommand::execute(){
198 if (abort == true) { return 0; }
201 SAbundVector* lastSAbund;
202 vector<SharedRAbundVector*> lastLookup;
204 //if the users entered no valid calculators don't execute command
205 if (vennCalculators.size() == 0) { return 0; }
207 if (format == "sharedfile") {
209 read = new ReadOTUFile(globaldata->inputFileName);
210 read->read(&*globaldata);
212 input = globaldata->ginput;
213 lookup = input->getSharedRAbundVectors();
215 }else if (format == "list") {
216 //you are using just a list file and have only one group
217 read = new ReadOTUFile(globaldata->inputFileName);
218 read->read(&*globaldata);
220 sabund = globaldata->sabund;
221 lastSAbund = globaldata->sabund;
222 input = globaldata->ginput;
225 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
226 set<string> processedLabels;
227 set<string> userLabels = labels;
228 set<int> userLines = lines;
230 if (format != "list") {
232 //as long as you are not at the end of the file or done wih the lines you want
233 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
235 if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
236 cout << lookup[0]->getLabel() << '\t' << count << endl;
237 processedLabels.insert(lookup[0]->getLabel());
238 userLabels.erase(lookup[0]->getLabel());
239 userLines.erase(count);
241 if (lookup.size() > 4) {
242 cout << "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." << endl;
243 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
245 venn->getPic(lookup, vennCalculators);
248 if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
249 cout << lastLookup[0]->getLabel() << '\t' << count << endl;
250 processedLabels.insert(lastLookup[0]->getLabel());
251 userLabels.erase(lastLookup[0]->getLabel());
253 if (lastLookup.size() > 4) {
254 cout << "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." << endl;
255 for (int i = lastLookup.size(); i > 4; i--) { lastLookup.pop_back(); } //no memmory leak because pop_back calls destructor
257 venn->getPic(lastLookup, vennCalculators);
260 //prevent memory leak
261 if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[i]; } }
264 //get next line to process
265 lookup = input->getSharedRAbundVectors();
269 //output error messages about any remaining user labels
270 set<string>::iterator it;
271 bool needToRun = false;
272 for (it = userLabels.begin(); it != userLabels.end(); it++) {
273 cout << "Your file does not include the label "<< *it;
274 if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
275 cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
278 cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
282 //run last line if you need to
283 if (needToRun == true) {
284 cout << lastLookup[0]->getLabel() << '\t' << count << endl;
285 if (lastLookup.size() > 4) {
286 cout << "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." << endl;
287 for (int i = lastLookup.size(); i > 3; i--) { delete lastLookup[i]; lastLookup.pop_back(); }
289 venn->getPic(lastLookup, vennCalculators);
292 for (int i = 0; i < lastLookup.size(); i++) { delete lastLookup[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 cout << sabund->getLabel() << '\t' << count << endl;
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(lastSAbund->getLabel()) != 1)) {
313 cout << lastSAbund->getLabel() << '\t' << count << endl;
314 venn->getPic(lastSAbund, vennCalculators);
316 processedLabels.insert(lastSAbund->getLabel());
317 userLabels.erase(lastSAbund->getLabel());
320 if (count != 1) { delete lastSAbund; }
323 sabund = input->getSAbundVector();
327 //output error messages about any remaining user labels
328 set<string>::iterator it;
329 bool needToRun = false;
330 for (it = userLabels.begin(); it != userLabels.end(); it++) {
331 cout << "Your file does not include the label "<< *it;
332 if (processedLabels.count(lastSAbund->getLabel()) != 1) {
333 cout << ". I will use " << lastSAbund->getLabel() << "." << endl;
336 cout << ". Please refer to " << lastSAbund->getLabel() << "." << endl;
340 //run last line if you need to
341 if (needToRun == true) {
342 cout << lastSAbund->getLabel() << '\t' << count << endl;
343 venn->getPic(lastSAbund, vennCalculators);
348 for (int i = 0; i < vennCalculators.size(); i++) { delete vennCalculators[i]; }
351 catch(exception& e) {
352 cout << "Standard Error: " << e.what() << " has occurred in the VennCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
356 cout << "An unknown error has occurred in the VennCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
361 //**********************************************************************************************************************