X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=formatphylip.cpp;h=60591178836ee793a83cbd3ec75776b463af4ead;hb=e8e13c129ba8184ec5932a090773f353f3ae3406;hp=206df7edfbd915f00947c46d6de07f44fc021c38;hpb=aa9238c0a9e6e7aa0ed8b8b606b08ad4fd7dcfe3;p=mothur.git

diff --git a/formatphylip.cpp b/formatphylip.cpp
index 206df7e..6059117 100644
--- a/formatphylip.cpp
+++ b/formatphylip.cpp
@@ -12,7 +12,7 @@
 
 /***********************************************************************/
 FormatPhylipMatrix::FormatPhylipMatrix(string df) : filename(df) {
-        openInputFile(filename, fileHandle);
+        m->openInputFile(filename, fileHandle);
 }
 /***********************************************************************/
 //not using nameMap
@@ -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);
@@ -37,11 +42,11 @@ int FormatPhylipMatrix::read(NameAssignment* nameMap){
 					fileHandle.close();  //reset file
 					
 					//open and get through numSeqs, code below formats rest of file
-					openInputFile(filename, fileHandle);
-					fileHandle >> nseqs; gobble(fileHandle);
+					m->openInputFile(filename, fileHandle);
+					fileHandle >> nseqs; m->gobble(fileHandle);
 					
 					distFile = filename + ".rowFormatted";
-					openOutputFile(distFile, out);
+					m->openOutputFile(distFile, out);
 					break;
 				}
 				if(d == '\n'){
@@ -59,7 +64,7 @@ int FormatPhylipMatrix::read(NameAssignment* nameMap){
 				
 				ofstream outTemp;
 				string tempFile = filename + ".temp";
-				openOutputFile(tempFile, outTemp);
+				m->openOutputFile(tempFile, outTemp);
                 
 				//convert to square column matrix
 				for(int i=1;i<nseqs;i++){
@@ -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;
 						
@@ -88,10 +93,10 @@ int FormatPhylipMatrix::read(NameAssignment* nameMap){
 				
 				//format from square column to rowFormatted
 				//sort file by first column so the distances for each row are together
-				string outfile = getRootName(tempFile) + "sorted.dist.temp";
+				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
@@ -99,14 +104,14 @@ 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;
-				openInputFile(outfile, in);
+				m->openInputFile(outfile, in);
 				
 				distFile = outfile + ".rowFormatted";
-				openOutputFile(distFile, out);
+				m->openOutputFile(distFile, out);
 				
 				rowPos.resize(nseqs, -1);
 				int currentRow;
@@ -123,9 +128,9 @@ 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; gobble(in);
+					in >> first >> second >> dist; m->gobble(in);
 					
 					if (first != currentRow) {
 						//save position in file of each new row
@@ -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;
 					
@@ -196,7 +201,7 @@ int FormatPhylipMatrix::read(NameAssignment* nameMap){
 						reading->update(index);
 					}
 					
-					gobble(fileHandle);
+					m->gobble(fileHandle);
 			
 					//save position in file of each new row
 					rowPos[i] = out.tellp();
@@ -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");