fixed bug with trim.seqs allfiles=t

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index c2ef698db8ed4d9c0769fcd4295a27a886c65bfc..5a0ea1281b3644e1c0b42035054f9f7f2e0cf0f6 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -1154,7 +1154,43 @@ vector<unsigned long int> MothurOut::divideFile(string filename, int& proc) {
                exit(1);
        }
 }
-
+/**************************************************************************************************/
+int MothurOut::divideFile(string filename, int& proc, vector<string>& files) {
+       try{
+               
+               vector<unsigned long int> filePos = divideFile(filename, proc);
+               
+               for (int i = 0; i < (filePos.size()-1); i++) {
+                       
+                       //read file chunk
+                       ifstream in;
+                       openInputFile(filename, in);
+                       in.seekg(filePos[i]);
+                       unsigned long int size = filePos[(i+1)] - filePos[i];
+                       char* chunk = new char[size];
+                       in.read(chunk, size);
+                       in.close();
+                       
+                       //open new file
+                       string fileChunkName = filename + "." + toString(i) + ".tmp";
+                       ofstream out; 
+                       openOutputFile(fileChunkName, out);
+                       
+                       out << chunk << endl;
+                       out.close();
+                       delete[] chunk;
+                       
+                       //save name
+                       files.push_back(fileChunkName);
+               }
+                               
+               return 0;
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "divideFile");
+               exit(1);
+       }
+}
 /***********************************************************************/
 
 bool MothurOut::isTrue(string f){
@@ -1193,6 +1229,33 @@ float MothurOut::ceilDist(float dist, int precision){
                exit(1);
        }
 }
+/**********************************************************************************************************************/
+int MothurOut::readNames(string namefile, map<string, string>& nameMap) { 
+       try {
+               
+               //open input file
+               ifstream in;
+               openInputFile(namefile, in);
+               
+               while (!in.eof()) {
+                       if (control_pressed) { break; }
+                       
+                       string firstCol, secondCol;
+                       in >> firstCol >> secondCol; gobble(in);
+                       
+                       nameMap[firstCol] = secondCol;
+               }
+               in.close();
+               
+               return 0;
+               
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "readNames");
+               exit(1);
+       }
+}
+
 /**********************************************************************************************************************/
 map<string, int> MothurOut::readNames(string namefile) { 
        try {