fixed issue in tree.shared when shared file was not sorted

[mothur.git] / trimseqscommand.h

diff --git a/trimseqscommand.h b/trimseqscommand.h
index 8d9a57a54ffd0db053956200602f3aa06fb4de5b..60d29f9e56024de7a0d6d39478ce12872788acd5 100644 (file)
--- a/trimseqscommand.h
+++ b/trimseqscommand.h
@@ -27,8 +27,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "trim.seqs";   }
        string getCommandCategory()             { return "Sequence Processing";         }
-       string getOutputFileNameTag(string, string);
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Trim.seqs"; }
        string getDescription()         { return "provides the preprocessing features needed to screen and sort pyrosequences"; }
 
@@ -61,7 +62,6 @@ private:
        vector<string> revPrimer, outputNames;
        set<string> filesToRemove;
        map<string, int> barcodes;
-    map<string, int> rbarcodes;
        vector<string> groupVector;
        map<string, int> primers;
     vector<string>  linker;
@@ -102,7 +102,6 @@ struct trimData {
        double qRollAverage, qThreshold, qWindowAverage, qAverage;
     vector<string> revPrimer;
        map<string, int> barcodes;
-    map<string, int> rbarcodes;
        map<string, int> primers;
     map<string, int> nameCount;
     vector<string>  linker;
@@ -116,7 +115,7 @@ struct trimData {
     
        trimData(){}
        trimData(string fn, string qn, string nf, string cf, string tn, string sn, string tqn, string sqn, string tnn, string snn, string tcn, string scn,string gn, vector<vector<string> > ffn, vector<vector<string> > qfn, vector<vector<string> > nfn, unsigned long long lstart, unsigned long long lend, unsigned long long qstart, unsigned long long qend,  MothurOut* mout,
-                      int pd, int bd, int ld, int sd, int td, map<string, int> pri, map<string, int> bar, map<string, int> rbar, vector<string> revP, vector<string> li, vector<string> spa, 
+                      int pd, int bd, int ld, int sd, int td, map<string, int> pri, map<string, int> bar, vector<string> revP, vector<string> li, vector<string> spa, 
                       vector<string> priNameVector, vector<string> barNameVector, bool cGroup, bool aFiles, bool keepF, int keepfi, int removeL,
                       int WindowStep, int WindowSize, int WindowAverage, bool trim, double Threshold, double Average, double RollAverage,
                       int minL, int maxA, int maxH, int maxL, bool fli, map<string, string> nm, map<string, int> ncount) {
@@ -149,7 +148,6 @@ struct trimData {
         sdiffs = sd;
         tdiffs = td;
         barcodes = bar;
-        rbarcodes = rbar;
         primers = pri;      numFPrimers = primers.size();
         revPrimer = revP;   numRPrimers = revPrimer.size();
         linker = li;        numLinkers = linker.size();
@@ -254,7 +252,7 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                }
                
                
-               TrimOligos trimOligos(pDataArray->pdiffs, pDataArray->bdiffs, pDataArray->ldiffs, pDataArray->sdiffs, pDataArray->primers, pDataArray->barcodes, pDataArray->rbarcodes, pDataArray->revPrimer, pDataArray->linker, pDataArray->spacer);
+               TrimOligos trimOligos(pDataArray->pdiffs, pDataArray->bdiffs, pDataArray->ldiffs, pDataArray->sdiffs, pDataArray->primers, pDataArray->barcodes, pDataArray->revPrimer, pDataArray->linker, pDataArray->spacer);
         
                pDataArray->count = pDataArray->lineEnd;
                for(int i = 0; i < pDataArray->lineEnd; i++){ //end is the number of sequences to process
@@ -299,12 +297,6 @@ static DWORD WINAPI MyTrimThreadFunction(LPVOID lpParam){
                                        else{ currentSeqsDiffs += success;  }
                                }
                 
-                               if(pDataArray->rbarcodes.size() != 0){
-                                       success = trimOligos.stripRBarcode(currSeq, currQual, barcodeIndex);
-                                       if(success > pDataArray->bdiffs)                {       trashCode += 'b';       }
-                                       else{ currentSeqsDiffs += success;  }
-                               }
-                
                 if(pDataArray->numSpacers != 0){
                                        success = trimOligos.stripSpacer(currSeq, currQual);
                                        if(success > pDataArray->sdiffs)                {       trashCode += 's';       }