#include <gnStringSpec.h>
Inheritance diagram for gnStringSpec:
Public Member Functions | |
virtual void | Clear () |
Clears all data from this spec. | |
gnStringSpec * | Clone () const |
virtual gnStringSpec * | CloneRange (const gnSeqI startI, const gnSeqI len) const |
Copies a specified range of bases and returns a pointer to the resulting gnStringSpec. | |
virtual gnBaseSource * | GetSource () const |
virtual gnSeqI | GetSourceLength () const |
Get the length of the source for this spec. | |
gnStringSpec (const gnStringSpec &s) | |
Copy constructor. | |
gnStringSpec (const string &m_string, const gnSeqI startI=0, const gnSeqI endI=GNSEQI_END, const boolean revComp=false) | |
Constructor, creates a gnStringSpec using sequence data in the given string. | |
gnStringSpec () | |
Empty constructor. | |
~gnStringSpec () | |
Protected Member Functions | |
virtual boolean | Read (const gnSeqI start, gnSeqC *buf, gnSeqI &bufLen) const |
all derived classes must implement this! it simply reads the specified bases into buf, disregarding circularity and reverse complement. | |
Protected Attributes | |
string | m_seqString |
For a more complete description see the gnBaseSpec documentation.
Definition at line 25 of file gnStringSpec.h.
|
Empty constructor. Definition at line 16 of file gnStringSpec.cpp. References gnContigSpec::Clear(). Referenced by Clone(), and CloneRange(). |
|
Constructor, creates a gnStringSpec using sequence data in the given string. A circular spec will be created if the end index is greater than the start.
References gnSeqI, and m_seqString. |
|
Copy constructor.
References gnBaseSpec::m_circular, gnContigSpec::m_length, gnBaseSpec::m_name, gnBaseSpec::m_reverseComplement, m_seqString, gnContigSpec::m_SourceContigIndex, gnBaseSpec::m_sourceName, and gnContigSpec::m_start. |
|
Definition at line 55 of file gnStringSpec.cpp. References Clear(). |
|
Clears all data from this spec.
Reimplemented from gnContigSpec. Definition at line 59 of file gnStringSpec.cpp. References gnContigSpec::Clear(), and m_seqString. Referenced by ~gnStringSpec(). |
|
Implements gnContigSpec. Definition at line 75 of file gnStringSpec.h. References gnStringSpec(). |
|
Copies a specified range of bases and returns a pointer to the resulting gnStringSpec. You must delete the copy when you are finished with it.
Implements gnContigSpec. Definition at line 65 of file gnStringSpec.cpp. References gnSeqI, gnStringSpec(), gnBaseSpec::m_circular, gnContigSpec::m_length, gnBaseSpec::m_name, gnBaseSpec::m_reverseComplement, m_seqString, gnContigSpec::m_SourceContigIndex, gnBaseSpec::m_sourceName, and gnContigSpec::m_start. |
|
Definition at line 84 of file gnStringSpec.h. |
|
Get the length of the source for this spec.
Implements gnContigSpec. Definition at line 80 of file gnStringSpec.h. References gnSeqI, and m_seqString. |
|
all derived classes must implement this! it simply reads the specified bases into buf, disregarding circularity and reverse complement.
Implements gnContigSpec. Definition at line 90 of file gnStringSpec.h. References gnSeqC, gnSeqI, and m_seqString. |
|
Definition at line 70 of file gnStringSpec.h. Referenced by Clear(), CloneRange(), GetSourceLength(), gnStringSpec(), and Read(). |