SliceData.hh Source File

00001 #ifndef SLICEDATA_HH
00002 #define SLICEDATA_HH 1
00003 
00008 #include <string>
00009 #include "Exceptions.hh"
00010 #include "Slice.h"
00011 #include "ReadData.hh"
00012 #include "ConsensusData.hh"
00013 
00026 namespace libSlice
00027 {
00028   class ConsensusData;
00029 
00038   class SliceData
00039   {
00040   public:
00041     SliceData(const ReadManager & readManager,
00042               const char * index, 
00043               const char * gindex,
00044               const char * existing,
00045               long sliceRangeIndex=0,
00046               long sliceRangeGindex=0);
00047 
00048     virtual ~SliceData();
00049 
00050     void addNuc     (const char * nucData);
00051     void addQualVal (const char * qualVal);
00052     void addReadId  (const char * readId);
00053 
00054 
00055     void print(ostream & out, const string & prefix = "");
00056     void printError(ostream & out) const;
00057     void printXML(ostream & out, const string & prefix = "    ");
00058 
00059     int getErrorCode() const;
00060     int getErrorOperation() const;
00061 
00062     void setDistributionTable(double freqA, double freqC,
00063                               double freqG, double freqT,
00064                               double freqGap);
00065 
00066     void setHighQualityThreshold(int highQualityThreshold);
00067     void setDoAmbiguity(int doAmbiguity);
00068     void setScoringModel(int scoringModel);
00069 
00070     ConsensusData doCalculations(bool recallEmpty = false);
00071 
00073     enum SliceErrorCode
00074     {
00075       SLICE_NOERROR = 0,
00076       SLICE_ERR_GETCONSENSUS,
00077       SLICE_ERR_QV_NONNUMERIC,
00078       SLICE_ERR_UNDERFLOW,
00079       SLICE_ERR_OVERFLOW,
00080       SLICE_ERR_NO_READID,
00081       SLICE_ERR_CALCULATION_NOT_DONE
00082     };
00083 
00085     enum StringOperation
00086     {
00087       STROP_NONE = 0,
00088       STROP_GET_QUAL_VAL,
00089       STROP_IS_REVERSE_COMPLIMENT
00090     };
00091 
00092     unsigned short   getDepth()                     const;
00093     ReadData *       getRead(unsigned short index)  const;
00094     long             getIndex()                     const;
00095     long             getGindex()                    const;
00096 
00097     char             getBase(unsigned short index);
00098     char             getQualVal(unsigned short index);
00099     char             getConsensus();
00100 
00101     static char      getBaseCompliment(char base);
00102 
00103     const string &   getNucData()                    const;
00104     const string &   getQualValData()                const;
00105     const string &   getReadIdData()                 const;
00106 
00107     void             resetIndex(long index, long gindex);
00108     void             resetReadId();
00109     void             resetQualVal();
00110     void             resetNuc();
00111     void             setConsensus(char consensus);
00112 
00113 
00114   private:
00115     const ReadManager & m_readManager;
00116 
00117     void           flattenSlice();
00118 
00119     char *         getBases(int len) const;
00120 
00121     char           getExisting()                    const;
00122     char *         getQualVals(int len);
00123     char *         getReverseCompliments(int len);
00124     char *         foreach(const string & data, int numresults,
00125                            StringOperation operation,
00126                            const char * underflowError,
00127                            const char * overflowError);
00128 
00129     libSlice_Slice * m_slice;
00130 
00131     long m_index;
00132     long m_gindex;
00133     string m_existing;
00134     string m_indexstr;
00135 
00136     string m_nucData;
00137     string m_qualValData;
00138     string m_readIdData;
00139 
00140     int    m_highQualityThreshold;
00141     int    m_doAmbiguity;
00142     int    m_scoringModel;
00143 
00144     libSlice_BaseDistribution m_distribution;
00145 
00146     SliceErrorCode  m_errorCode;
00147     StringOperation m_errorOperation;
00148     string          m_errorData;
00149   };
00150 }
00151 
00152 ostream & operator<< (ostream & os, libSlice::SliceData & slice);
00153 ostream & operator<< (ostream & os, libSlice::SliceData * slice);
00154 
00155 
00156 #endif
00157 
00158