added smart distance feature and optimized all commands using line by line processing

[mothur.git] / mothur.h

diff --git a/mothur.h b/mothur.h
index 2c9595ebe53c4055179f2297372bb1e691fff8ab..07bb971347d974066ab5449614172c5e68d4c2a6 100644 (file)
--- a/mothur.h
+++ b/mothur.h
@@ -73,6 +73,19 @@ inline void convert(const string& s, T& x, bool failIfLeftoverChars = true){
 }
 //**********************************************************************************************************************
 
+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);
@@ -465,8 +478,87 @@ inline bool inUsersGroups(string groupname, vector<string> Groups) {
        }
 }
 
-/**************************************************************************************************/
+/***********************************************************************/
+//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