X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=formatcolumn.cpp;h=6b29f90464f3259c6c625421d9ee1cadbc8b2ef8;hb=e10c72304ee071c0c40e0218a06d89dc4731cbc2;hp=e68d85d71c32df15ca56cbee916c6c9dd1072df1;hpb=e1cf60b82a48d4d96e3a696a2d221c56cfb0b298;p=mothur.git

diff --git a/formatcolumn.cpp b/formatcolumn.cpp
index e68d85d..6b29f90 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;
@@ -35,21 +35,22 @@ 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();  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; }
-			
-			if(distance < cutoff && itA != itB){
-							
+		
+			if((distance < cutoff) && (itA != itB)){
 				if(refRow == refCol){		// in other words, if we haven't loaded refRow and refCol...
 					refRow = itA->second;
 					refCol = itB->second;
@@ -67,21 +68,21 @@ void FormatColumnMatrix::read(NameAssignment* nameMap){
 				
 				reading->update(itA->second * nseqs / 2);
 			}
-			gobble(fileHandle);
+			m->gobble(fileHandle);
 		}
 		out.close();
 		fileHandle.close();
-		
+	
 		string squareFile;
 		if(lt == 0){  // oops, it was square
 			squareFile = filename;
 		}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
@@ -89,13 +90,14 @@ void FormatColumnMatrix::read(NameAssignment* nameMap){
 			system(command.c_str());
 		#endif
 		
+		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;
@@ -112,7 +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(); m->mothurRemove(distFile); m->mothurRemove(tempOutFile); m->mothurRemove(outfile); delete reading; return 0; }
+			
+			in >> first >> second >> dist; m->gobble(in);
 			
 			if (first != currentRow) {
 				//save position in file of each new row
@@ -129,10 +134,13 @@ void FormatColumnMatrix::read(NameAssignment* nameMap){
 				rowMap.clear();
 				
 				//save row you just read
-				rowMap[second] = dist;
-
+				if (dist < cutoff) {
+					rowMap[second] = dist;
+				}
 			}else{
-				rowMap[second] = dist;
+				if (dist < cutoff) {
+					rowMap[second] = dist;
+				}
 			}
 		}
 		
@@ -151,16 +159,23 @@ void FormatColumnMatrix::read(NameAssignment* nameMap){
 		in.close();
 		out.close();
 		
+		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) {  m->mothurRemove(distFile);  return 0; }
+
+		return 1;
 
 	}
 	catch(exception& e) {
-		errorOut(e, "FormatColumnMatrix", "read");
+		m->errorOut(e, "FormatColumnMatrix", "read");
 		exit(1);
 	}
 }