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/*
* sharedutilities.cpp
* Mothur
*
* Created by Sarah Westcott on 4/9/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "sharedutilities.h"
#include "sharedrabundvector.h"
#include "sharedordervector.h"
/**************************************************************************************************/
void SharedUtil::getSharedVectors(vector<string> Groups, vector<SharedRAbundVector*>& lookup, SharedOrderVector* order) {
try {
//delete each sharedrabundvector in lookup
for (int j = 0; j < lookup.size(); j++) {
delete lookup[j];
}
lookup.clear();
sort(Groups.begin(), Groups.end());
//create and initialize vector of sharedvectors, one for each group
for (int i = 0; i < Groups.size(); i++) {
SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins());
temp->setLabel(order->getLabel());
temp->setGroup(Groups[i]);
lookup.push_back(temp);
}
int numSeqs = order->size();
//sample all the members
for(int i=0;i<numSeqs;i++){
//get first sample
individual chosen = order->get(i);
int abundance;
//set info for sharedvector in chosens group
for (int j = 0; j < lookup.size(); j++) {
if (chosen.group == lookup[j]->getGroup()) {
abundance = lookup[j]->getAbundance(chosen.bin);
lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
break;
}
}
}
}
catch(exception& e) {
m->errorOut(e, "SharedUtil", "getSharedVectors");
exit(1);
}
}
/**************************************************************************************************/
void SharedUtil::getSharedVectorswithReplacement(vector<string> Groups, vector<SharedRAbundVector*>& lookup, SharedOrderVector* order) {
try {
//delete each sharedrabundvector in lookup
for (int j = 0; j < lookup.size(); j++) {
delete lookup[j];
}
lookup.clear();
//create and initialize vector of sharedvectors, one for each group
for (int i = 0; i < Groups.size(); i++) {
SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins());
temp->setLabel(order->getLabel());
temp->setGroup(Groups[i]);
lookup.push_back(temp);
}
int numSeqs = order->size();
//sample all the members
for(int i=0;i<numSeqs;i++){
//get random number
int random = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
individual chosen = order->get(random);
int abundance;
//set info for sharedvector in chosens group
for (int j = 0; j < lookup.size(); j++) {
if (chosen.group == lookup[j]->getGroup()) {
abundance = lookup[j]->getAbundance(chosen.bin);
lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
break;
}
}
}
}
catch(exception& e) {
m->errorOut(e, "SharedUtil", "getSharedVectorswithReplacement");
exit(1);
}
}
/**************************************************************************************************/
//need to have mode because different commands require different number of valid groups
void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups) {
try {
sort(userGroups.begin(), userGroups.end());
sort(allGroups.begin(), allGroups.end());
if (userGroups.size() != 0) {
if (userGroups[0] != "all") {
//check that groups are valid
for (int i = 0; i < userGroups.size(); i++) {
if (isValidGroup(userGroups[i], allGroups) != true) {
m->mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
// erase the invalid group from userGroups
userGroups.erase(userGroups.begin()+i);
i--;
}
}
//if the user only entered invalid groups
if (userGroups.size() == 0) {
m->mothurOut("You provided no valid groups. I will run the command using all the groups in your file."); m->mothurOutEndLine();
for (int i = 0; i < allGroups.size(); i++) {
userGroups.push_back(allGroups[i]);
}
}
}else{//user has enter "all" and wants the default groups
userGroups.clear();
for (int i = 0; i < allGroups.size(); i++) {
userGroups.push_back(allGroups[i]);
}
}
}else { //the user has not entered groups
for (int i = 0; i < allGroups.size(); i++) {
userGroups.push_back(allGroups[i]);
}
}
}
catch(exception& e) {
m->errorOut(e, "SharedUtil", "setGroups");
exit(1);
}
}
/**************************************************************************************************/
//need to have mode because different commands require different number of valid groups
void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups, string mode) {
try {
sort(userGroups.begin(), userGroups.end());
sort(allGroups.begin(), allGroups.end());
if (userGroups.size() != 0) {
if (userGroups[0] != "all") {
//check that groups are valid
for (int i = 0; i < userGroups.size(); i++) {
if (isValidGroup(userGroups[i], allGroups) != true) {
m->mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
// erase the invalid group from userGroups
userGroups.erase(userGroups.begin()+i);
i--;
}
}
}else{//user has enter "all" and wants the default groups
userGroups.clear();
for (int i = 0; i < allGroups.size(); i++) {
userGroups.push_back(allGroups[i]);
}
}
}else { //the user has not entered groups
for (int i = 0; i < allGroups.size(); i++) {
userGroups.push_back(allGroups[i]);
}
}
if ((mode == "collect") || (mode == "rarefact") || (mode == "summary") || (mode == "treegroup")) {
//if the user only entered invalid groups
if ((userGroups.size() == 0) || (userGroups.size() == 1)) {
m->mothurOut("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."); m->mothurOutEndLine();
for (int i = 0; i < allGroups.size(); i++) {
userGroups.push_back(allGroups[i]);
}
}
}
}
catch(exception& e) {
m->errorOut(e, "SharedUtil", "setGroups");
exit(1);
}
}
/**************************************************************************************/
//for parsimony and unifrac commands you set pairwise groups as well as an allgroups in calc
void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups, string& label, int& numGroups, string mode){ //globaldata->Groups, your tree or group map, allgroups, mode
try {
sort(userGroups.begin(), userGroups.end());
sort(allGroups.begin(), allGroups.end());
numGroups = 0;
label = "";
//if the user has not entered specific groups to analyze then do them all
if (userGroups.size() != 0) {
if (userGroups[0] != "all") {
//check that groups are valid
for (int i = 0; i < userGroups.size(); i++) {
if (isValidGroup(userGroups[i], allGroups) != true) {
m->mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
// erase the invalid group from globaldata->Groups
userGroups.erase(userGroups.begin()+i);
i--;
}
}
}else { //users wants all groups
userGroups.clear();
for (int i=0; i < allGroups.size(); i++) {
if (allGroups[i] != "xxx") {
userGroups.push_back(allGroups[i]);
}
}
}
}else { //the user has not entered groups
for (int i=0; i < allGroups.size(); i++) {
if (allGroups[i] != "xxx") {
if (mode == "weighted") {
userGroups.push_back(allGroups[i]);
}else {
numGroups = 1;
label += allGroups[i] + "-";
}
}
}
//rip extra - off allgroups
label = label.substr(0, label.length()-1);
if ((mode != "weighted") && (allGroups.size() > 10)) { label = "merged"; }
}
if (mode == "weighted") {
//if the user only entered invalid groups
if (userGroups.size() == 0) {
for (int i=0; i < allGroups.size(); i++) {
if (allGroups[i] != "xxx") {
userGroups.push_back(allGroups[i]);
}
}
m->mothurOut("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."); m->mothurOutEndLine();
}else if (userGroups.size() == 1) {
m->mothurOut("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."); m->mothurOutEndLine();
userGroups.clear();
for (int i=0; i < allGroups.size(); i++) {
if (allGroups[i] != "xxx") {
userGroups.push_back(allGroups[i]);
}
}
}
numGroups = userGroups.size();
}else if ((mode == "unweighted") || (mode == "parsimony")) {
//if the user only entered invalid groups
if ((userGroups.size() == 0) && (numGroups == 0)) {
m->mothurOut("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."); m->mothurOutEndLine();
for (int i = 0; i < allGroups.size(); i++) {
if (allGroups[i] != "xxx") {
userGroups.push_back(allGroups[i]);
}
}
}
if (numGroups != 1) { numGroups = userGroups.size(); }
}
}
catch(exception& e) {
m->errorOut(e, "SharedUtil", "setGroups");
exit(1);
}
}
/**************************************************************************************/
void SharedUtil::getCombos(vector<string>& groupComb, vector<string> userGroups, int& numComp) { //groupcomb, globaldata->Groups, numcomb
try {
sort(userGroups.begin(), userGroups.end());
//calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
numComp = 0;
for (int i=0; i< userGroups.size(); i++) {
numComp += i;
for (int l = 0; l < i; l++) {
if (userGroups[i] > userGroups[l]) {
//set group comparison labels
groupComb.push_back(userGroups[l] + "-" + userGroups[i]);
}else{
groupComb.push_back(userGroups[i] + "-" + userGroups[l]);
}
}
}
}
catch(exception& e) {
m->errorOut(e, "SharedUtil", "getCombos");
exit(1);
}
}
/**************************************************************************************/
bool SharedUtil::isValidGroup(string groupname, vector<string> groups) {
try {
for (int i = 0; i < groups.size(); i++) {
if (groupname == groups[i]) { return true; }
}
return false;
}
catch(exception& e) {
m->errorOut(e, "SharedUtil", "isValidGroup");
exit(1);
}
}
/**************************************************************************************/
void SharedUtil::updateGroupIndex(vector<string>& userGroups, map<string, int>& index) {
try {
index.clear();
for (int i = 0; i < userGroups.size(); i++) {
index[userGroups[i]] = i;
}
}
catch(exception& e) {
m->errorOut(e, "SharedUtil", "updateGroupIndex");
exit(1);
}
}
/**************************************************************************************/
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