---

gnStringSpec Class Reference

gnStringSpec stores a sequence and annotation data in memory. More...

#include <gnStringSpec.h>

Inheritance diagram for gnStringSpec::

List of all members.

Public Methods
	gnStringSpec ()
	Empty constructor. More...
	gnStringSpec (const string &m_string, const gnSeqI start=0, const gnSeqI endI=GNSEQI_END, const boolean revComp=false)
	Constructor, creates a gnStringSpec using sequence data in the given string. More...
	gnStringSpec (const gnStringSpec &s)
	Copy constructor. More...
	~gnStringSpec ()
gnStringSpec*	Clone () const
virtual void	Clear ()
	Clears all data from this spec. More...
virtual gnSeqI	GetSourceLength () const
	Get the length of the source for this spec. More...
virtual gnBaseSource*	GetSource () 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. More...
Protected Methods
virtual boolean	Read (const gnSeqI start, gnSeqC *buf, uint32 &bufLen) const
	all derived classes must implement this! it simply reads the specified bases into buf, disregarding circularity and reverse complement. More...
Protected Attributes
string	m_seqString

---

Detailed Description

gnStringSpec stores a sequence and annotation data in memory.

For a more complete description see the gnBaseSpec documentation.

Definition at line 26 of file gnStringSpec.h.

---

Constructor & Destructor Documentation

gnStringSpec::gnStringSpec ( )

Empty constructor. Definition at line 17 of file gnStringSpec.cpp. Referenced by Clone(), and CloneRange().

gnStringSpec::gnStringSpec ( const string & m_string, const gnSeqI start = 0, const gnSeqI endI = GNSEQI_END, const boolean revComp = false )

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. Parameters: m_string   The string to read base pairs from. startI   The index to start reading base pairs from the string. endI   The index to stop reading base pairs from the string. revComp   True if the sequence is read reverse complement. Definition at line 22 of file gnStringSpec.cpp.

gnStringSpec::gnStringSpec ( const gnStringSpec & s )

Copy constructor. Parameters: s   the gnStringSpec to copy. Definition at line 45 of file gnStringSpec.cpp.

gnStringSpec::~gnStringSpec ( )

Definition at line 56 of file gnStringSpec.cpp.

---

Member Function Documentation

void gnStringSpec::Clear ( ) [virtual]

Clears all data from this spec. Reimplemented from gnContigSpec. Definition at line 60 of file gnStringSpec.cpp. Referenced by gnStringSpec(), and ~gnStringSpec().

gnStringSpec * gnStringSpec::Clone ( ) const [inline, virtual]

Reimplemented from gnContigSpec. Definition at line 76 of file gnStringSpec.h.

gnStringSpec * gnStringSpec::CloneRange ( const gnSeqI startI, const gnSeqI len ) const [virtual]

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. Parameters: startI   The first base pair to copy len   The length of the piece to copy Returns: A copy of the gnStringSpec containing only the specified bases Definition at line 66 of file gnStringSpec.cpp.

gnBaseSource * gnStringSpec::GetSource ( ) const [inline, virtual]

Definition at line 85 of file gnStringSpec.h.

gnSeqI gnStringSpec::GetSourceLength ( ) const [inline, virtual]

Get the length of the source for this spec. Returns: The source length. Reimplemented from gnContigSpec. Definition at line 81 of file gnStringSpec.h.

boolean gnStringSpec::Read ( const gnSeqI start, gnSeqC * buf, uint32 & bufLen ) const [inline, protected, virtual]

all derived classes must implement this! it simply reads the specified bases into buf, disregarding circularity and reverse complement. Reimplemented from gnContigSpec. Definition at line 91 of file gnStringSpec.h.

---

Member Data Documentation

string gnStringSpec::m_seqString [protected]

Definition at line 71 of file gnStringSpec.h.

---

The documentation for this class was generated from the following files:

• gnStringSpec.h
• gnStringSpec.cpp

---