X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=formatphylip.cpp;fp=formatphylip.cpp;h=206df7edfbd915f00947c46d6de07f44fc021c38;hb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;hp=aaf540aed0d800d111e1a8a7703520640a28d240;hpb=182db2b6f1747bc1e0b8cd3eceec8751abdd31d5;p=mothur.git

diff --git a/formatphylip.cpp b/formatphylip.cpp
index aaf540a..206df7e 100644
--- a/formatphylip.cpp
+++ b/formatphylip.cpp
@@ -16,7 +16,7 @@ FormatPhylipMatrix::FormatPhylipMatrix(string df) : filename(df) {
 }
 /***********************************************************************/
 //not using nameMap
-void FormatPhylipMatrix::read(NameAssignment* nameMap){
+int FormatPhylipMatrix::read(NameAssignment* nameMap){
 	try {
         
 			float distance;
@@ -63,11 +63,15 @@ void FormatPhylipMatrix::read(NameAssignment* nameMap){
                 
 				//convert to square column matrix
 				for(int i=1;i<nseqs;i++){
+				
 					fileHandle >> name;
 					
 					list->set(i, name);
 					
 					for(int j=0;j<i;j++){
+					
+						if (m->control_pressed) { outTemp.close(); remove(tempFile.c_str()); fileHandle.close();  delete reading; return 0; }
+											
 						fileHandle >> distance;
 						
 						if (distance == -1) { distance = 1000000; }
@@ -95,6 +99,7 @@ void FormatPhylipMatrix::read(NameAssignment* nameMap){
 					system(command.c_str());
 				#endif
 				
+				if (m->control_pressed) { remove(tempFile.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;
@@ -118,6 +123,8 @@ void FormatPhylipMatrix::read(NameAssignment* nameMap){
 				for(int k = 0; k < firstString.length(); k++)  {   in.putback(firstString[k]);  }
 				
 				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);
 					
 					if (first != currentRow) {
@@ -160,6 +167,9 @@ void FormatPhylipMatrix::read(NameAssignment* nameMap){
 				
 				remove(tempFile.c_str());
 				remove(outfile.c_str());
+				
+				if (m->control_pressed) {  remove(distFile.c_str());   delete reading; return 0; }
+
 			}
 			else{ //square matrix convert directly to formatted row file
 				int index = nseqs;
@@ -173,6 +183,8 @@ void FormatPhylipMatrix::read(NameAssignment* nameMap){
 					list->set(i, name);
 					
 					for(int j=0;j<nseqs;j++){
+						if (m->control_pressed) {  fileHandle.close(); out.close(); remove(distFile.c_str());   delete reading; return 0; }
+						
 						fileHandle >> distance;
 					
 						if (distance == -1) { distance = 1000000; }
@@ -202,11 +214,16 @@ void FormatPhylipMatrix::read(NameAssignment* nameMap){
 			}
 			reading->finish();
 			delete reading;
-			
-			list->setLabel("0");
 			fileHandle.close();
 			out.close();
 			
+			if (m->control_pressed) { remove(distFile.c_str());  return 0; }
+			
+			list->setLabel("0");
+			
+			return 1;
+			
+			
 	}
 	catch(exception& e) {
                m->errorOut(e, "FormatPhylipMatrix", "read");