moved utilities out of mothur.h and into mothurOut class.

[mothur.git] / hcluster.cpp

diff --git a/hcluster.cpp b/hcluster.cpp
index 9466483c779ce0b32698c8469c6224ea3c63b724..e1830cd8fbaacaf518f17b74a8822b475e485b53 100644 (file)
--- a/hcluster.cpp
+++ b/hcluster.cpp
@@ -27,7 +27,7 @@ HCluster::HCluster(RAbundVector* rav, ListVector* lv, string ms, string d, NameA
                }
                
                if (method != "average") {
-                       openInputFile(distfile, filehandle);
+                       m->openInputFile(distfile, filehandle);
                }else{  
                        processFile();  
                }
@@ -389,7 +389,7 @@ vector<seqDist> HCluster::getSeqsFNNN(){
                //get entry
                while (!filehandle.eof()) {
                        
-                       filehandle >> firstName >> secondName >> distance;    gobble(filehandle); 
+                       filehandle >> firstName >> secondName >> distance;    m->gobble(filehandle); 
        
                        //save first one
                        if (prevDistance == -1) { prevDistance = distance; }
@@ -438,7 +438,7 @@ vector<seqDist> HCluster::getSeqsAN(){
                vector<seqDist> sameSeqs;
                prevDistance = -1;
                
-               openInputFile(distfile, filehandle, "no error"); 
+               m->openInputFile(distfile, filehandle, "no error"); 
                
                //is the smallest value in mergedMin or the distfile?
                float mergedMinDist = 10000;
@@ -446,7 +446,7 @@ vector<seqDist> HCluster::getSeqsAN(){
                if (mergedMin.size() > 0) { mergedMinDist = mergedMin[0].dist;  }
                        
                if (!filehandle.eof()) {  
-                       filehandle >> firstName >> secondName >> distance;    gobble(filehandle);
+                       filehandle >> firstName >> secondName >> distance;    m->gobble(filehandle);
                        //save first one
                        if (prevDistance == -1) { prevDistance = distance; } 
                        if (distance != -1) { //-1 means skip me
@@ -469,7 +469,7 @@ vector<seqDist> HCluster::getSeqsAN(){
                        //get entry
                        while (!filehandle.eof()) {
                                
-                               filehandle >> firstName >> secondName >> distance;    gobble(filehandle); 
+                               filehandle >> firstName >> secondName >> distance;    m->gobble(filehandle); 
                                
                                if (prevDistance == -1) { prevDistance = distance; }
                                
@@ -511,13 +511,13 @@ int HCluster::combineFile() {
                
                string tempDistFile = distfile + ".temp";
                ofstream out;
-               openOutputFile(tempDistFile, out);
+               m->openOutputFile(tempDistFile, out);
                
                //FILE* in;
                //in = fopen(distfile.c_str(), "rb");
        
                ifstream in;
-               openInputFile(distfile, in);
+               m->openInputFile(distfile, in);
                
                int first, second;
                float dist;
@@ -550,7 +550,7 @@ int HCluster::combineFile() {
                           //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);
+                          in >> first >> second >> dist; m->gobble(in);
                           
                           if (m->control_pressed) { in.close(); out.close(); remove(tempDistFile.c_str()); return 0; }
                           
@@ -688,7 +688,7 @@ seqDist HCluster::getNextDist(char* buffer, int& index, int size){
                        if ((buffer[index] == 10) || (buffer[index] == 13)) { //newline in unix or windows
                                gotDist = true;
                                
-                               //gobble space
+                               //m->gobble space
                                while (index < size) {          
                                        if (isspace(buffer[index])) { index++; }
                                        else { break; }         
@@ -741,17 +741,17 @@ int HCluster::processFile() {
                float distance;
                
                ifstream in;
-               openInputFile(distfile, in);
+               m->openInputFile(distfile, in);
                
                ofstream out;
                string outTemp = distfile + ".temp";
-               openOutputFile(outTemp, out);
+               m->openOutputFile(outTemp, out);
        
                //get entry
                while (!in.eof()) {
                        if (m->control_pressed) { in.close(); out.close(); remove(outTemp.c_str()); return 0; }
                        
-                       in >> firstName >> secondName >> distance;    gobble(in);               
+                       in >> firstName >> secondName >> distance;    m->gobble(in);            
                        
                        map<string,int>::iterator itA = nameMap->find(firstName);
                        map<string,int>::iterator itB = nameMap->find(secondName);