added phylip as output file type for commands that output distance matrices. added...

[mothur.git] / formatcolumn.cpp

diff --git a/formatcolumn.cpp b/formatcolumn.cpp
index e68d85d71c32df15ca56cbee916c6c9dd1072df1..6b29f90464f3259c6c625421d9ee1cadbc8b2ef8 100644 (file)
--- 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);
        }
 }