ReadData.hh Source File

00001 #ifndef READDATA_HH
00002 #define READDATA_HH 1
00003 
00008 #include <string>
00009 #include <map>
00010 #include <map>
00011 #include <vector>
00012 
00013 using namespace std;
00014 
00015 /*
00016 template<> struct hash< std::string >
00017 {
00018   size_t operator()( const std::string& x ) const
00019   {
00020           return hash< const char* >()( x.c_str() );
00021   }
00022 };
00023 */
00024 
00025 namespace libSlice
00026 {
00027   using std::string;
00028   using std::map;
00029   using std::vector;
00030 
00034   class ReadData
00035   {
00036   public:
00037     ReadData(const char * id, 
00038              const char * seqname,
00039              const char * dir, 
00040              const char * chem);
00041 
00042     void addClrData (const char * left,
00043                      const char * right);
00044 
00045     void setClrData(long int clrleft, long int clrright);
00046     void setSeqData(long int seqleft, long int seqright);
00047 
00048     void addNucData (const char * buffer, bool isLeft);
00049     void addQualData(const char * buffer, bool isLeft);
00050 
00051     void flushTrimmedSeq();
00052     void flushTrimmedSeqSide(bool flushLeft);
00053 
00054     void reverseCompliment();
00055 
00056     void resetId(const string & id);
00057 
00058     char           isReverseCompliment()                  const;
00059 
00060     void           printXML(ostream & out, 
00061                             const string & prefix="    ") const;
00062 
00063     long           getSeqleft()                           const;
00064     long           getSeqright()                          const;
00065     long           getClrleft()                           const;
00066     long           getClrright()                          const;
00067 
00068     const string & getId()                                const;
00069     const string & getSeqname()                           const;
00070     const string & getChem()                              const;
00071     const string & getRawNucData(bool getLeft)            const;
00072     const string & getRawQualData(bool getLeft)           const;
00073 
00074     const string   getNucData(bool getLeft)               const;
00075     const string   getQualData(bool getLeft)              const;
00076 
00077   private:
00078     void validateSeqdata()                                const;
00079     void parseDirection();
00080 
00081     string m_id;
00082     string m_seqname;
00083     string m_dir;
00084     string m_chem;
00085 
00086     string m_leftnuc;
00087     string m_leftqual;
00088     string m_rightnuc;
00089     string m_rightqual;
00090 
00091     long m_seqleft;
00092     long m_seqright;
00093     long m_clrleft;
00094     long m_clrright;
00095 
00096     char m_rc;
00097   };
00098 
00100   typedef map<string, ReadData *> ReadMap;
00101 
00106   class ReadManager
00107   {
00108   public:
00109     ReadManager();
00110     ~ReadManager();
00111 
00112     int size() const;
00113 
00114     ReadData * addReadData(const char * id, 
00115                            const char * seqname,
00116                            const char * dir, 
00117                            const char * chem);
00118 
00119     void       insertRead(ReadData * rd);
00120 
00121     void       resetReadId(ReadData * rd, const string & id);
00122     void       removeRead(const string & id);
00123 
00124     ReadData * getNextRead();
00125     void       resetReadIterator();
00126 
00127     void       printXML(ostream & out, const string & prefix="  ") const;
00128 
00129     ReadData * find(const string & readId)                         const;
00130 
00131   private:
00132 
00133     ReadMap m_readMap;
00134     ReadMap::const_iterator m_readIterator;
00135   };
00136 }
00137 
00138 #endif