changed random forest output filename

[mothur.git] / sffinfocommand.h

diff --git a/sffinfocommand.h b/sffinfocommand.h
index 219e125943a812ac9bfdd026fe0608cdb2a8f5fe..5ec6e72239d0772548ce10f584ebccb435230d25 100644 (file)
--- a/sffinfocommand.h
+++ b/sffinfocommand.h
@@ -17,7 +17,7 @@
 struct CommonHeader {
        unsigned int magicNumber;
        string version;
-       unsigned long int indexOffset;
+       unsigned long long indexOffset;
        unsigned int indexLength;
        unsigned int numReads;
        unsigned short headerLength;
@@ -40,6 +40,9 @@ struct Header {
        unsigned short clipAdapterLeft;
        unsigned short clipAdapterRight;
        string name; //length depends on nameLength
+       string timestamp;
+       string region;
+       string xy;
        
        Header() { headerLength=0; nameLength=0; numBases=0; clipQualLeft=0; clipQualRight=0; clipAdapterLeft=0; clipAdapterRight=0; }
        ~Header() { } 
@@ -60,24 +63,59 @@ class SffInfoCommand : public Command {
        
 public:
        SffInfoCommand(string);
-       ~SffInfoCommand();
-       int execute();
-       void help();
+       SffInfoCommand();
+       ~SffInfoCommand(){}
        
-private:
-       string sffFilename, outputDir;
-       vector<string> filenames, outputNames;
-       bool abort;
+       vector<string> setParameters();
+       string getCommandName()                 { return "sffinfo";                                     }
+       string getCommandCategory()             { return "Sequence Processing";         }
+       
+       string getHelpString(); 
+    string getOutputPattern(string);   
+       string getCitation() { return "http://www.mothur.org/wiki/Sffinfo"; }
+       string getDescription()         { return "extract sequences reads from a .sff file"; }
+
+       int execute(); 
+       void help() { m->mothurOut(getHelpString()); }  
        
-       int extractSffInfo(string, string);
+private:
+       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, 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&);
-       int printSeqData(ofstream&, seqRead&);
-               
+       int printSffTxtSeqData(ofstream&, seqRead&, Header&);
+       int printFlowSeqData(ofstream&, seqRead&, Header&);
+       int printFastaSeqData(ofstream&, seqRead&, Header&);
+       int printQualSeqData(ofstream&, seqRead&, Header&);
+       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&);
+       vector<unsigned short> parseHeaderLineToFloatVector(ifstream&, int);
+       vector<unsigned int> parseHeaderLineToIntVector(ifstream&, int);
+       string parseHeaderLineToString(ifstream&);
 };
 
 /**********************************************************/