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, string mode) {
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 }else{//user has enter "all" and wants the default groups
128 for (int i = 0; i < allGroups.size(); i++) {
129 userGroups.push_back(allGroups[i]);
132 }else { //the user has not entered groups
133 for (int i = 0; i < allGroups.size(); i++) {
134 userGroups.push_back(allGroups[i]);
138 if (mode == "venn") {
139 //if the user only entered invalid groups
140 if (userGroups.size() == 0) {
141 if (allGroups.size() > 4) {
142 cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using the first four groups in your groupfile." << endl;
143 for (int i = 0; i < 4; i++) {
144 userGroups.push_back(allGroups[i]);
147 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;
148 for (int i = 0; i < allGroups.size(); i++) {
149 userGroups.push_back(allGroups[i]);
154 //check to make sure their are only 4 groups
155 if (userGroups.size() > 4) {
156 cout << "You may only use up to 4 groups at a time with this command. I will choose the first four and disregard the rest." << endl;
157 for (int i = 4; i < userGroups.size(); i++) {
158 userGroups.erase(userGroups.begin()+i);
161 }else if (mode == "heat") {
162 //if the user only entered invalid groups
163 if (userGroups.size() == 0) {
164 cout << "When using the groups parameter you must have at least 1 valid groups. I will run the command using all the groups in your groupfile." << endl;
165 for (int i = 0; i < allGroups.size(); i++) {
166 userGroups.push_back(allGroups[i]);
169 }else if ((mode == "collect") || (mode == "rarefact") || (mode == "summary") || (mode == "treegroup")) {
170 //if the user only entered invalid groups
171 if ((userGroups.size() == 0) || (userGroups.size() == 1)) {
172 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;
173 for (int i = 0; i < allGroups.size(); i++) {
174 userGroups.push_back(allGroups[i]);
180 catch(exception& e) {
181 cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
185 cout << "An unknown error has occurred in the SharedUtil class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
191 /**************************************************************************************/
192 //for parsimony and unifrac commands you set pairwise groups as well as an allgroups in calc
193 void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups, string& label, int& numGroups, string mode){ //globaldata->Groups, your tree or group map, allgroups, mode
197 //if the user has not entered specific groups to analyze then do them all
198 if (userGroups.size() != 0) {
199 if (userGroups[0] != "all") {
200 //check that groups are valid
201 for (int i = 0; i < userGroups.size(); i++) {
202 if (isValidGroup(userGroups[i], allGroups) != true) {
203 cout << userGroups[i] << " is not a valid group, and will be disregarded." << endl;
204 // erase the invalid group from globaldata->Groups
205 userGroups.erase(userGroups.begin()+i);
209 }else { //users wants all groups
211 for (int i=0; i < allGroups.size(); i++) {
212 if (allGroups[i] != "xxx") {
213 userGroups.push_back(allGroups[i]);
214 label += allGroups[i] + "-";
218 }else { //the user has not entered groups
219 for (int i=0; i < allGroups.size(); i++) {
220 if (allGroups[i] != "xxx") {
221 label += allGroups[i] + "-";
222 if (mode == "weighted") {
223 userGroups.push_back(allGroups[i]);
232 if (mode == "weighted") {
233 //if the user only entered invalid groups
234 if (userGroups.size() == 0) {
235 for (int i=0; i < allGroups.size(); i++) {
236 if (allGroups[i] != "xxx") {
237 userGroups.push_back(allGroups[i]);
240 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;
241 }else if (userGroups.size() == 1) {
242 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;
244 for (int i=0; i < allGroups.size(); i++) {
245 if (allGroups[i] != "xxx") {
246 userGroups.push_back(allGroups[i]);
250 numGroups = userGroups.size();
252 }else if ((mode == "unweighted") || (mode == "parsimony")) {
253 //if the user only entered invalid groups
254 if ((userGroups.size() == 0) && (numGroups == 0)) {
255 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;
256 for (int i = 0; i < allGroups.size(); i++) {
257 if (allGroups[i] != "xxx") {
258 userGroups.push_back(allGroups[i]);
259 label += allGroups[i] + "-";
263 for (int i = 0; i < userGroups.size(); i++) {
264 label += userGroups[i] + "-";
268 //rip extra - off allgroups
269 label = label.substr(0, label.length()-1);
271 if (numGroups != 1) { numGroups = userGroups.size(); }
275 catch(exception& e) {
276 cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
280 cout << "An unknown error has occurred in the SharedUtil class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
284 /**************************************************************************************/
285 void SharedUtil::getCombos(vector<string>& groupComb, vector<string> userGroups, int& numComp) { //groupcomb, globaldata->Groups, numcomb
287 //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
289 for (int i=0; i< userGroups.size(); i++) {
291 for (int l = i+1; l < userGroups.size(); l++) {
292 //set group comparison labels
293 groupComb.push_back(userGroups[i] + "-" + userGroups[l]);
297 catch(exception& e) {
298 cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function getCombos. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
302 cout << "An unknown error has occurred in the SharedUtil class function getCombos. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
306 /**************************************************************************************/
307 bool SharedUtil::isValidGroup(string groupname, vector<string> groups) {
309 for (int i = 0; i < groups.size(); i++) {
310 if (groupname == groups[i]) { return true; }
315 catch(exception& e) {
316 cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function isValidGroup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
320 cout << "An unknown error has occurred in the SharedUtil class function isValidGroup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
325 /**************************************************************************************/
326 void SharedUtil::updateGroupIndex(vector<string>& userGroups, map<string, int>& index) {
329 for (int i = 0; i < userGroups.size(); i++) {
330 index[userGroups[i]] = i;
333 catch(exception& e) {
334 cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function updateGroupIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
338 cout << "An unknown error has occurred in the SharedUtil class function updateGroupIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";