added MPI code, broke up chimera.seqs into 5 separated commands, added parse.sff...

[mothur.git] / fullmatrix.cpp

diff --git a/fullmatrix.cpp b/fullmatrix.cpp
index 72866491648e1fb02f681c1ca5842fdbba8e58a2..43c6f2e30a6dc04458e5aab7c42a8ada3636dae5 100644 (file)
--- a/fullmatrix.cpp
+++ b/fullmatrix.cpp
@@ -44,6 +44,7 @@ FullMatrix::FullMatrix(ifstream& filehandle) {
                                
                                for(int i=0;i<numSeqs;i++){
                                        filehandle >> matrix[0][i];
+                                       if (globaldata->sim) {  matrix[0][i] = 1.0 - matrix[0][i];  }
                                }
                                break;
                        }
@@ -93,6 +94,7 @@ int FullMatrix::readSquareMatrix(ifstream& filehandle) {
                                if (m->control_pressed) { delete reading;  return 0; }
                                
                                filehandle >> matrix[i][j];
+                               if (globaldata->sim) {  matrix[i][j] = 1.0 - matrix[i][j];  }
                                
                                count++;
                                reading->update(count);
@@ -135,8 +137,10 @@ int FullMatrix::readLTMatrix(ifstream& filehandle) {
                                if (m->control_pressed) { delete reading;  return 0; }
                                
                                filehandle >> distance;
-               
+                               if (globaldata->sim) {  distance = 1.0 - distance;  }
+                               
                                matrix[i][j] = distance;  matrix[j][i] = distance;
+                               
                                count++;
                                reading->update(count);
                        }