gnStringSpec.h Source File

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_