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

[mothur.git] / formatphylip.cpp

diff --git a/formatphylip.cpp b/formatphylip.cpp
index 206df7edfbd915f00947c46d6de07f44fc021c38..60a3b4136810515bc628b334d948fb0d957605d2 100644 (file)
--- a/formatphylip.cpp
+++ b/formatphylip.cpp
@@ -12,7 +12,7 @@
 
 /***********************************************************************/
 FormatPhylipMatrix::FormatPhylipMatrix(string df) : filename(df) {
-        openInputFile(filename, fileHandle);
+        m->openInputFile(filename, fileHandle);
 }
 /***********************************************************************/
 //not using nameMap
@@ -37,11 +37,11 @@ int FormatPhylipMatrix::read(NameAssignment* nameMap){
                                        fileHandle.close();  //reset file
                                        
                                        //open and get through numSeqs, code below formats rest of file
-                                       openInputFile(filename, fileHandle);
-                                       fileHandle >> nseqs; gobble(fileHandle);
+                                       m->openInputFile(filename, fileHandle);
+                                       fileHandle >> nseqs; m->gobble(fileHandle);
                                        
                                        distFile = filename + ".rowFormatted";
-                                       openOutputFile(distFile, out);
+                                       m->openOutputFile(distFile, out);
                                        break;
                                }
                                if(d == '\n'){
@@ -59,7 +59,7 @@ int FormatPhylipMatrix::read(NameAssignment* nameMap){
                                
                                ofstream outTemp;
                                string tempFile = filename + ".temp";
-                               openOutputFile(tempFile, outTemp);
+                               m->openOutputFile(tempFile, outTemp);
                 
                                //convert to square column matrix
                                for(int i=1;i<nseqs;i++){
@@ -88,7 +88,7 @@ int FormatPhylipMatrix::read(NameAssignment* nameMap){
                                
                                //format from square column to rowFormatted
                                //sort file by first column so the distances for each row are together
-                               string outfile = getRootName(tempFile) + "sorted.dist.temp";
+                               string outfile = m->getRootName(tempFile) + "sorted.dist.temp";
                                
                                //use the unix sort 
                                #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
@@ -103,10 +103,10 @@ int FormatPhylipMatrix::read(NameAssignment* nameMap){
 
                                //output to new file distance for each row and save positions in file where new row begins
                                ifstream in;
-                               openInputFile(outfile, in);
+                               m->openInputFile(outfile, in);
                                
                                distFile = outfile + ".rowFormatted";
-                               openOutputFile(distFile, out);
+                               m->openOutputFile(distFile, out);
                                
                                rowPos.resize(nseqs, -1);
                                int currentRow;
@@ -125,7 +125,7 @@ int FormatPhylipMatrix::read(NameAssignment* nameMap){
                                while(!in.eof()) {
                                        if (m->control_pressed) { in.close(); out.close(); remove(tempFile.c_str()); remove(distFile.c_str()); remove(outfile.c_str());  delete reading; return 0; }
 
-                                       in >> first >> second >> dist; gobble(in);
+                                       in >> first >> second >> dist; m->gobble(in);
                                        
                                        if (first != currentRow) {
                                                //save position in file of each new row
@@ -196,7 +196,7 @@ int FormatPhylipMatrix::read(NameAssignment* nameMap){
                                                reading->update(index);
                                        }
                                        
-                                       gobble(fileHandle);
+                                       m->gobble(fileHandle);
                        
                                        //save position in file of each new row
                                        rowPos[i] = out.tellp();