added shannonrange calc.

[mothur.git] / filterseqscommand.cpp

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index b17d9ed6799d9c8287664cf63241b0fde01bf40e..4ac3381d384edf1979f78c911381e040666b8afe 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -558,7 +558,7 @@ int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_Fil
 
                        }
                        
-                       if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
+                       if((i+1) % 100 == 0){   cout << (i+1) << endl;          }
                }
                
                if(outputString != ""){ //output to file 
@@ -572,7 +572,7 @@ int FilterSeqsCommand::driverMPIRun(int start, int num, MPI_File& inMPI, MPI_Fil
                        delete buf;
                }
                
-               if((num) % 100 != 0){   cout << (num) << endl;   m->mothurOutJustToLog(toString(num) + "\n");   }
+               if((num) % 100 != 0){   cout << (num) << endl;          }
                        
                return 0;
        }
@@ -623,10 +623,10 @@ int FilterSeqsCommand::driverRunFilter(string F, string outputFilename, string i
                        #endif
                        
                        //report progress
-                       if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
+                       if((count) % 100 == 0){ m->mothurOutJustToScreen(toString(count)+"\n");         }
                }
                //report progress
-               if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
+               if((count) % 100 != 0){ m->mothurOutJustToScreen(toString(count)+"\n");                 }
                
                
                out.close();
@@ -990,7 +990,8 @@ int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair*
                                        
                        Sequence seq(in); m->gobble(in);
                        if (seq.getName() != "") {
-                                       if (seq.getAligned().length() != alignmentLength) { m->mothurOut("Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true;  }
+                    if (m->debug) { m->mothurOut("[DEBUG]: " + seq.getName() + " length = " + toString(seq.getAligned().length())); m->mothurOutEndLine();}
+                                       if (seq.getAligned().length() != alignmentLength) { m->mothurOut("[ERROR]: Sequences are not all the same length, please correct."); m->mothurOutEndLine(); m->control_pressed = true;  }
                                        
                                        if(trump != '*')                        {       F.doTrump(seq);         }
                                        if(m->isTrue(vertical) || soft != 0)    {       F.getFreqs(seq);        }
@@ -1006,10 +1007,10 @@ int FilterSeqsCommand::driverCreateFilter(Filters& F, string filename, linePair*
                        #endif
                        
                        //report progress
-                       if((count) % 100 == 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
+                       if((count) % 100 == 0){ m->mothurOutJustToScreen(toString(count)+"\n");                 }
                }
                //report progress
-               if((count) % 100 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine();           }
+               if((count) % 100 != 0){ m->mothurOutJustToScreen(toString(count)+"\n");         }
                in.close();
                
                return count;
@@ -1052,11 +1053,11 @@ int FilterSeqsCommand::MPICreateFilter(int start, int num, Filters& F, MPI_File&
                        cout.flush();
                                                
                        //report progress
-                       if((i+1) % 100 == 0){   cout << (i+1) << endl;   m->mothurOutJustToLog(toString(i+1) + "\n");   }
+                       if((i+1) % 100 == 0){   cout << (i+1) << endl;          }
                }
                
                //report progress
-               if((num) % 100 != 0){   cout << num << endl; m->mothurOutJustToLog(toString(num) + "\n");       }
+               if((num) % 100 != 0){   cout << num << endl;    }
                
                return 0;
        }