X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=formatcolumn.cpp;h=2bbcf518b864aa5a5656a271f2922c531e74af11;hb=df905918ace8537273616b4120d404ebd29dc9cc;hp=a11601b74004d2429b985a1aa1e6fe4114457855;hpb=832d53a9dfac6b1795735eec643d8cf627b0d8e3;p=mothur.git

diff --git a/formatcolumn.cpp b/formatcolumn.cpp
index a11601b..2bbcf51 100644
--- a/formatcolumn.cpp
+++ b/formatcolumn.cpp
@@ -12,11 +12,11 @@
 
 /***********************************************************************/
 FormatColumnMatrix::FormatColumnMatrix(string df) : filename(df){
-	openInputFile(filename, fileHandle);
+	m->openInputFile(filename, fileHandle);
 }
 /***********************************************************************/
 
-void FormatColumnMatrix::read(NameAssignment* nameMap){
+int FormatColumnMatrix::read(NameAssignment* nameMap){
 	try {		
 
 		string firstName, secondName;
@@ -35,10 +35,12 @@ void 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; }
+		
 			fileHandle >> firstName >> secondName >> distance;	// get the row and column names and distance
 	
 			map<string,int>::iterator itA = nameMap->find(firstName);
@@ -66,7 +68,7 @@ void FormatColumnMatrix::read(NameAssignment* nameMap){
 				
 				reading->update(itA->second * nseqs / 2);
 			}
-			gobble(fileHandle);
+			m->gobble(fileHandle);
 		}
 		out.close();
 		fileHandle.close();
@@ -77,7 +79,7 @@ void 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)
@@ -88,13 +90,14 @@ void 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; }
 
 		//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;
@@ -111,7 +114,10 @@ void FormatColumnMatrix::read(NameAssignment* nameMap){
 		for(int k = 0; k < firstString.length(); k++)  {   in.putback(firstString[k]);  }
 		
 		while(!in.eof()) {
-			in >> first >> second >> dist; gobble(in);
+			
+			if (m->control_pressed) { in.close(); out.close(); remove(distFile.c_str()); remove(tempOutFile.c_str()); remove(outfile.c_str()); delete reading; return 0; }
+			
+			in >> first >> second >> dist; m->gobble(in);
 			
 			if (first != currentRow) {
 				//save position in file of each new row
@@ -153,16 +159,23 @@ void 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; }
 		
 		remove(tempOutFile.c_str());
 		remove(outfile.c_str());
 		
 		reading->finish();
+		
+		delete reading;
 		list->setLabel("0");
+		
+		if (m->control_pressed) {  remove(distFile.c_str());  return 0; }
+
+		return 1;
 
 	}
 	catch(exception& e) {
-		errorOut(e, "FormatColumnMatrix", "read");
+		m->errorOut(e, "FormatColumnMatrix", "read");
 		exit(1);
 	}
 }