changing command name classify.shared to classifyrf.shared

[mothur.git] / sffinfocommand.h

diff --git a/sffinfocommand.h b/sffinfocommand.h
index e33bd59b8559bfda513c07d29f2356831e5cd4c8..5ec6e72239d0772548ce10f584ebccb435230d25 100644 (file)
--- a/sffinfocommand.h
+++ b/sffinfocommand.h
@@ -12,25 +12,23 @@
 
 #include "command.hpp"
 
-#define SFF_MAGIC   0x2e736666 /* ".sff" */
-#define SFF_VERSION "\0\0\0\1"
 
 /**********************************************************/
 struct CommonHeader {
        unsigned int magicNumber;
-       char* version;
-       unsigned long int indexOffset;
+       string version;
+       unsigned long long indexOffset;
        unsigned int indexLength;
        unsigned int numReads;
        unsigned short headerLength;
        unsigned short keyLength;
        unsigned short numFlowsPerRead;
-       char flogramFormatCode;
-       char* flowChars; //length depends on number flow reads
-       char* keySequence; //length depends on key length
+       int flogramFormatCode;
+       string flowChars; //length depends on number flow reads
+       string keySequence; //length depends on key length
        
-       CommonHeader(){ magicNumber=0; version=NULL; indexOffset=0; indexLength=0; numReads=0; headerLength=0; keyLength=0; numFlowsPerRead=0; flogramFormatCode='s'; flowChars=NULL; keySequence=NULL; }
-       ~CommonHeader() { if (version != NULL) { delete [] version; } if (flowChars != NULL) { delete [] flowChars; } if (keySequence != NULL) { delete [] keySequence; } }
+       CommonHeader(){ magicNumber=0; indexOffset=0; indexLength=0; numReads=0; headerLength=0; keyLength=0; numFlowsPerRead=0; flogramFormatCode='s'; } 
+       ~CommonHeader() { }
 };
 /**********************************************************/
 struct Header {
@@ -41,20 +39,23 @@ struct Header {
        unsigned short clipQualRight;
        unsigned short clipAdapterLeft;
        unsigned short clipAdapterRight;
-       char* name; //length depends on nameLength
+       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; name=NULL; }
-       ~Header() { if (name != NULL) { delete [] name; } }
+       Header() { headerLength=0; nameLength=0; numBases=0; clipQualLeft=0; clipQualRight=0; clipAdapterLeft=0; clipAdapterRight=0; }
+       ~Header() { } 
 };
 /**********************************************************/
 struct seqRead {
        vector<unsigned short> flowgram;
        vector<unsigned int> flowIndex;
-       char* bases;
+       string bases;
        vector<unsigned int> qualScores;
        
-       seqRead() { bases=NULL; }
-       ~seqRead() { if (bases != NULL) { delete [] bases; } }
+       seqRead() { } 
+       ~seqRead() { } 
 };
 /**********************************************************/
 
@@ -62,24 +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);
-       int readCommonHeader(ifstream&, CommonHeader*);
-       int readHeader(ifstream&, Header*);
-       int readSeqData(ifstream&, seqRead*, int, int);
+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, Header&);
+       int decodeName(string&, string&, string&, string);
+    bool readOligos(string oligosFile);
        
-       int printCommonHeader(ofstream&, CommonHeader*, bool); //bool is debug mode
-       int printHeader(ofstream&, Header*, bool);
-       int printSeqData(ofstream&, seqRead*, bool);
-               
+       int printCommonHeader(ofstream&, CommonHeader&); 
+       int printHeader(ofstream&, Header&);
+       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&);
 };
 
 /**********************************************************/