added create.database command. fixed help in get.sharedseqs. added new constructor...

[mothur.git] / trimflowscommand.cpp

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 00c4d94e1027c63d8a0c324167bb3d7ec8e4c570..0557c71bda3453068175fe3d405ff87972df80e1 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -207,6 +207,8 @@ TrimFlowsCommand::TrimFlowsCommand(string option)  {
 
                        numFPrimers = 0;
                        numRPrimers = 0;
+            numLinkers = 0;
+            numSpacers = 0;
                }
                
        }
@@ -387,7 +389,7 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN
                int count = 0;
                bool moreSeqs = 1;
                
-               TrimOligos trimOligos(pdiffs, bdiffs, primers, barcodes, revPrimer);
+               TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer);
                
                while(moreSeqs) {
                                
@@ -542,9 +544,8 @@ void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
 
                                }
                                else if(type == "REVERSE"){
-                                       Sequence oligoRC("reverse", oligo);
-                                       oligoRC.reverseComplement();
-                                       revPrimer.push_back(oligoRC.getUnaligned());
+                                       string oligoRC = reverseOligo(oligo);
+                                       revPrimer.push_back(oligoRC);
                                }
                                else if(type == "BARCODE"){
                                        oligosFile >> group;
@@ -633,6 +634,47 @@ void TrimFlowsCommand::getOligos(vector<vector<string> >& outFlowFileNames){
                exit(1);
        }
 }
+//********************************************************************/
+string TrimFlowsCommand::reverseOligo(string oligo){
+       try {
+        string reverse = "";
+        
+        for(int i=oligo.length()-1;i>=0;i--){
+            
+            if(oligo[i] == 'A')                {       reverse += 'T'; }
+            else if(oligo[i] == 'T'){  reverse += 'A'; }
+            else if(oligo[i] == 'U'){  reverse += 'A'; }
+            
+            else if(oligo[i] == 'G'){  reverse += 'C'; }
+            else if(oligo[i] == 'C'){  reverse += 'G'; }
+            
+            else if(oligo[i] == 'R'){  reverse += 'Y'; }
+            else if(oligo[i] == 'Y'){  reverse += 'R'; }
+            
+            else if(oligo[i] == 'M'){  reverse += 'K'; }
+            else if(oligo[i] == 'K'){  reverse += 'M'; }
+            
+            else if(oligo[i] == 'W'){  reverse += 'W'; }
+            else if(oligo[i] == 'S'){  reverse += 'S'; }
+            
+            else if(oligo[i] == 'B'){  reverse += 'V'; }
+            else if(oligo[i] == 'V'){  reverse += 'B'; }
+            
+            else if(oligo[i] == 'D'){  reverse += 'H'; }
+            else if(oligo[i] == 'H'){  reverse += 'D'; }
+            
+            else                                               {       reverse += 'N'; }
+        }
+        
+        
+        return reverse;
+    }
+       catch(exception& e) {
+               m->errorOut(e, "TrimFlowsCommand", "reverseOligo");
+               exit(1);
+       }
+}
+
 /**************************************************************************************************/
 vector<unsigned long long> TrimFlowsCommand::getFlowFileBreaks() {