added *.count.summary file to count.groups command. added deltaq and insert parameter...

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index 1b72137a66d6cd8038446dbc823033bb3293869d..dc77490e4b9bba1bc9bf6e4c16b0f402985c73d1 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -1430,6 +1430,83 @@ vector<unsigned long long> MothurOut::divideFile(string filename, int& proc) {
        }
 }
 /**************************************************************************************************/
+
+vector<unsigned long long> MothurOut::divideFilePerLine(string filename, int& proc) {
+       try{
+               vector<unsigned long long> filePos;
+               filePos.push_back(0);
+               
+               FILE * pFile;
+               unsigned long long size;
+               
+               filename = getFullPathName(filename);
+        
+               //get num bytes in file
+               pFile = fopen (filename.c_str(),"rb");
+               if (pFile==NULL) perror ("Error opening file");
+               else{
+                       fseek (pFile, 0, SEEK_END);
+                       size=ftell (pFile);
+                       fclose (pFile);
+               }
+               
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+        
+               //estimate file breaks
+               unsigned long long chunkSize = 0;
+               chunkSize = size / proc;
+        
+               //file to small to divide by processors
+               if (chunkSize == 0)  {  proc = 1;       filePos.push_back(size); return filePos;        }
+        
+               //for each process seekg to closest file break and search for next '>' char. make that the filebreak
+               for (int i = 0; i < proc; i++) {
+                       unsigned long long spot = (i+1) * chunkSize;
+                       
+                       ifstream in;
+                       openInputFile(filename, in);
+                       in.seekg(spot);
+                       
+                       //look for next line break
+                       unsigned long long newSpot = spot;
+                       while (!in.eof()) {
+                char c = in.get();
+                               
+                               if ((c == '\n') || (c == '\r') || (c == '\f'))  { gobble(in); newSpot = in.tellg(); break; }
+                else if (int(c) == -1) { break; }
+            }
+            
+                       //there was not another line before the end of the file
+                       unsigned long long sanityPos = in.tellg();
+            
+                       if (sanityPos == -1) {  break;  }
+                       else {  filePos.push_back(newSpot);  }
+                       
+                       in.close();
+               }
+               
+               //save end pos
+               filePos.push_back(size);
+               
+               //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--; }
+               }
+        
+               proc = (filePos.size() - 1);
+#else
+               mothurOut("[ERROR]: Windows version should not be calling the divideFile function."); mothurOutEndLine();
+               proc=1;
+               filePos.push_back(size);
+#endif
+               return filePos;
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "divideFile");
+               exit(1);
+       }
+}
+/**************************************************************************************************/
 int MothurOut::divideFile(string filename, int& proc, vector<string>& files) {
        try{
                
@@ -2643,7 +2720,7 @@ void MothurOut::splitAtDash(string& estim, vector<string>& container) {
                string individual = "";
                int estimLength = estim.size();
                bool prevEscape = false;
-               for(int i=0;i<estimLength;i++){
+               /*for(int i=0;i<estimLength;i++){
                        if(prevEscape){
                                individual += estim[i];
                                prevEscape = false;
@@ -2662,7 +2739,28 @@ void MothurOut::splitAtDash(string& estim, vector<string>& container) {
                                        prevEscape = false;
                                }
                        }
-               }
+               }*/
+        
+        
+        for(int i=0;i<estimLength;i++){
+            if(estim[i] == '-'){
+                if (prevEscape) {  individual += estim[i]; prevEscape = false;  } //add in dash because it was escaped.
+                else {
+                    container.push_back(individual);
+                    individual = "";
+                }
+            }else if(estim[i] == '\\'){
+                if (i < estimLength-1) { 
+                    if (estim[i+1] == '-') { prevEscape=true; }  //are you a backslash before a dash, if yes ignore
+                    else { individual += estim[i]; prevEscape = false;  } //if no, add in
+                }else { individual += estim[i]; }
+            }else {
+                individual += estim[i];
+            }
+        }
+        
+
+        
                container.push_back(individual);
        }
        catch(exception& e) {
@@ -2743,6 +2841,7 @@ void MothurOut::splitAtDash(string& estim, set<int>& container) {
                exit(1);
        }       
 }
+
 /***********************************************************************/
 string MothurOut::makeList(vector<string>& names) {
        try {
@@ -2810,11 +2909,11 @@ void MothurOut::splitAtChar(string& prefix, string& suffix, char c){
                        string space = " ";
                        while(suffix.at(0) == ' ')
                                suffix = suffix.substr(1, suffix.length());
-               }
+               }else {  suffix = "";  }
         
-       }
+    }
        catch(exception& e) {
-               errorOut(e, "MothurOut", "splitAtComma");
+               errorOut(e, "MothurOut", "splitAtChar");
                exit(1);
        }       
 }
@@ -2830,7 +2929,7 @@ void MothurOut::splitAtComma(string& prefix, string& suffix){
                        string space = " ";
                        while(suffix.at(0) == ' ')
                                suffix = suffix.substr(1, suffix.length());
-               }
+               }else {  suffix = "";  }
 
        }
        catch(exception& e) {