SequenceListImpl Class Reference

#include <sequence_list_impl.hh>

Public Types

typedef
SequenceImplListConstIterator 
ConstIterator
typedef SequenceImplListIterator Iterator

Public Member Functions

 SequenceListImpl ()
void AddSequence (const SequenceImplPtr &sequence)
int GetCount () const
SequenceImplPtrGetSequence (int i)
const SequenceImplPtrGetSequence (unsigned int i) const
void RemoveSequence (int index)
int GetPos (int seq_index, int residue_index) const
int GetResidueIndex (int seq_index, int pos) const
SequenceImplPtr FindSequence (const String &name) const
int FindSequenceIndex (const String &name) const
String ToString (int width=80) const
SequenceListImplPtr Slice (int first, int n) const
int GetMinLength () const
int GetMaxLength () const
bool SequencesHaveEqualLength () const
Real GetCoverage (int seq_index) const
SequenceListImplPtr Copy () const
Iterator Begin ()
Iterator End ()
ConstIterator Begin () const
ConstIterator End () const

Detailed Description

Definition at line 33 of file sequence_list_impl.hh.


Member Typedef Documentation

Definition at line 35 of file sequence_list_impl.hh.

Definition at line 36 of file sequence_list_impl.hh.


Constructor & Destructor Documentation

SequenceListImpl (  )  [inline]

Definition at line 37 of file sequence_list_impl.hh.


Member Function Documentation

void AddSequence ( const SequenceImplPtr sequence  ) 

add sequence

ConstIterator Begin (  )  const [inline]

Definition at line 89 of file sequence_list_impl.hh.

Iterator Begin (  )  [inline]

Definition at line 87 of file sequence_list_impl.hh.

SequenceListImplPtr Copy (  )  const
ConstIterator End (  )  const [inline]

Definition at line 90 of file sequence_list_impl.hh.

Iterator End (  )  [inline]

Definition at line 88 of file sequence_list_impl.hh.

SequenceImplPtr FindSequence ( const String name  )  const
int FindSequenceIndex ( const String name  )  const
int GetCount (  )  const [inline]

get number of sequences in list

Definition at line 42 of file sequence_list_impl.hh.

Real GetCoverage ( int  seq_index  )  const
int GetMaxLength (  )  const
int GetMinLength (  )  const
int GetPos ( int  seq_index,
int  residue_index 
) const
int GetResidueIndex ( int  seq_index,
int  pos 
) const
const SequenceImplPtr& GetSequence ( unsigned int  i  )  const [inline]

Definition at line 52 of file sequence_list_impl.hh.

SequenceImplPtr& GetSequence ( int  i  )  [inline]

Definition at line 44 of file sequence_list_impl.hh.

void RemoveSequence ( int  index  ) 
bool SequencesHaveEqualLength (  )  const [inline]

Definition at line 78 of file sequence_list_impl.hh.

SequenceListImplPtr Slice ( int  first,
int  n 
) const
String ToString ( int  width = 80  )  const

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