*
*/
-/* This file contains all the standard incudes we use in the project. */
+/* This file contains all the standard incudes we use in the project as well as some common utilities. */
//io libraries
#include <math.h>
#include <algorithm>
+typedef unsigned long long ull;
+
+
+/***********************************************************************/
+
+// snagged from http://www.parashift.com/c++-faq-lite/misc-technical-issues.html#faq-39.2
+// works for now, but there should be a way to do it without killing the whole program
+
+class BadConversion : public runtime_error {
+public:
+ BadConversion(const string& s) : runtime_error(s){ }
+};
+
+//**********************************************************************************************************************
+
+template<typename T>
+inline void convert(const string& s, T& x, bool failIfLeftoverChars = true){
+ istringstream i(s);
+ char c;
+ 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;
+}
+
+//**********************************************************************************************************************
+
+template<typename T>
+string toString(const T&x){
+ stringstream output;
+ output << x;
+ return output.str();
+}
+
+//**********************************************************************************************************************
+
+template<typename T>
+string toHex(const T&x){
+ stringstream output;
+
+ output << hex << x;
+
+ return output.str();
+}
+
+//**********************************************************************************************************************
+
+template<typename T>
+string toString(const T&x, int i){
+ stringstream output;
+
+ output.precision(i);
+ output << fixed << x;
+
+ return output.str();
+}
+
+
+/***********************************************************************/
+
+inline void gobble(istream& f){
+
+ char d;
+ while(isspace(d=f.get())) {;}
+ f.putback(d);
+
+}
+
+/***********************************************************************/
+
+inline float roundDist(float dist, int precision){
+
+ return int(dist * precision + 0.5)/float(precision);
+
+}
+
+/***********************************************************************/
+
+inline int getNumNames(string names){
+
+ int count = 0;
+
+ if(names != ""){
+ count = 1;
+ for(int i=0;i<names.size();i++){
+ if(names[i] == ','){
+ count++;
+ }
+ }
+ }
+
+ return count;
+
+}
+
+/**************************************************************************************************/
+
+inline vector<vector<double> > binomial(int maxOrder){
+
+ vector<vector<double> > binomial(maxOrder+1);
+
+ for(int i=0;i<=maxOrder;i++){
+ binomial[i].resize(maxOrder+1);
+ binomial[i][0]=1;
+ binomial[0][i]=0;
+ }
+ binomial[0][0]=1;
+
+ binomial[1][0]=1;
+ binomial[1][1]=1;
+
+ for(int i=2;i<=maxOrder;i++){
+ binomial[1][i]=0;
+ }
+
+ for(int i=2;i<=maxOrder;i++){
+ for(int j=1;j<=maxOrder;j++){
+ if(i==j){ binomial[i][j]=1; }
+ if(j>i) { binomial[i][j]=0; }
+ else { binomial[i][j]=binomial[i-1][j-1]+binomial[i-1][j]; }
+ }
+ }
+
+ return binomial;
+}
+
+/***********************************************************************/
+
+inline string getRootName(string longName){
+
+ string rootName = longName;
+
+ if(longName.find_last_of(".") != longName.npos){
+ int pos = longName.find_last_of('.')+1;
+ rootName = longName.substr(0, pos);
+ }
+
+ return rootName;
+}
+/***********************************************************************/
+
+inline string getSimpleName(string longName){
+
+ string simpleName = longName;
+
+ if(longName.find_last_of("/") != longName.npos){
+ int pos = longName.find_last_of('/')+1;
+ simpleName = longName.substr(pos, longName.length());
+ }
+
+ return simpleName;
+}
+
+/***********************************************************************/
+
+inline string getPathName(string longName){
+
+ string rootPathName = longName;
+
+ if(longName.find_last_of("/") != longName.npos){
+ int pos = longName.find_last_of('/')+1;
+ rootPathName = longName.substr(0, pos);
+ }
+
+ return rootPathName;
+}
+
+/***********************************************************************/
+
+inline int openInputFile(string fileName, ifstream& fileHandle){
+
+ fileHandle.open(fileName.c_str());
+ if(!fileHandle) {
+ cerr << "Error: Could not open " << fileName << endl;
+ return 1;
+ }
+ else {
+ return 0;
+ }
+
+}
+
+/***********************************************************************/
+
+inline int openOutputFile(string fileName, ofstream& fileHandle){
+
+ fileHandle.open(fileName.c_str(), ios::trunc);
+ if(!fileHandle) {
+ cerr << "Error: Could not open " << fileName << endl;
+ return 1;
+ }
+ else {
+ return 0;
+ }
+
+}
+
+/***********************************************************************/
+
+//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 mothur class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the mothur 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 mothur class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the mothur 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 mothur class Function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the mothur class function splitAtDash. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+
+}
+/***********************************************************************/
+//This function parses the a string and puts peices in a vector
+inline void splitAtComma(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 comma 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 mothur class Function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the mothur class function splitAtComma. 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 mothur class Function splitAtComma. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the mothur 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 mothur class Function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the mothur class function splitAtEquals. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+
+}
+/**************************************************************************************************/
+
+inline bool inUsersGroups(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) {
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function inUsersGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the mothur class function inUsersGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+
#endif
projects / mothur.git / blobdiff