gnStringSpec.h Source File

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# gnStringSpec.h

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    00001
    00002 // File:            gnStringSpec.h
    00003 // Purpose:         implements gnContigSpec for strings
    00004 // Description:
    00005 // Changes:
    00006 // Version:         libGenome 0.1.0
    00007 // Author:          Aaron Darling
    00008 // Last Edited:     April 15, 2001, 10:34:50pm
    00009 // Modified by:
    00010 // Copyright:       (c) Aaron Darling
    00011 // Licenses:        Proprietary
    00013 #ifndef _gnStringSpec_h_
    00014 #define _gnStringSpec_h_
    00015
    00016 #include "gn/gnDefs.h"
    00017
    00018 #include <string>
    00019 #include "gn/gnContigSpec.h"
    00020 #include "gn/gnBaseSource.h"
    00021
    00026 class GNDLLEXPORT gnStringSpec : public gnContigSpec
    00027 {
    00028 public:
    00032         gnStringSpec();
    00041         gnStringSpec( const string& m_string, const gnSeqI start=0, const gnSeqI endI=GNSEQI_END, const boolean revComp = false);
    00046         gnStringSpec( const gnStringSpec& s );
    00047         ~gnStringSpec();
    00048 // Clone
    00049         gnStringSpec* Clone() const;
    00050         virtual void Clear();
    00051 // Value Access methods
    00052
    00053         virtual gnSeqI GetSourceLength() const;
    00054
    00055
    00056 // Source Spec Specific functions
    00057         virtual gnBaseSource *GetSource() const;
    00058
    00067         virtual gnStringSpec* CloneRange( const gnSeqI startI, const gnSeqI len ) const;
    00068
    00069 protected:
    00070         virtual boolean Read(const gnSeqI start, gnSeqC* buf, uint32& bufLen ) const;
    00071         string m_seqString;
    00072
    00073 }; // class gnStringSpec
    00074
    00075 inline
    00076 gnStringSpec* gnStringSpec::Clone() const
    00077 {
    00078         return new gnStringSpec( *this );
    00079 }
    00080 inline
    00081 gnSeqI gnStringSpec::GetSourceLength() const{
    00082         return m_seqString.length();
    00083 }
    00084 inline
    00085 gnBaseSource* gnStringSpec::GetSource() const
    00086 {
    00087         return NULL;
    00088 }
    00089
    00090 inline
    00091 boolean gnStringSpec::Read(const gnSeqI start, gnSeqC* buf, uint32& bufLen) const{
    00092         memcpy(buf, m_seqString.data() + start, bufLen);
    00093         return true;
    00094 }
    00095
    00096 #endif
    00097         // _gnStringSpec_h_