rewrote metastats command in c++, added mothurRemove function to handle ~ error....

[mothur.git] / bellerophon.cpp

diff --git a/bellerophon.cpp b/bellerophon.cpp
index 761d291da566aa1495b4f4a8e75079f1a619a617..207fa51583b0835810ffaf1e52db88e95252346b 100644 (file)
--- a/bellerophon.cpp
+++ b/bellerophon.cpp
@@ -75,7 +75,7 @@ Bellerophon::Bellerophon(string name, bool filterSeqs,  bool c, int win, int inc
 }
 
 //***************************************************************************************************************
-int Bellerophon::print(ostream& out, ostream& outAcc) {
+int Bellerophon::print(ostream& out, ostream& outAcc, string s) {
        try {
                int above1 = 0;
                
@@ -130,7 +130,7 @@ int Bellerophon::print(ostream& out, ostream& outAcc) {
 }
 #ifdef USE_MPI
 //***************************************************************************************************************
-int Bellerophon::print(MPI_File& out, MPI_File& outAcc) {
+int Bellerophon::print(MPI_File& out, MPI_File& outAcc, string s) {
        try {
        
                int pid;
@@ -535,7 +535,6 @@ int Bellerophon::createSparseMatrix(int startSeq, int endSeq, SparseMatrix* spar
 int Bellerophon::generatePreferences(vector<SeqMap> left, vector<SeqMap> right, int mid){
        try {
                
-               float dme = 0.0;
                SeqMap::iterator itR;
                SeqMap::iterator itL;
                
@@ -678,7 +677,7 @@ int Bellerophon::writePrefs(string file, linePair tempLine) {
                        
                        for (int j = 0; j < numSeqs; j++) {
                                
-                               if (m->control_pressed) { outTemp.close(); remove(file.c_str()); return 0; }
+                               if (m->control_pressed) { outTemp.close(); m->mothurRemove(file); return 0; }
                                
                                outTemp << pref[i][j].name << '\t' << pref[i][j].leftParent << '\t' << pref[i][j].rightParent << '\t';
                                outTemp << pref[i][j].score << '\t' << pref[i][j].closestLeft << '\t' << pref[i][j].closestRight << '\t' << pref[i][j].midpoint <<  endl;
@@ -710,7 +709,7 @@ int Bellerophon::readPrefs(string file) {
                        
                        for (int j = 0; j < numSeqs; j++) {
                                
-                               if (m->control_pressed) { inTemp.close(); remove(file.c_str()); return 0; }
+                               if (m->control_pressed) { inTemp.close(); m->mothurRemove(file); return 0; }
                        
                                inTemp >> pref[i][j].name >> pref[i][j].leftParent >> pref[i][j].rightParent;
                                inTemp >> pref[i][j].score >> pref[i][j].closestLeft >> pref[i][j].closestRight >> pref[i][j].midpoint;
@@ -720,7 +719,7 @@ int Bellerophon::readPrefs(string file) {
                
                inTemp.close();
                
-               remove(file.c_str());
+               m->mothurRemove(file);
                
                return 0;
        }