--- /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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