fix trim.seqs / qualscores bug

[mothur.git] / shhhercommand.h

diff --git a/shhhercommand.h b/shhhercommand.h
index b423b4d320acd81ecb1c2e67b1f4ba6c3ad9d3fc..acceb7fdba0aa19c3e5f8b032d11d5ad872dca5c 100644 (file)
--- a/shhhercommand.h
+++ b/shhhercommand.h
@@ -33,25 +33,27 @@ private:
        int abort;
        map<string, vector<string> > outputTypes;
        
-       string outputDir, flowFileName, flowFilesFileName, lookupFileName;
+       string outputDir, flowFileName, flowFilesFileName, lookupFileName, compositeFASTAFileName;
+
        int processors, maxIters;
        float cutoff, sigma, minDelta;
        
        vector<int> nSeqsBreaks;
        vector<int> nOTUsBreaks;
-       vector<double> flowDataPrI;
-       vector<short> flowDataIntI;
-       vector<int> lengths;
-       vector<string> seqNameVector;
        vector<double> singleLookUp;
        vector<double> jointLookUp;
+       
+       vector<string> seqNameVector;
+       vector<int> lengths;
+       vector<short> flowDataIntI;
+       vector<double> flowDataPrI;
        map<string, int> nameMap;
        vector<int> otuData;
        vector<int> cumNumSeqs;
        vector<int> nSeqsPerOTU;
        vector<vector<int> > aaP;       //tMaster->aanP:        each row is a different otu / each col contains the sequence indices
-       vector<int> seqNumber;          //tMaster->anP:         the sequence id number sorted by OTU
        vector<vector<int> > aaI;       //tMaster->aanI:        that are in each otu - can't differentiate between aaP and aaI 
+       vector<int> seqNumber;          //tMaster->anP:         the sequence id number sorted by OTU
        vector<int> seqIndex;           //tMaster->anI;         the index that corresponds to seqNumber
        vector<double> dist;            //adDist - distance of sequences to centroids
        vector<short> change;           //did the centroid sequence change? 0 = no; 1 = yes
@@ -60,9 +62,9 @@ private:
        vector<double> singleTau;       //tMaster->adTau:       1-D Tau vector (1xnumSeqs)
        vector<short> uniqueFlowgrams;
        vector<int> uniqueCount;
-       vector<int> uniqueLengths;
        vector<int> mapSeqToUnique;
        vector<int> mapUniqueToSeq;
+       vector<int> uniqueLengths;
        
        int numSeqs, numUniques, numOTUs, numFlowCells;
        
@@ -110,4 +112,5 @@ private:
 };
 
 
-#endif
\ No newline at end of file
+#endif
+