working on windows paralellization, added trimOligos class to be used by trim.flows...

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index cdde507ce4464ef9da5d8f5041d56ae73818941f..c80bff27e4ab69bf26d0fddaae534fe625f6df0b 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -1050,19 +1050,27 @@ string MothurOut::sortFile(string distFile, string outputDir){
        }       
 }
 /**************************************************************************************************/
-vector<unsigned long int> MothurOut::setFilePosFasta(string filename, int& num) {
+vector<unsigned long long> MothurOut::setFilePosFasta(string filename, int& num) {
        try {
-                       vector<unsigned long int> positions;
+                       vector<unsigned long long> positions;
                        ifstream inFASTA;
-                       openInputFile(filename, inFASTA);
+                       //openInputFile(filename, inFASTA);
+                       inFASTA.open(filename.c_str(), ios::binary);
                                                
                        string input;
+                       unsigned long long count = 0;
                        while(!inFASTA.eof()){
-                               input = getline(inFASTA); 
-                               if (input.length() != 0) {
-                                       if(input[0] == '>'){    unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1); }
+                               //input = getline(inFASTA); 
+                               //cout << input << '\t' << inFASTA.tellg() << endl;
+                               //if (input.length() != 0) {
+                               //      if(input[0] == '>'){    unsigned long int pos = inFASTA.tellg(); positions.push_back(pos - input.length() - 1);  cout << (pos - input.length() - 1) << endl; }
+                               //}
+                               //gobble(inFASTA); //has to be here since windows line endings are 2 characters and mess up the positions
+                               char c = inFASTA.get(); count++;
+                               if (c == '>') {
+                                       positions.push_back(count-1);
+                                       //cout << count << endl;
                                }
-                               gobble(inFASTA); //has to be here since windows line endings are 2 characters and mess up the positions
                        }
                        inFASTA.close();
                
@@ -1080,7 +1088,7 @@ vector<unsigned long int> MothurOut::setFilePosFasta(string filename, int& num)
                                fclose (pFile);
                        }*/
                        
-                       unsigned long int size = positions[(positions.size()-1)];
+                       unsigned long long size = positions[(positions.size()-1)];
                        ifstream in;
                        openInputFile(filename, in);
                        
@@ -1093,6 +1101,7 @@ vector<unsigned long int> MothurOut::setFilePosFasta(string filename, int& num)
                        in.close();
                
                        positions.push_back(size);
+                       positions[0] = 0;
                
                        return positions;
        }
@@ -1102,31 +1111,51 @@ vector<unsigned long int> MothurOut::setFilePosFasta(string filename, int& num)
        }
 }
 /**************************************************************************************************/
-vector<unsigned long int> MothurOut::setFilePosEachLine(string filename, int& num) {
+vector<unsigned long long> MothurOut::setFilePosEachLine(string filename, int& num) {
        try {
                        filename = getFullPathName(filename);
                        
-                       vector<unsigned long int> positions;
+                       vector<unsigned long long> positions;
                        ifstream in;
-                       openInputFile(filename, in);
-                               
+                       //openInputFile(filename, in);
+                       in.open(filename.c_str(), ios::binary);
+               
                        string input;
+                       unsigned long long count = 0;
+                       positions.push_back(0);
+               
                        while(!in.eof()){
-                               unsigned long int lastpos = in.tellg();
-                               input = getline(in); 
-                               if (input.length() != 0) {
-                                       unsigned long int pos = in.tellg(); 
-                                       if (pos != -1) { positions.push_back(pos - input.length() - 1); }
-                                       else {  positions.push_back(lastpos);  }
+                               //unsigned long long lastpos = in.tellg();
+                               //input = getline(in); 
+                               //if (input.length() != 0) {
+                                       //unsigned long long pos = in.tellg(); 
+                                       //if (pos != -1) { positions.push_back(pos - input.length() - 1);       }
+                                       //else {  positions.push_back(lastpos);  }
+                               //}
+                               //gobble(in); //has to be here since windows line endings are 2 characters and mess up the positions
+                               
+                               
+                               //getline counting reads
+                               char d = in.get(); count++;
+                               while ((d != '\n') && (d != '\r') && (d != '\f') && (d != in.eof()))    {
+                                       //get next character
+                                       d = in.get(); 
+                                       count++;
+                               }
+                               
+                               if (!in.eof()) {
+                                       d=in.get(); count++;
+                                       while(isspace(d) && (d != in.eof()))            { d=in.get(); count++;}
                                }
-                               gobble(in); //has to be here since windows line endings are 2 characters and mess up the positions
+                               positions.push_back(count-1);
+                               cout << count-1 << endl;
                        }
                        in.close();
                
-                       num = positions.size();
+                       num = positions.size()-1;
                
                        FILE * pFile;
-                       unsigned long int size;
+                       unsigned long long size;
                        
                        //get num bytes in file
                        pFile = fopen (filename.c_str(),"rb");
@@ -1137,7 +1166,7 @@ vector<unsigned long int> MothurOut::setFilePosEachLine(string filename, int& nu
                                fclose (pFile);
                        }
                
-                       positions.push_back(size);
+                       positions[(positions.size()-1)] = size;
                
                        return positions;
        }
@@ -1148,14 +1177,14 @@ vector<unsigned long int> MothurOut::setFilePosEachLine(string filename, int& nu
 }
 /**************************************************************************************************/
 
-vector<unsigned long int> MothurOut::divideFile(string filename, int& proc) {
+vector<unsigned long long> MothurOut::divideFile(string filename, int& proc) {
        try{
        
-               vector<unsigned long int> filePos;
+               vector<unsigned long long> filePos;
                filePos.push_back(0);
                
                FILE * pFile;
-               unsigned long int size;
+               unsigned long long size;
                
                filename = getFullPathName(filename);
                
@@ -1169,7 +1198,7 @@ vector<unsigned long int> MothurOut::divideFile(string filename, int& proc) {
                }
        
                //estimate file breaks
-               unsigned long int chunkSize = 0;
+               unsigned long long chunkSize = 0;
                chunkSize = size / proc;
 
                //file to small to divide by processors
@@ -1177,21 +1206,21 @@ vector<unsigned long int> MothurOut::divideFile(string filename, int& proc) {
        
                //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 int spot = (i+1) * chunkSize;
+                       unsigned long long spot = (i+1) * chunkSize;
                        
                        ifstream in;
                        openInputFile(filename, in);
                        in.seekg(spot);
                        
                        //look for next '>'
-                       unsigned long int newSpot = spot;
+                       unsigned long long newSpot = spot;
                        while (!in.eof()) {
                           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();
+                       unsigned long long sanityPos = in.tellg();
 
                        if (sanityPos == -1) {  break;  }
                        else {  filePos.push_back(newSpot);  }
@@ -1220,7 +1249,7 @@ vector<unsigned long int> MothurOut::divideFile(string filename, int& proc) {
 int MothurOut::divideFile(string filename, int& proc, vector<string>& files) {
        try{
                
-               vector<unsigned long int> filePos = divideFile(filename, proc);
+               vector<unsigned long long> filePos = divideFile(filename, proc);
                
                for (int i = 0; i < (filePos.size()-1); i++) {
                        
@@ -1228,7 +1257,7 @@ int MothurOut::divideFile(string filename, int& proc, vector<string>& files) {
                        ifstream in;
                        openInputFile(filename, in);
                        in.seekg(filePos[i]);
-                       unsigned long int size = filePos[(i+1)] - filePos[i];
+                       unsigned long long size = filePos[(i+1)] - filePos[i];
                        char* chunk = new char[size];
                        in.read(chunk, size);
                        in.close();