X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=formatcolumn.cpp;h=6b29f90464f3259c6c625421d9ee1cadbc8b2ef8;hb=b866e1519a60681527244036428104ad1cb90c93;hp=64b85317d1303658627f4ed6cfde1f99b51d3677;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git

diff --git a/formatcolumn.cpp b/formatcolumn.cpp
index 64b8531..6b29f90 100644
--- a/formatcolumn.cpp
+++ b/formatcolumn.cpp
@@ -12,7 +12,7 @@
 
 /***********************************************************************/
 FormatColumnMatrix::FormatColumnMatrix(string df) : filename(df){
-	openInputFile(filename, fileHandle);
+	m->openInputFile(filename, fileHandle);
 }
 /***********************************************************************/
 
@@ -35,18 +35,18 @@ int FormatColumnMatrix::read(NameAssignment* nameMap){
 		
 		ofstream out;
 		string tempOutFile = filename + ".temp";
-		openOutputFile(tempOutFile, out);
+		m->openOutputFile(tempOutFile, out);
 	
 		while(fileHandle && lt == 1){  //let's assume it's a triangular matrix...
 		
-			if (m->control_pressed) { out.close(); remove(tempOutFile.c_str()); fileHandle.close();  delete reading; return 0; }
+			if (m->control_pressed) { out.close();  m->mothurRemove(tempOutFile); fileHandle.close();  delete reading; return 0; }
 		
 			fileHandle >> firstName >> secondName >> distance;	// get the row and column names and distance
 	
 			map<string,int>::iterator itA = nameMap->find(firstName);
 			map<string,int>::iterator itB = nameMap->find(secondName);
-			if(itA == nameMap->end()){	cerr << "AAError: Sequence '" << firstName << "' was not found in the names file, please correct\n"; exit(1);	}
-			if(itB == nameMap->end()){	cerr << "ABError: Sequence '" << secondName << "' was not found in the names file, please correct\n"; exit(1);	}
+			if(itA == nameMap->end()){  m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the names file, please correct\n"); exit(1);  }
+			if(itB == nameMap->end()){  m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the names file, please correct\n"); exit(1);  }
 
 			if (distance == -1) { distance = 1000000; }
 		
@@ -68,7 +68,7 @@ int FormatColumnMatrix::read(NameAssignment* nameMap){
 				
 				reading->update(itA->second * nseqs / 2);
 			}
-			gobble(fileHandle);
+			m->gobble(fileHandle);
 		}
 		out.close();
 		fileHandle.close();
@@ -79,10 +79,10 @@ int FormatColumnMatrix::read(NameAssignment* nameMap){
 		}else{ squareFile = tempOutFile; }
 		
 		//sort file by first column so the distances for each row are together
-		string outfile = getRootName(squareFile) + "sorted.dist.temp";
+		string outfile = m->getRootName(squareFile) + "sorted.dist.temp";
 		
 		//use the unix sort 
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			string command = "sort -n " + squareFile + " -o " + outfile;
 			system(command.c_str());
 		#else //sort using windows sort
@@ -90,14 +90,14 @@ int FormatColumnMatrix::read(NameAssignment* nameMap){
 			system(command.c_str());
 		#endif
 		
-		if (m->control_pressed) { remove(tempOutFile.c_str()); remove(outfile.c_str()); delete reading; return 0; }
+		if (m->control_pressed) { m->mothurRemove(tempOutFile); m->mothurRemove(outfile); delete reading; return 0; }
 
 		//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;
@@ -115,9 +115,9 @@ int FormatColumnMatrix::read(NameAssignment* nameMap){
 		
 		while(!in.eof()) {
 			
-			if (m->control_pressed) { in.close(); out.close(); remove(distFile.c_str()); remove(tempOutFile.c_str()); remove(outfile.c_str()); delete reading; return 0; }
+			if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(distFile); m->mothurRemove(tempOutFile); m->mothurRemove(outfile); 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
@@ -159,17 +159,17 @@ int FormatColumnMatrix::read(NameAssignment* nameMap){
 		in.close();
 		out.close();
 		
-		if (m->control_pressed) {  remove(distFile.c_str()); remove(tempOutFile.c_str()); remove(outfile.c_str());  delete reading; return 0; }
+		if (m->control_pressed) {  m->mothurRemove(distFile); m->mothurRemove(tempOutFile); m->mothurRemove(outfile);  delete reading; return 0; }
 		
-		remove(tempOutFile.c_str());
-		remove(outfile.c_str());
+		m->mothurRemove(tempOutFile);
+		m->mothurRemove(outfile);
 		
 		reading->finish();
 		
 		delete reading;
 		list->setLabel("0");
 		
-		if (m->control_pressed) {  remove(distFile.c_str());  return 0; }
+		if (m->control_pressed) {  m->mothurRemove(distFile);  return 0; }
 
 		return 1;