added out.hierarchy command

[mothur.git] / hcluster.cpp

diff --git a/hcluster.cpp b/hcluster.cpp
index 259036f0f02a42beb95926f9ce59a4140164840e..db937851dfae88802dd27ee9dcb65d8beeb60d0f 100644 (file)
--- a/hcluster.cpp
+++ b/hcluster.cpp
@@ -503,18 +503,21 @@ vector<seqDist> HCluster::getSeqsAN(){
 /***********************************************************************/
 void HCluster::combineFile() {
        try {
-               int bufferSize = 64000;  //512k - this should be a variable that the user can set to optimize code to their hardware
-               char* inputBuffer;
-               inputBuffer = new char[bufferSize];
-               size_t numRead;
+               //int bufferSize = 64000;  //512k - this should be a variable that the user can set to optimize code to their hardware
+               //char* inputBuffer;
+               //inputBuffer = new char[bufferSize];
+               //size_t numRead;
                
                string tempDistFile = distfile + ".temp";
                ofstream out;
                openOutputFile(tempDistFile, out);
                
-               FILE* in;
-               in = fopen(distfile.c_str(), "rb");
+               //FILE* in;
+               //in = fopen(distfile.c_str(), "rb");
        
+               ifstream in;
+               openInputFile(distfile, in);
+               
                int first, second;
                float dist;
                
@@ -524,28 +527,30 @@ void HCluster::combineFile() {
                                
                //go through file pulling out distances related to rows merging
                //if mergedMin contains distances add those back into file
-               bool done = false;
-               partialDist = "";
-               while ((numRead = fread(inputBuffer, 1, bufferSize, in)) != 0) {
+               //bool done = false;
+               //partialDist = "";
+               //while ((numRead = fread(inputBuffer, 1, bufferSize, in)) != 0) {
 //cout << "number of char read = " << numRead << endl;
 //cout << inputBuffer << endl;
-                       if (numRead < bufferSize) { done = true; }
+                       //if (numRead < bufferSize) { done = true; }
                        
                        //parse input into individual distances
-                       int spot = 0;
-                       string outputString = "";
-                       while(spot < numRead) {
+                       //int spot = 0;
+                       //string outputString = "";
+                       //while(spot < numRead) {
        //cout << "spot = " << spot << endl;
-                          seqDist nextDist = getNextDist(inputBuffer, spot, bufferSize);
+                        //  seqDist nextDist = getNextDist(inputBuffer, spot, bufferSize);
                           
                           //you read a partial distance
-                          if (nextDist.seq1 == -1) { break;  }
-                          
-                          first = nextDist.seq1; second = nextDist.seq2; dist = nextDist.dist;
+                         // if (nextDist.seq1 == -1) { break;  }
+                       while (!in.eof()) {
+                               //first = nextDist.seq1; second = nextDist.seq2; dist = nextDist.dist;
        //cout << "next distance = " << first << '\t' << second << '\t' << dist << endl;                   
                           //since file is sorted and mergedMin is sorted 
                           //you can put the smallest distance from each through the code below and keep the file sorted
                           
+                          in >> first >> second >> dist; gobble(in);
+                          
                           //while there are still values in mergedMin that are smaller than the distance read from file
                           while (count < mergedMin.size())  {
                           
@@ -563,7 +568,8 @@ void HCluster::combineFile() {
                                                }else if (mergedMin[count].seq2 == smallRow) {
                                                        smallRowColValues[0][mergedMin[count].seq1] = mergedMin[count].dist;
                                                }else { //if no, write to temp file
-                                                       outputString += toString(mergedMin[count].seq1) + '\t' + toString(mergedMin[count].seq2) + '\t' + toString(mergedMin[count].dist) + '\n';
+                                                       //outputString += toString(mergedMin[count].seq1) + '\t' + toString(mergedMin[count].seq2) + '\t' + toString(mergedMin[count].dist) + '\n';
+                                                       out << mergedMin[count].seq1 << '\t' << mergedMin[count].seq2 << '\t' << mergedMin[count].dist << endl;
                                                }
                                                count++;
                                        }else{   break; }
@@ -582,14 +588,16 @@ void HCluster::combineFile() {
                                        smallRowColValues[0][first] = dist;
                           
                           }else { //if no, write to temp file
-                                       outputString += toString(first) + '\t' + toString(second) + '\t' + toString(dist) + '\n';
+                                       //outputString += toString(first) + '\t' + toString(second) + '\t' + toString(dist) + '\n';
+                                       out << first << '\t' << second << '\t' << dist << endl;
                           }
                        }
                        
-                       out << outputString;
-                       if(done) { break; }
-               }
-               fclose(in);
+                       //out << outputString;
+                       //if(done) { break; }
+               //}
+               //fclose(in);
+               in.close();
                
                //if values in mergedMin are larger than the the largest in file then
                while (count < mergedMin.size())  {  
@@ -644,7 +652,7 @@ void HCluster::combineFile() {
                exit(1);
        }
 }
-/***********************************************************************/
+/***********************************************************************
 seqDist HCluster::getNextDist(char* buffer, int& index, int size){
        try {
                seqDist next;