fixed linking error in collect, collectshared, and errorcheckor

[mothur.git] / utilities.hpp

diff --git a/utilities.hpp b/utilities.hpp
index 16e762c295708ddbc3c0cd4835cd4b60bc8e9162..8f5009ffc4f0306a5da950e75a541aaa56cfb572 100644 (file)
--- a/utilities.hpp
+++ b/utilities.hpp
@@ -10,6 +10,7 @@ using namespace std;
 #include <cmath>
 #include <vector>
 #include <stdexcept>
+#include <set>
 
 typedef unsigned long long ull;
 
@@ -32,6 +33,19 @@ inline void convert(const string& s, T& x, bool failIfLeftoverChars = true){
        if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
                throw BadConversion(s);
 }
+//**********************************************************************************************************************
+
+template<typename T>
+inline bool convertTest(const string& s, T& x, bool failIfLeftoverChars = true){
+       istringstream i(s);
+       char c;
+       if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
+       {
+               cout << "'" << s << "' is unable to be converted into an integer.\n";
+               return false;
+       } 
+       return true;
+}
 
 //**********************************************************************************************************************
 
@@ -57,7 +71,7 @@ string toString(const T&x, int i){
 
 /***********************************************************************/
 
-inline void gobble(ifstream& f){
+inline void gobble(istream& f){
        
        char d;
     while(isspace(d=f.get()))          {;}
@@ -196,4 +210,138 @@ inline int openOutputFile(string fileName, ofstream& fileHandle){
 
 /***********************************************************************/
 
+//This function parses the estimator options and puts them in a vector
+inline void splitAtDash(string& estim, vector<string>& container) {
+       try {
+               string individual;
+               
+               while (estim.find_first_of('-') != -1) {
+                       individual = estim.substr(0,estim.find_first_of('-'));
+                       if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
+                               estim = estim.substr(estim.find_first_of('-')+1, estim.length());
+                               container.push_back(individual);
+                       }
+               }
+               //get last one
+               container.push_back(estim);
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the utilities class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the utilities class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+
+}
+
+/***********************************************************************/
+//This function parses the label options and puts them in a set
+inline void splitAtDash(string& estim, set<string>& container) {
+       try {
+               string individual;
+               
+               while (estim.find_first_of('-') != -1) {
+                       individual = estim.substr(0,estim.find_first_of('-'));
+                       if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
+                               estim = estim.substr(estim.find_first_of('-')+1, estim.length());
+                               container.insert(individual);
+                       }
+               }
+               //get last one
+               container.insert(estim);
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the utilities class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the utilities class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+
+}
+/***********************************************************************/
+//This function parses the line options and puts them in a set
+inline void splitAtDash(string& estim, set<int>& container) {
+       try {
+               string individual;
+               int lineNum;
+               
+               while (estim.find_first_of('-') != -1) {
+                       individual = estim.substr(0,estim.find_first_of('-'));
+                       if ((estim.find_first_of('-')+1) <= estim.length()) { //checks to make sure you don't have dash at end of string
+                               estim = estim.substr(estim.find_first_of('-')+1, estim.length());
+                               convert(individual, lineNum); //convert the string to int
+                               container.insert(lineNum);
+                       }
+               }
+               //get last one
+               convert(estim, lineNum); //convert the string to int
+               container.insert(lineNum);
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the utilities class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the utilities class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+
+}
+/***********************************************************************/
+
+//This function splits up the various option parameters
+inline void splitAtComma(string& prefix, string& suffix){
+       try {
+               prefix = suffix.substr(0,suffix.find_first_of(','));
+               if ((suffix.find_first_of(',')+2) <= suffix.length()) {  //checks to make sure you don't have comma at end of string
+                       suffix = suffix.substr(suffix.find_first_of(',')+1, suffix.length());
+                       string space = " ";
+                       while(suffix.at(0) == ' ')
+                               suffix = suffix.substr(1, suffix.length());
+               }
+
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the utilities class Function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the utilities class function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+
+}
+/***********************************************************************/
+
+//This function separates the key value from the option value i.e. dist=96_...
+inline void splitAtEquals(string& key, string& value){         
+       try {
+               if(value.find_first_of('=') != -1){
+                       key = value.substr(0,value.find_first_of('='));
+                       if ((value.find_first_of('=')+1) <= value.length()) {
+                               value = value.substr(value.find_first_of('=')+1, value.length());
+                       }
+               }else{
+                       key = value;
+                       value = 1;
+               }
+       }
+       catch(exception& e) {
+               cout << "Standard Error: " << e.what() << " has occurred in the utilities class Function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+       catch(...) {
+               cout << "An unknown error has occurred in the utilities class function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+               exit(1);
+       }
+
+}
+/*******************************************************/
+
+
+
 #endif