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++) {
71 //create and initialize vector of sharedvectors, one for each group
72 for (int i = 0; i < Groups.size(); i++) {
73 SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins());
74 temp->setLabel(order->getLabel());
75 temp->setGroup(Groups[i]);
76 lookup.push_back(temp);
79 int numSeqs = order->size();
81 //sample all the members
82 for(int i=0;i<numSeqs;i++){
84 int random = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
85 individual chosen = order->get(random);
88 //set info for sharedvector in chosens group
89 for (int j = 0; j < lookup.size(); j++) {
90 if (chosen.group == lookup[j]->getGroup()) {
91 abundance = lookup[j]->getAbundance(chosen.bin);
92 lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
100 cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function getSharedVectorswithReplacement. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
104 cout << "An unknown error has occurred in the SharedUtil class function getSharedVectorswithReplacement. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
109 /**************************************************************************************************/
110 //need to have mode because different commands require different number of valid groups
111 void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups) {
113 if (userGroups.size() != 0) {
114 if (userGroups[0] != "all") {
115 //check that groups are valid
116 for (int i = 0; i < userGroups.size(); i++) {
117 if (isValidGroup(userGroups[i], allGroups) != true) {
118 cout << userGroups[i] << " is not a valid group, and will be disregarded." << endl;
119 // erase the invalid group from userGroups
120 userGroups.erase(userGroups.begin()+i);
125 //if the user only entered invalid groups
126 if (userGroups.size() == 0) {
127 cout << "You provided no valid groups. I will run the command using all the groups in your groupfile." << endl;
128 for (int i = 0; i < allGroups.size(); i++) {
129 userGroups.push_back(allGroups[i]);
133 }else{//user has enter "all" and wants the default groups
135 for (int i = 0; i < allGroups.size(); i++) {
136 userGroups.push_back(allGroups[i]);
139 }else { //the user has not entered groups
140 for (int i = 0; i < allGroups.size(); i++) {
141 userGroups.push_back(allGroups[i]);
146 catch(exception& e) {
147 cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
151 cout << "An unknown error has occurred in the SharedUtil class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
156 /**************************************************************************************************/
157 //need to have mode because different commands require different number of valid groups
158 void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups, string mode) {
160 if (userGroups.size() != 0) {
161 if (userGroups[0] != "all") {
162 //check that groups are valid
163 for (int i = 0; i < userGroups.size(); i++) {
164 if (isValidGroup(userGroups[i], allGroups) != true) {
165 cout << userGroups[i] << " is not a valid group, and will be disregarded." << endl;
166 // erase the invalid group from userGroups
167 userGroups.erase(userGroups.begin()+i);
172 }else{//user has enter "all" and wants the default groups
174 for (int i = 0; i < allGroups.size(); i++) {
175 userGroups.push_back(allGroups[i]);
178 }else { //the user has not entered groups
179 for (int i = 0; i < allGroups.size(); i++) {
180 userGroups.push_back(allGroups[i]);
184 if ((mode == "collect") || (mode == "rarefact") || (mode == "summary") || (mode == "treegroup")) {
185 //if the user only entered invalid groups
186 if ((userGroups.size() == 0) || (userGroups.size() == 1)) {
187 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;
188 for (int i = 0; i < allGroups.size(); i++) {
189 userGroups.push_back(allGroups[i]);
195 catch(exception& e) {
196 cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
200 cout << "An unknown error has occurred in the SharedUtil class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
207 /**************************************************************************************/
208 //for parsimony and unifrac commands you set pairwise groups as well as an allgroups in calc
209 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";