5 * Created by Sarah Westcott on 4/9/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "sharedutilities.h"
11 #include "sharedrabundvector.h"
12 #include "sharedordervector.h"
14 /**************************************************************************************************/
16 void SharedUtil::getSharedVectors(vector<string> Groups, vector<SharedRAbundVector*>& lookup, SharedOrderVector* order) {
19 //delete each sharedrabundvector in lookup
20 for (int j = 0; j < lookup.size(); j++) {
26 //create and initialize vector of sharedvectors, one for each group
27 for (int i = 0; i < Groups.size(); i++) {
28 SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins());
29 temp->setLabel(order->getLabel());
30 temp->setGroup(Groups[i]);
31 lookup.push_back(temp);
34 int numSeqs = order->size();
35 //sample all the members
36 for(int i=0;i<numSeqs;i++){
38 individual chosen = order->get(i);
41 //set info for sharedvector in chosens group
42 for (int j = 0; j < lookup.size(); j++) {
43 if (chosen.group == lookup[j]->getGroup()) {
44 abundance = lookup[j]->getAbundance(chosen.bin);
45 lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
52 cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
56 cout << "An unknown error has occurred in the SharedUtil class function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
60 /**************************************************************************************************/
62 void SharedUtil::getSharedVectorswithReplacement(vector<string> Groups, vector<SharedRAbundVector*>& lookup, SharedOrderVector* order) {
65 //delete each sharedrabundvector in lookup
66 for (int j = 0; j < lookup.size(); j++) {
72 //create and initialize vector of sharedvectors, one for each group
73 for (int i = 0; i < Groups.size(); i++) {
74 SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins());
75 temp->setLabel(order->getLabel());
76 temp->setGroup(Groups[i]);
77 lookup.push_back(temp);
80 int numSeqs = order->size();
82 //sample all the members
83 for(int i=0;i<numSeqs;i++){
85 int random = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
86 individual chosen = order->get(random);
89 //set info for sharedvector in chosens group
90 for (int j = 0; j < lookup.size(); j++) {
91 if (chosen.group == lookup[j]->getGroup()) {
92 abundance = lookup[j]->getAbundance(chosen.bin);
93 lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
100 catch(exception& e) {
101 cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function getSharedVectorswithReplacement. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
105 cout << "An unknown error has occurred in the SharedUtil class function getSharedVectorswithReplacement. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
110 /**************************************************************************************************/
111 //need to have mode because different commands require different number of valid groups
112 void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups) {
114 if (userGroups.size() != 0) {
115 if (userGroups[0] != "all") {
116 //check that groups are valid
117 for (int i = 0; i < userGroups.size(); i++) {
118 if (isValidGroup(userGroups[i], allGroups) != true) {
119 cout << userGroups[i] << " is not a valid group, and will be disregarded." << endl;
120 // erase the invalid group from userGroups
121 userGroups.erase(userGroups.begin()+i);
126 //if the user only entered invalid groups
127 if (userGroups.size() == 0) {
128 cout << "You provided no valid groups. I will run the command using all the groups in your groupfile." << endl;
129 for (int i = 0; i < allGroups.size(); i++) {
130 userGroups.push_back(allGroups[i]);
134 }else{//user has enter "all" and wants the default groups
136 for (int i = 0; i < allGroups.size(); i++) {
137 userGroups.push_back(allGroups[i]);
140 }else { //the user has not entered groups
141 for (int i = 0; i < allGroups.size(); i++) {
142 userGroups.push_back(allGroups[i]);
147 catch(exception& e) {
148 cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
152 cout << "An unknown error has occurred in the SharedUtil class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
157 /**************************************************************************************************/
158 //need to have mode because different commands require different number of valid groups
159 void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups, string mode) {
161 if (userGroups.size() != 0) {
162 if (userGroups[0] != "all") {
163 //check that groups are valid
164 for (int i = 0; i < userGroups.size(); i++) {
165 if (isValidGroup(userGroups[i], allGroups) != true) {
166 cout << userGroups[i] << " is not a valid group, and will be disregarded." << endl;
167 // erase the invalid group from userGroups
168 userGroups.erase(userGroups.begin()+i);
173 }else{//user has enter "all" and wants the default groups
175 for (int i = 0; i < allGroups.size(); i++) {
176 userGroups.push_back(allGroups[i]);
179 }else { //the user has not entered groups
180 for (int i = 0; i < allGroups.size(); i++) {
181 userGroups.push_back(allGroups[i]);
185 if ((mode == "collect") || (mode == "rarefact") || (mode == "summary") || (mode == "treegroup")) {
186 //if the user only entered invalid groups
187 if ((userGroups.size() == 0) || (userGroups.size() == 1)) {
188 cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
189 for (int i = 0; i < allGroups.size(); i++) {
190 userGroups.push_back(allGroups[i]);
196 catch(exception& e) {
197 cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
201 cout << "An unknown error has occurred in the SharedUtil class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
208 /**************************************************************************************/
209 //for parsimony and unifrac commands you set pairwise groups as well as an allgroups in calc
210 void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups, string& label, int& numGroups, string mode){ //globaldata->Groups, your tree or group map, allgroups, mode
214 //if the user has not entered specific groups to analyze then do them all
215 if (userGroups.size() != 0) {
216 if (userGroups[0] != "all") {
217 //check that groups are valid
218 for (int i = 0; i < userGroups.size(); i++) {
219 if (isValidGroup(userGroups[i], allGroups) != true) {
220 cout << userGroups[i] << " is not a valid group, and will be disregarded." << endl;
221 // erase the invalid group from globaldata->Groups
222 userGroups.erase(userGroups.begin()+i);
226 }else { //users wants all groups
228 for (int i=0; i < allGroups.size(); i++) {
229 if (allGroups[i] != "xxx") {
230 userGroups.push_back(allGroups[i]);
234 }else { //the user has not entered groups
235 for (int i=0; i < allGroups.size(); i++) {
236 if (allGroups[i] != "xxx") {
237 if (mode == "weighted") {
238 userGroups.push_back(allGroups[i]);
241 label += allGroups[i] + "-";
245 //rip extra - off allgroups
246 label = label.substr(0, label.length()-1);
249 if (mode == "weighted") {
250 //if the user only entered invalid groups
251 if (userGroups.size() == 0) {
252 for (int i=0; i < allGroups.size(); i++) {
253 if (allGroups[i] != "xxx") {
254 userGroups.push_back(allGroups[i]);
257 cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
258 }else if (userGroups.size() == 1) {
259 cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
261 for (int i=0; i < allGroups.size(); i++) {
262 if (allGroups[i] != "xxx") {
263 userGroups.push_back(allGroups[i]);
267 numGroups = userGroups.size();
269 }else if ((mode == "unweighted") || (mode == "parsimony")) {
270 //if the user only entered invalid groups
271 if ((userGroups.size() == 0) && (numGroups == 0)) {
272 cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile." << endl;
273 for (int i = 0; i < allGroups.size(); i++) {
274 if (allGroups[i] != "xxx") {
275 userGroups.push_back(allGroups[i]);
280 if (numGroups != 1) { numGroups = userGroups.size(); }
283 catch(exception& e) {
284 cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
288 cout << "An unknown error has occurred in the SharedUtil class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
292 /**************************************************************************************/
293 void SharedUtil::getCombos(vector<string>& groupComb, vector<string> userGroups, int& numComp) { //groupcomb, globaldata->Groups, numcomb
295 //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
297 for (int i=0; i< userGroups.size(); i++) {
299 for (int l = i+1; l < userGroups.size(); l++) {
300 //set group comparison labels
301 groupComb.push_back(userGroups[i] + "-" + userGroups[l]);
305 catch(exception& e) {
306 cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function getCombos. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
310 cout << "An unknown error has occurred in the SharedUtil class function getCombos. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
314 /**************************************************************************************/
315 bool SharedUtil::isValidGroup(string groupname, vector<string> groups) {
317 for (int i = 0; i < groups.size(); i++) {
318 if (groupname == groups[i]) { return true; }
323 catch(exception& e) {
324 cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function isValidGroup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
328 cout << "An unknown error has occurred in the SharedUtil class function isValidGroup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
333 /**************************************************************************************/
334 void SharedUtil::updateGroupIndex(vector<string>& userGroups, map<string, int>& index) {
337 for (int i = 0; i < userGroups.size(); i++) {
338 index[userGroups[i]] = i;
341 catch(exception& e) {
342 cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function updateGroupIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
346 cout << "An unknown error has occurred in the SharedUtil class function updateGroupIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";