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core::sequence::CompositeSequence Class Reference

#include <CompositeSequence.hh>

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Collaboration diagram for core::sequence::CompositeSequence:
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Public Member Functions

 CompositeSequence ()
 ctors More...
 
 CompositeSequence (CompositeSequence const &src)
 copy ctor More...
 
core::Size n_seqs () const
 
utility::vector1< SequenceOPseqs () const
 
void add_sequence (SequenceOP seq)
 
virtual Size length () const
 Returns the number of characters in this object. More...
 
virtual void delete_position (core::Size pos)
 Deletes the given position from the Sequence and shifts everything else back by one. More...
 
virtual void insert_char (core::Size pos, char new_char)
 Inserts a character at the given position. More...
 
SequenceOP seq (core::Size idx) const
 
CompositeSequenceoperator= (CompositeSequence const &rhs)
 assignment operator. More...
 
virtual ~CompositeSequence ()
 dtor More...
 
virtual SequenceOP clone () const
 Returns an owning pointer to a new CompositeSequence object, with data that is a deep copy of the information in this object. More...
 
virtual std::string to_string () const
 
virtual std::string type () const
 
- Public Member Functions inherited from core::sequence::Sequence
 Sequence ()
 ctor More...
 
 Sequence (std::string seq, std::string id, core::Size start=1)
 
 Sequence (core::pose::Pose const &pose)
 
 Sequence (Sequence const &src)
 copy constructor. More...
 
virtual ~Sequence ()
 dtor More...
 
virtual void read_from_file (utility::file::FileName const &)
 initializes this sequence object from a file. More...
 
void sequence (std::string sequence)
 sets sequence to the given value. More...
 
void id (std::string new_id)
 sets id to the given value. More...
 
void start (core::Size new_start)
 sets starting index to the given value. More...
 
void gap_char (char gap_char)
 sets gap_char to the given value. More...
 
core::Size ungapped_length () const
 Returns the number of characters in this object, ignoring gaps. More...
 
core::Size start () const
 Returns the start of this object. More...
 
std::string id () const
 Returns the id of this object. More...
 
char gap_char () const
 Returns the character used to represent a gap for this object. More...
 
std::string ungapped_sequence () const
 Returns the string representing this sequence without gaps. More...
 
std::string sequence () const
 Returns the full sequence, which may include gaps. More...
 
Sequenceoperator= (Sequence const &rhs)
 assignment operator. More...
 
bool operator< (const Sequence &s) const
 Returns true if this Sequence object's id is lexicographically less than the given Sequence object's id, returns false otherwise. Uses C++ string < operator to compare this Sequence object's id() to the given Sequence object's id(). More...
 
bool operator== (const Sequence &s) const
 Returns true if the given Sequence object is equal to this Sequence object. Tests for string equality of id(), start(), and sequence(), and returns false if any of these are not equal. More...
 
char operator[] (core::Size pos) const
 Returns the character at the given sequence position. More...
 
char at (core::Size pos) const
 
void insert_gap (core::Size pos)
 Inserts a gap at the given position, where insert_gap( 0 ) inserts the character at the beginning of the sequence, and insert_gap( length() ) inserts the character at the end of the sequence. More...
 
void append_char (char new_char)
 Append a character. More...
 
void append_gap ()
 Append a gap. More...
 
bool is_gap (core::Size pos) const
 Returns true if this position in the sequence represents a gap, returns false otherwise. More...
 
void read_data (std::istream &in)
 Initializes the information in this sequence from the given std::istream. The istream should yield three pieces of information in the following order: More...
 
core::Size resnum (core::Size idx) const
 Returns the index of the given sequence position, which is the position in the sequence minus any gaps that occur earlier in the sequence. For example, if the sequence is —AT, resnum(5) will return 2. Returns 0 for unaligned positions. More...
 

Private Types

typedef std::string string
 

Private Attributes

utility::vector1< SequenceOPseqs_
 

Member Typedef Documentation

typedef std::string core::sequence::CompositeSequence::string
private

Constructor & Destructor Documentation

core::sequence::CompositeSequence::CompositeSequence ( )
inline

ctors

Referenced by clone().

core::sequence::CompositeSequence::CompositeSequence ( CompositeSequence const &  src)
inline

copy ctor

core::sequence::CompositeSequence::~CompositeSequence ( )
virtual

dtor

Member Function Documentation

void core::sequence::CompositeSequence::add_sequence ( SequenceOP  seq)
SequenceOP core::sequence::CompositeSequence::clone ( ) const
virtual

Returns an owning pointer to a new CompositeSequence object, with data that is a deep copy of the information in this object.

Reimplemented from core::sequence::Sequence.

References CompositeSequence().

void core::sequence::CompositeSequence::delete_position ( core::Size  pos)
virtual

Deletes the given position from the Sequence and shifts everything else back by one.

Reimplemented from core::sequence::Sequence.

References core::sequence::Sequence::delete_position(), n_seqs(), and seqs_.

void core::sequence::CompositeSequence::insert_char ( core::Size  pos,
char  new_char 
)
virtual

Inserts a character at the given position.

Reimplemented from core::sequence::Sequence.

References core::sequence::Sequence::insert_char(), n_seqs(), and seqs_.

Size core::sequence::CompositeSequence::length ( ) const
virtual

Returns the number of characters in this object.

Reimplemented from core::sequence::Sequence.

References seqs_.

Referenced by add_sequence().

core::Size core::sequence::CompositeSequence::n_seqs ( ) const

References seqs_.

Referenced by delete_position(), and insert_char().

CompositeSequence& core::sequence::CompositeSequence::operator= ( CompositeSequence const &  rhs)
inline
SequenceOP core::sequence::CompositeSequence::seq ( core::Size  idx) const

References seqs_.

Referenced by operator=().

utility::vector1< SequenceOP > core::sequence::CompositeSequence::seqs ( ) const

References seqs_.

Referenced by operator=().

std::string core::sequence::CompositeSequence::to_string ( ) const
virtual
std::string core::sequence::CompositeSequence::type ( ) const
virtual

Reimplemented from core::sequence::Sequence.

Member Data Documentation

utility::vector1< SequenceOP > core::sequence::CompositeSequence::seqs_
private

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