changed random forest output filename

[mothur.git] / sffinfocommand.h

diff --git a/sffinfocommand.h b/sffinfocommand.h
index 4e72a960a7bb07d4e94df795bea462519f6d777a..5ec6e72239d0772548ce10f584ebccb435230d25 100644 (file)
--- a/sffinfocommand.h
+++ b/sffinfocommand.h
@@ -69,8 +69,9 @@ public:
        vector<string> setParameters();
        string getCommandName()                 { return "sffinfo";                                     }
        string getCommandCategory()             { return "Sequence Processing";         }
-       string getOutputFileNameTag(string, string);
+       
        string getHelpString(); 
+    string getOutputPattern(string);   
        string getCitation() { return "http://www.mothur.org/wiki/Sffinfo"; }
        string getDescription()         { return "extract sequences reads from a .sff file"; }
 
@@ -78,18 +79,24 @@ public:
        void help() { m->mothurOut(getHelpString()); }  
        
 private:
-       string sffFilename, sfftxtFilename, outputDir, accnosName;
-       vector<string> filenames, outputNames, accnosFileNames;
-       bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos;
-       int mycount;
+       string sffFilename, sfftxtFilename, outputDir, accnosName, currentFileName, oligosfile, noMatchFile;
+       vector<string> filenames, outputNames, accnosFileNames, oligosFileNames;
+       bool abort, fasta, qual, trim, flow, sfftxt, hasAccnos, hasOligos;
+       int mycount, split, numFPrimers, numLinkers, numSpacers, pdiffs, bdiffs, ldiffs, sdiffs, tdiffs;
        set<string> seqNames;
+    map<string, int> barcodes;
+    map<string, int> primers;
+    vector<string> linker, spacer, primerNameVector, barcodeNameVector, revPrimer;
+    vector<vector<int> > numSplitReads;
+    vector<vector<string> > filehandles, filehandlesHeaders;
     
        //extract sff file functions
-       int extractSffInfo(string, string);
+       int extractSffInfo(string, string, string);
        int readCommonHeader(ifstream&, CommonHeader&);
-       int readHeader(ifstream&, Header&);
-       int readSeqData(ifstream&, seqRead&, int, int);
+       //int readHeader(ifstream&, Header&);
+       int readSeqData(ifstream&, seqRead&, int, Header&);
        int decodeName(string&, string&, string&, string);
+    bool readOligos(string oligosFile);
        
        int printCommonHeader(ofstream&, CommonHeader&); 
        int printHeader(ofstream&, Header&);
@@ -100,6 +107,9 @@ private:
        int readAccnosFile(string);
        int parseSffTxt();
        bool sanityCheck(Header&, seqRead&);
+    int adjustCommonHeader(CommonHeader);
+    int findGroup(Header header, seqRead read, int& barcode, int& primer);
+    string reverseOligo(string oligo);
     
        //parsesfftxt file functions
        int parseHeaderLineToInt(ifstream&);