added split.groups command

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index 0c3ef3d9cddf5cc90544d9a6d0117882d60db6b6..aab9945230f680e4ce106e4266ff66ba5ee7c34e 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -276,8 +276,9 @@ int MothurOut::openOutputFileAppend(string fileName, ofstream& fileHandle){
 /***********************************************************************/
 void MothurOut::gobble(istream& f){
        try {
+               
                char d;
-               while(isspace(d=f.get()))               {;}
+               while(isspace(d=f.get()))               { ;}
                f.putback(d);
        }
        catch(exception& e) {
@@ -984,7 +985,7 @@ vector<unsigned long int> MothurOut::divideFile(string filename, int& proc) {
                //estimate file breaks
                unsigned long int chunkSize = 0;
                chunkSize = size / proc;
-       
+
                //file to small to divide by processors
                if (chunkSize == 0)  {  proc = 1;       filePos.push_back(size); return filePos;        }
        
@@ -1002,7 +1003,7 @@ vector<unsigned long int> MothurOut::divideFile(string filename, int& proc) {
                           char c = in.get();
                           if (c == '>') {   in.putback(c); newSpot = in.tellg(); break;  }
                        }
-                       
+               
                        //there was not another sequence before the end of the file
                        unsigned long int sanityPos = in.tellg();
 
@@ -1017,7 +1018,7 @@ vector<unsigned long int> MothurOut::divideFile(string filename, int& proc) {
 
                //sanity check filePos
                for (int i = 0; i < (filePos.size()-1); i++) {
-                       if (filePos[(i+1)] <= filePos[i]) {  filePos.erase(filePos.begin()+(i+1)); i--; }
+                       if (filePos[(i+1)] <= filePos[i]) {  cout << "erasing " << (i+1) << endl; filePos.erase(filePos.begin()+(i+1)); i--; }
                }
 
                proc = (filePos.size() - 1);
@@ -1181,7 +1182,20 @@ void MothurOut::getNumSeqs(ifstream& file, int& numSeqs){
 //This function parses the estimator options and puts them in a vector
 void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbol) {
        try {
-               string individual;
+               string individual = "";
+               int estimLength = estim.size();
+               for(int i=0;i<estimLength;i++){
+                       if(estim[i] == symbol){
+                               container.push_back(individual);
+                               individual = "";                                
+                       }
+                       else{
+                               individual += estim[i];
+                       }
+               }
+               container.push_back(individual);
+
+               /*
                
                while (estim.find_first_of(symbol) != -1) {
                        individual = estim.substr(0,estim.find_first_of(symbol));
@@ -1191,7 +1205,7 @@ void MothurOut::splitAtChar(string& estim, vector<string>& container, char symbo
                        }
                }
                //get last one
-               container.push_back(estim);
+               container.push_back(estim); */
        }
        catch(exception& e) {
                errorOut(e, "MothurOut", "splitAtChar");