added SequenceCountParser class to parse the count table by group. added count parame...

[mothur.git] / formatphylip.cpp

diff --git a/formatphylip.cpp b/formatphylip.cpp
index 60a3b4136810515bc628b334d948fb0d957605d2..60591178836ee793a83cbd3ec75776b463af4ead 100644 (file)
--- 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");