modified trim.seqs command

[mothur.git] / trimseqscommand.cpp

diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 40b3b4fbd11c711965ddddf531ee07d95e246c67..95a85ac23b3a347e25cbc11c03350ef49ae7cb58 100644 (file)
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -7,7 +7,6 @@
  *
  */
 
-#include "sequence.hpp"
 #include "trimseqscommand.h"
 
 //***************************************************************************************************************
@@ -15,11 +14,7 @@
 TrimSeqsCommand::TrimSeqsCommand(){
        try {
                
-               oligos = 0;
-               forwardPrimerMismatch = 0;
-               reversePrimerMismatch = 0;
-               barcodeMismatch = 0;
-               
+               oligos = 0;             
                totalBarcodeCount = 0;
                matchBarcodeCount = 0;
                
@@ -28,18 +23,10 @@ TrimSeqsCommand::TrimSeqsCommand(){
                        cout << "you need to at least enter a fasta file name" << endl;
                }
                
-               if(isTrue(globaldata->getFlip()))       {       flip = 1;       }
-               
-               if(globaldata->getOligosFile() != ""){
-                       oligos = 1;
-                       forwardPrimerMismatch = atoi(globaldata->getForwardMismatch().c_str());
-                       reversePrimerMismatch = atoi(globaldata->getReverseMismatch().c_str());
-                       barcodeMismatch = atoi(globaldata->getBarcodeMismatch().c_str());
-               }
-               
-               if(!flip && !oligos)    {       cout << "what was the point?" << endl;                                                  }
+               if(isTrue(globaldata->getFlip()))               {       flip = 1;                               }
+               if(globaldata->getOligosFile() != "")   {       oligos = 1;                             }
+               if(!flip && !oligos)                                    {       cout << "huh?" << endl; }
 
-               
        }
        catch(exception& e) {
                cout << "Standard Error: " << e.what() << " has occurred in the TrimSeqsCommand class Function TrimSeqsCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
@@ -80,6 +67,7 @@ int TrimSeqsCommand::execute(){
                
                while(!inFASTA.eof()){
                        Sequence currSeq(inFASTA);
+                       string origSeq = currSeq.getUnaligned();
                        string group;
                        string trashCode = "";
 
@@ -103,6 +91,7 @@ int TrimSeqsCommand::execute(){
                        }
                        else{
                                currSeq.setName(currSeq.getName() + '|' + trashCode);
+                               currSeq.setUnaligned(origSeq);
                                currSeq.printSequence(scrapFASTA);
                        }
                        
@@ -210,8 +199,8 @@ bool TrimSeqsCommand::stripForward(Sequence& seq){
                        success = 1;
                        break;
                }
-               
        }
+       
        totalFPrimerCount++;
        return success;
        
@@ -238,8 +227,8 @@ bool TrimSeqsCommand::stripReverse(Sequence& seq){
                        success = 1;
                        break;
                }
-               
-       }
+       }       
+       
        totalRPrimerCount++;
        return success;