/* This file contains all the standard incudes we use in the project as well as some common utilities. */
+//#include <cstddef>
//io libraries
#include <iostream>
typedef unsigned long long ull;
-
+struct IntNode {
+ int lvalue;
+ int rvalue;
+ int lcoef;
+ int rcoef;
+ IntNode* left;
+ IntNode* right;
+};
+
/***********************************************************************/
// snagged from http://www.parashift.com/c++-faq-lite/misc-technical-issues.html#faq-39.2
}
//**********************************************************************************************************************
+template<typename T>
+inline bool convertTestFloat(const string& s, T& x, bool failIfLeftoverChars = true){
+ istringstream i(s);
+ char c;
+ if (!(i >> x) || (failIfLeftoverChars && i.get(c)))
+ {
+ return false;
+ }
+ return true;
+}
+
+//**********************************************************************************************************************
+
template<typename T>
inline bool convertTest(const string& s, T& x, bool failIfLeftoverChars = true){
istringstream i(s);
return output.str();
}
-
//**********************************************************************************************************************
template<typename T>
return simpleName;
}
+/***********************************************************************/
+
+inline int factorial(int num){
+ int total = 1;
+
+ for (int i = 1; i <= num; i++) {
+ total *= i;
+ }
+
+ return total;
+}
+/**************************************************************************************************
+
+double min(double x, double y)
+{
+ if(x<y){ return x; }
+ else { return y; }
+}
/***********************************************************************/
string rootPathName = longName;
- if(longName.find_last_of("/") != longName.npos){
+ if(longName.find_last_of('/') != longName.npos){
int pos = longName.find_last_of('/')+1;
rootPathName = longName.substr(0, pos);
}
/***********************************************************************/
+inline string getExtension(string longName){
+
+ string extension = longName;
+
+ if(longName.find_last_of('.') != longName.npos){
+ int pos = longName.find_last_of('.');
+ extension = longName.substr(pos, longName.length());
+ }
+
+ return extension;
+}
+
+/***********************************************************************/
+
inline int openInputFile(string fileName, ifstream& fileHandle){
fileHandle.open(fileName.c_str());
return 0;
}
+}
+/***********************************************************************/
+
+inline int openOutputFileAppend(string fileName, ofstream& fileHandle){
+
+ fileHandle.open(fileName.c_str(), ios::app);
+ if(!fileHandle) {
+ cerr << "Error: Could not open " << fileName << endl;
+ return 1;
+ }
+ else {
+ return 0;
+ }
+
+}
+
+
+/***********************************************************************/
+
+inline int getNumSeqs(ifstream& file){
+
+ int numSeqs = count(istreambuf_iterator<char>(file),istreambuf_iterator<char>(), '>');
+ file.seekg(0);
+ return numSeqs;
+
}
/***********************************************************************/
}
}
-/**************************************************************************************************/
+/***********************************************************************/
+//this function determines if the user has given us labels that are smaller than the given label.
+//if so then it returns true so that the calling function can run the previous valid distance.
+//it's a "smart" distance function. It also checks for invalid labels.
+inline bool anyLabelsToProcess(string label, set<string>& userLabels, string errorOff) {
+ try {
+ set<string>::iterator it;
+ vector<float> orderFloat;
+ map<string, float> userMap; //the conversion process removes trailing 0's which we need to put back
+ map<string, float>::iterator it2;
+ float labelFloat;
+ bool smaller = false;
+
+ //unique is the smallest line
+ if (label == "unique") { return false; }
+ else { convert(label, labelFloat); }
+
+ //go through users set and make them floats
+ for(it = userLabels.begin(); it != userLabels.end(); ++it) {
+
+ float temp;
+ if ((*it != "unique") && (convertTestFloat(*it, temp) == true)){
+ convert(*it, temp);
+ orderFloat.push_back(temp);
+ userMap[*it] = temp;
+ }else if (*it == "unique") {
+ orderFloat.push_back(-1.0);
+ userMap["unique"] = -1.0;
+ }else {
+ if (errorOff == "") { cout << *it << " is not a valid label." << endl; }
+ userLabels.erase(*it);
+ it--;
+ }
+ }
+
+ //sort order
+ sort(orderFloat.begin(), orderFloat.end());
+
+ /*************************************************/
+ //is this label bigger than any of the users labels
+ /*************************************************/
+
+ //loop through order until you find a label greater than label
+ for (int i = 0; i < orderFloat.size(); i++) {
+ if (orderFloat[i] < labelFloat) {
+ smaller = true;
+ if (orderFloat[i] == -1) {
+ if (errorOff == "") { cout << "Your file does not include the label unique." << endl; }
+ userLabels.erase("unique");
+ }
+ else {
+ if (errorOff == "") { cout << "Your file does not include the label "; }
+ string s = "";
+ for (it2 = userMap.begin(); it2!= userMap.end(); it2++) {
+ if (it2->second == orderFloat[i]) {
+ s = it2->first;
+ //remove small labels
+ userLabels.erase(s);
+ break;
+ }
+ }
+ if (errorOff == "") { cout << s << ". I will use the next smallest distance. " << endl; }
+ }
+ //since they are sorted once you find a bigger one stop looking
+ }else { break; }
+ }
+
+ return smaller;
+
+ }
+ catch(exception& e) {
+ cout << "Standard Error: " << e.what() << " has occurred in the mothur class Function anyLabelsToProcess. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+ catch(...) {
+ cout << "An unknown error has occurred in the mothur class function anyLabelsToProcess. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ exit(1);
+ }
+}
+/**************************************************************************************************/
#endif
projects / mothur.git / blobdiff