changed reading of name file to use buffered reads. note the splitAtWhiteSpace functi...

[mothur.git] / mothurout.cpp

diff --git a/mothurout.cpp b/mothurout.cpp
index 6ecb86f94e5533165551ed5ae571f0c51f3c9ff9..f98bea8ca92fbb387ad0d3727dbfbc858da49583 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -1092,11 +1092,14 @@ int MothurOut::appendFiles(string temp, string filename) {
                
                int numLines = 0;
                if (ableToOpen == 0) { //you opened it
-                       while(!input.eof()){
-                char c = input.get();
-                               if(input.eof())         {       break;                  }
-                               else                            {       output << c;    if (c == '\n') {numLines++;} }
-                       }
+            
+            char buffer[4096];        
+            while (!input.eof()) {
+                input.read(buffer, 4096);
+                output.write(buffer, input.gcount());
+                //count number of lines
+                for (int i = 0; i < input.gcount(); i++) {  if (buffer[i] == '\n') {numLines++;} }
+            }
                        input.close();
                }
                
@@ -1454,6 +1457,30 @@ float MothurOut::ceilDist(float dist, int precision){
                exit(1);
        }
 }
+/***********************************************************************/
+
+vector<string> MothurOut::splitWhiteSpace(string& rest, char buffer[], int size){
+       try {
+        vector<string> pieces;
+        
+        for (int i = 0; i < size; i++) {
+            if (!isspace(buffer[i]))  { rest += buffer[i];  }
+            else {
+                pieces.push_back(rest);  rest = "";
+                while (i < size) {  //gobble white space
+                    if (isspace(buffer[i])) { i++; }
+                    else { rest = buffer[i];  break; } //cout << "next piece buffer = " << nextPiece << endl;
+                } 
+            }
+        }
+        
+        return pieces;
+       }
+       catch(exception& e) {
+               errorOut(e, "MothurOut", "parsePieces");
+               exit(1);
+       }
+}
 /**********************************************************************************************************************/
 int MothurOut::readNames(string namefile, map<string, string>& nameMap) { 
        try {
@@ -1461,14 +1488,25 @@ int MothurOut::readNames(string namefile, map<string, string>& nameMap) {
                //open input file
                ifstream in;
                openInputFile(namefile, in);
-               
+
+        string rest = "";
+        char buffer[4096];
+        bool pairDone = false;
+        bool columnOne = true;
+        string firstCol, secondCol;
+        
                while (!in.eof()) {
                        if (control_pressed) { break; }
                        
-                       string firstCol, secondCol;
-                       in >> firstCol >> secondCol; gobble(in);
-                       
-                       nameMap[firstCol] = secondCol;
+            in.read(buffer, 4096);
+            vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+             
+            for (int i = 0; i < pieces.size(); i++) {
+                if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
+                else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+                
+                if (pairDone) { nameMap[firstCol] = secondCol; pairDone = false; }
+            }
                }
                in.close();
                
@@ -1488,21 +1526,33 @@ int MothurOut::readNames(string namefile, map<string, vector<string> >& nameMap)
                ifstream in;
                openInputFile(namefile, in);
                
+        string rest = "";
+        char buffer[4096];
+        bool pairDone = false;
+        bool columnOne = true;
+        string firstCol, secondCol;
+        
                while (!in.eof()) {
                        if (control_pressed) { break; }
                        
-                       string firstCol, secondCol;
-                       in >> firstCol >> secondCol; gobble(in);
-                       
-                       vector<string> temp;
-                       splitAtComma(secondCol, temp);
-                       
-                       nameMap[firstCol] = temp;
+            in.read(buffer, 4096);
+            vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+            
+            for (int i = 0; i < pieces.size(); i++) {
+                if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
+                else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+                
+                if (pairDone) { 
+                    vector<string> temp;
+                    splitAtComma(secondCol, temp);
+                    nameMap[firstCol] = temp;
+                    pairDone = false;  
+                } 
+            }
                }
                in.close();
-               
+        
                return nameMap.size();
-               
        }
        catch(exception& e) {
                errorOut(e, "MothurOut", "readNames");
@@ -1519,18 +1569,30 @@ map<string, int> MothurOut::readNames(string namefile) {
                ifstream in;
                openInputFile(namefile, in);
                
+        string rest = "";
+        char buffer[4096];
+        bool pairDone = false;
+        bool columnOne = true;
+        string firstCol, secondCol;
+        
                while (!in.eof()) {
                        if (control_pressed) { break; }
                        
-                       string firstCol, secondCol;
-                       in >> firstCol;  gobble(in);
-            in >> secondCol; gobble(in);
-                       
-                       int num = getNumNames(secondCol);
-                       
-                       nameMap[firstCol] = num;
+            in.read(buffer, 4096);
+            vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+            
+            for (int i = 0; i < pieces.size(); i++) {
+                if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
+                else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+                
+                if (pairDone) { 
+                    int num = getNumNames(secondCol);
+                    nameMap[firstCol] = num;
+                    pairDone = false;  
+                } 
+            }
                }
-               in.close();
+        in.close();
                
                return nameMap;
                
@@ -1549,27 +1611,41 @@ int MothurOut::readNames(string namefile, vector<seqPriorityNode>& nameVector, m
                ifstream in;
                openInputFile(namefile, in);
                
+        string rest = "";
+        char buffer[4096];
+        bool pairDone = false;
+        bool columnOne = true;
+        string firstCol, secondCol;
+        
                while (!in.eof()) {
                        if (control_pressed) { break; }
                        
-                       string firstCol, secondCol;
-                       in >> firstCol >> secondCol; gobble(in);
-                       
-                       int num = getNumNames(secondCol);
-                       
-                       map<string, string>::iterator it = fastamap.find(firstCol);
-                       if (it == fastamap.end()) {
-                               error = 1;
-                               mothurOut("[ERROR]: " + firstCol + " is not in your fastafile, but is in your namesfile, please correct."); mothurOutEndLine();
-                       }else {
-                               seqPriorityNode temp(num, it->second, firstCol);
-                               nameVector.push_back(temp);
-                       }
+            in.read(buffer, 4096);
+            vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+            
+            for (int i = 0; i < pieces.size(); i++) {
+                if (columnOne) {  firstCol = pieces[i]; columnOne=false; }
+                else  { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+                
+                if (pairDone) { 
+                    int num = getNumNames(secondCol);
+                    
+                    map<string, string>::iterator it = fastamap.find(firstCol);
+                    if (it == fastamap.end()) {
+                        error = 1;
+                        mothurOut("[ERROR]: " + firstCol + " is not in your fastafile, but is in your namesfile, please correct."); mothurOutEndLine();
+                    }else {
+                        seqPriorityNode temp(num, it->second, firstCol);
+                        nameVector.push_back(temp);
+                    }
+                    
+                    pairDone = false;  
+                } 
+            }
                }
-               in.close();
-               
+        in.close();
+        
                return error;
-               
        }
        catch(exception& e) {
                errorOut(e, "MothurOut", "readNames");