X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=formatphylip.cpp;h=60591178836ee793a83cbd3ec75776b463af4ead;hb=c7e8c2d15bd7cedcfdf18675cb0ea1a0dcd0e3c0;hp=60a3b4136810515bc628b334d948fb0d957605d2;hpb=260ae19c36cb11a53ddc5a75b5e507f8dd8b31d6;p=mothur.git

diff --git a/formatphylip.cpp b/formatphylip.cpp
index 60a3b41..6059117 100644
--- a/formatphylip.cpp
+++ b/formatphylip.cpp
@@ -24,7 +24,12 @@ int FormatPhylipMatrix::read(NameAssignment* nameMap){
 			string name;
 			ofstream out;
 			
-			fileHandle >> nseqs >> name;
+			string numTest;
+			fileHandle >> numTest >> name;
+			
+			if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
+			else { convert(numTest, nseqs); }
+		
 						
 			list = new ListVector(nseqs);
 			list->set(0, name);
@@ -70,7 +75,7 @@ int FormatPhylipMatrix::read(NameAssignment* nameMap){
 					
 					for(int j=0;j<i;j++){
 					
-						if (m->control_pressed) { outTemp.close(); remove(tempFile.c_str()); fileHandle.close();  delete reading; return 0; }
+						if (m->control_pressed) { outTemp.close(); m->mothurRemove(tempFile); fileHandle.close();  delete reading; return 0; }
 											
 						fileHandle >> distance;
 						
@@ -91,7 +96,7 @@ int FormatPhylipMatrix::read(NameAssignment* nameMap){
 				string outfile = m->getRootName(tempFile) + "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 " + tempFile + " -o " + outfile;
 					system(command.c_str());
 				#else //sort using windows sort
@@ -99,7 +104,7 @@ int 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; }
+				if (m->control_pressed) { m->mothurRemove(tempFile); 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;
@@ -123,7 +128,7 @@ int 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; }
+					if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(tempFile); m->mothurRemove(distFile); m->mothurRemove(outfile);  delete reading; return 0; }
 
 					in >> first >> second >> dist; m->gobble(in);
 					
@@ -165,10 +170,10 @@ int FormatPhylipMatrix::read(NameAssignment* nameMap){
 				in.close();
 				out.close();
 				
-				remove(tempFile.c_str());
-				remove(outfile.c_str());
+				m->mothurRemove(tempFile);
+				m->mothurRemove(outfile);
 				
-				if (m->control_pressed) {  remove(distFile.c_str());   delete reading; return 0; }
+				if (m->control_pressed) {  m->mothurRemove(distFile);   delete reading; return 0; }
 
 			}
 			else{ //square matrix convert directly to formatted row file
@@ -183,7 +188,7 @@ int 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; }
+						if (m->control_pressed) {  fileHandle.close(); out.close(); m->mothurRemove(distFile);   delete reading; return 0; }
 						
 						fileHandle >> distance;
 					
@@ -217,7 +222,7 @@ int FormatPhylipMatrix::read(NameAssignment* nameMap){
 			fileHandle.close();
 			out.close();
 			
-			if (m->control_pressed) { remove(distFile.c_str());  return 0; }
+			if (m->control_pressed) { m->mothurRemove(distFile);  return 0; }
 			
 			list->setLabel("0");