addition of trim.flows

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 9fc3abb8422341e755a1e54da38453002cf01dce..b40b7e5b0123d848a26df5afd803f3625df9a4a8 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -11,6 +11,7 @@
 #include "needlemanoverlap.hpp"
 
 //**********************************************************************************************************************
+
 vector<string> TrimSeqsCommand::getValidParameters(){  
        try {
                string Array[] =  {"fasta", "flip", "oligos", "maxambig", "maxhomop", "group","minlength", "maxlength", "qfile", 
@@ -25,7 +26,9 @@ vector<string> TrimSeqsCommand::getValidParameters(){
                exit(1);
        }
 }
+
 //**********************************************************************************************************************
+
 TrimSeqsCommand::TrimSeqsCommand(){    
        try {
                abort = true;
@@ -40,7 +43,9 @@ TrimSeqsCommand::TrimSeqsCommand(){
                exit(1);
        }
 }
+
 //**********************************************************************************************************************
+
 vector<string> TrimSeqsCommand::getRequiredParameters(){       
        try {
                string Array[] =  {"fasta"};
@@ -52,7 +57,9 @@ vector<string> TrimSeqsCommand::getRequiredParameters(){
                exit(1);
        }
 }
+
 //**********************************************************************************************************************
+
 vector<string> TrimSeqsCommand::getRequiredFiles(){    
        try {
                vector<string> myArray;
@@ -63,6 +70,7 @@ vector<string> TrimSeqsCommand::getRequiredFiles(){
                exit(1);
        }
 }
+
 //***************************************************************************************************************
 
 TrimSeqsCommand::TrimSeqsCommand(string option)  {
@@ -254,6 +262,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
                exit(1);
        }
 }
+
 //**********************************************************************************************************************
 
 void TrimSeqsCommand::help(){
@@ -1433,6 +1442,7 @@ bool TrimSeqsCommand::compareDNASeq(string oligo, string seq){
        }
 
 }
+
 //***************************************************************************************************************
 
 int TrimSeqsCommand::countDiffs(string oligo, string seq){