+++ /dev/null
-/*
- * 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();
-
- //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 groupfile."); 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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