added countable class to read and store count file. added count parameter to make...

[mothur.git] / sharedutilities.cpp

diff --git a/sharedutilities.cpp b/sharedutilities.cpp
index 15f16a6f1942921ca41098dd502750d68c75ce3e..151b254c7ca983abe1568a962aba5eef0e2f5ead 100644 (file)
--- a/sharedutilities.cpp
+++ b/sharedutilities.cpp
@@ -102,6 +102,10 @@ void SharedUtil::getSharedVectorswithReplacement(vector<string> Groups, vector<S
 //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
@@ -144,6 +148,10 @@ void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups
 //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
@@ -190,6 +198,9 @@ void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups
 //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 = "";
 
@@ -271,6 +282,7 @@ void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups
 /**************************************************************************************/
 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++) { 
@@ -305,7 +317,7 @@ bool SharedUtil::isValidGroup(string groupname, vector<string> groups) {
        }
 }
 
-/**************************************************************************************
+/**************************************************************************************/
 void SharedUtil::updateGroupIndex(vector<string>& userGroups, map<string, int>& index) {
        try {
                index.clear();