AMOS::Contig_t Class Reference

A tiling of assembled sequence reads. More...

#include <Contig_AMOS.hh>

Inheritance diagram for AMOS::Contig_t:

[legend]Collaboration diagram for AMOS::Contig_t:

[legend]List of all members.


Public Member Functions
	Contig_t ()
	Constructs an empty Contig_t object.
	Contig_t (const Contig_t &source)
	Copy constructor.
	~Contig_t ()
	Destroys a Contig_t object.
virtual void	clear ()
	Clears all object data, reinitializes the object.
Pos_t	gap2ungap (Pos_t gap) const
	Translates a gapped position to an ungapped position.
Pos_t	ungap2gap (Pos_t ungap) const
	Translates an ungapped position to a gapped position.
virtual NCode_t	getNCode () const
	Get the AMOS NCode type identifier.
const std::vector< Tile_t > &	getReadTiling () const
	Get the tiling of underlying reads.
std::vector< Tile_t > &	getReadTiling ()
Size_t	getSpan () const
	Get the span of the read layout.
Size_t	getUngappedLength () const
	Get the ungapped consensus length.
std::string	getUngappedQualString () const
	Get the ungapped quality score string.
std::string	getUngappedQualString (Range_t range) const
	Get an ungapped quality score substring.
std::string	getUngappedSeqString () const
	Get the ungapped sequence base string.
std::string	getUngappedSeqString (Range_t range) const
	Get an ungapped sequence base substring.
virtual void	readMessage (const Message_t &msg)
	Reads in data from a Message object.
bool	readUMD (std::istream &in)
	Read a UMD contig message from an input stream.
void	setReadTiling (const std::vector< Tile_t > &reads)
	Set the tiling of underlying reads.
void	setReadTiling (const Layout_t &layout)
	Set the tiling of underlying reads.
virtual void	writeMessage (Message_t &msg) const
	Writes data to a Message object.
void	writeUMD (std::ostream &out) const
	Write a UMD contig message to an output stream.
std::pair< char, char >	getBase (Pos_t index) const
	Get a single base and its quality score.
Size_t	getLength () const
	Get the length of the sequence.
std::string	getQualString () const
	Get the quality score string.
std::string	getQualString (Range_t range) const
	Get a quality score substring.
std::string	getSeqString () const
	Get the sequence base string.
std::string	getSeqString (Range_t range) const
	Get a sequence base substring.
bool	isCompressed () const
	Checks if the sequence data is compressed.
void	setBase (char seqchar, char qualchar, Pos_t index)
	Set a sequence base and its quality score.
void	setSequence (const char seq, const char qual)
	Set the entire sequence.
void	setSequence (const std::string &seq, const std::string &qual)
	Set the entire sequence.
const std::string &	getComment () const
	Get the comment string.
const Status_t	getStatus () const
	Get the status value.
void	setComment (const std::string &comment)
	Set the comment string.
void	setStatus (Status_t status)
	Set the status value.
const std::string &	getEID () const
	Get the external ID.
ID_t	getIID () const
	Get the internal ID.
bool	isRemoved () const
	Check if the object is waiting to be removed from the bank.
bool	isModified () const
	Check if the object has been modified.
bool	isFlagA () const
	Check the value of flag A.
bool	isFlagB () const
	Check the value of flag B.
void	setEID (const std::string &eid)
	Set the external ID.
void	setFlagA (bool flag)
	Set flag A.
void	setFlagB (bool flag)
	Set flag B.
void	setIID (ID_t iid)
	Set the internal ID.
Static Public Attributes
const NCode_t	NCODE = M_CONTIG
	The NCode type identifier for this object.
Protected Member Functions
virtual void	readRecord (std::istream &fix, std::istream &var)
	Read selected class members from a biserial record.
virtual void	writeRecord (std::ostream &fix, std::ostream &var) const
	Write selected class members to a biserial record.
Static Protected Member Functions
uint8_t	compress (char seqchar, char qualchar)
	Compresses a sequence char and quality char into a single byte.
std::pair< char, char >	uncompress (uint8_t byte)
	Uncompresses a byte into a sequence and quality char.
Protected Attributes
uint8_t *	seq_m
	compressed seq and qual data or uncompressed seq
uint8_t *	qual_m
	uncompressed qual data
Size_t	length_m
	length of the sequence and quality data
ID_t	iid_m
	internal ID (integer AMOS identifier)
std::string	eid_m
	external ID (anything you want sans newlines)
BankFlags_t	flags_m
	bank flags, derived classes may use "nibble"
Static Protected Attributes
const uint8_t	COMPRESS_BIT = 0x1
	compressed sequence flag
const uint8_t	ADENINE_BITS = 0x0
	'A' bit
const uint8_t	CYTOSINE_BITS = 0x40
	'C' bit
const uint8_t	GUANINE_BITS = 0x80
	'G' bit
const uint8_t	THYMINE_BITS = 0xC0
	'T' bit
const uint8_t	SEQ_BITS = 0xC0
	sequence bit mask
const uint8_t	QUAL_BITS = 0x3F
	quality bit mask

Detailed Description

A tiling of assembled sequence reads.

A Contig_t consists of a consensus sequence with quality scores and a tiling of underlying reads that produce the consensus. The consensus sequence is stored as a 'gapped consensus'. That is the gaps are stored as gap characters in the consensus sequence instead of as a position list. The ungapped version of the consensus can be generated with the getUngapped... methods. Gap characters should be '-' but '*' is also accepted. The compress and uncompress methods inherited from Sequence_t are made private because they would corrupt the gap characters.

Definition at line 35 of file Contig_AMOS.hh.

Constructor & Destructor Documentation

AMOS::Contig_t::Contig_t ( ) [inline]

Constructs an empty Contig_t object.
Definition at line 75 of file Contig_AMOS.hh.

AMOS::Contig_t::Contig_t ( const Contig_t & source ) [inline]

Copy constructor.
Definition at line 84 of file Contig_AMOS.hh.

AMOS::Contig_t::~Contig_t ( ) [inline]

Destroys a Contig_t object.
Definition at line 93 of file Contig_AMOS.hh.

Member Function Documentation

virtual void AMOS::Contig_t::clear ( ) [inline, virtual]

Clears all object data, reinitializes the object.
All data will be cleared, but object compression status will remain unchanged. Use the compress/uncompress members to change this info.
Reimplemented from AMOS::Sequence_t.
Definition at line 100 of file Contig_AMOS.hh.
References AMOS::Sequence_t::clear().
Referenced by readMessage(), readUMD(), and writeMessage().

uint8_t AMOS::Sequence_t::compress ( char seqchar,

char qualchar

) [inline, static, protected, inherited]

Compresses a sequence char and quality char into a single byte.

Note:
Must work with uncompress(uint8_t) method

Parameters:

seqchar The sequence base character (case insensitive)

qualchar The quality score character

Returns:
The compressed byte
Definition at line 64 of file Sequence_AMOS.hh.
References AMOS::Sequence_t::ADENINE_BITS, AMOS::Char2Qual(), AMOS::Sequence_t::CYTOSINE_BITS, AMOS::Sequence_t::GUANINE_BITS, AMOS::Sequence_t::SEQ_BITS, and AMOS::Sequence_t::THYMINE_BITS.
Referenced by AMOS::Sequence_t::clear().

Pos_t Contig_t::gap2ungap ( Pos_t gap ) const

Translates a gapped position to an ungapped position.
This method requires linear time. If the gapped position points to a gap the returned ungapped position will point to the position immediately following the gap.

Parameters:

The gapped position

Precondition:
gap < getLength( )

Returns:
The ungapped position
Definition at line 23 of file Contig_AMOS.cc.
References AMOS::Pos_t.

std::pair<char, char> AMOS::Sequence_t::getBase ( Pos_t index ) const [inline, inherited]

Get a single base and its quality score.
Retrieves and uncompresses the sequence base for the requested index.

Parameters:

index The index of the requested base

Precondition:
index >= 0 && index < length

Exceptions:

ArgumentException_t

Returns:
The requested (uppercase) base character and its quality score
Definition at line 203 of file Sequence_AMOS.hh.
References AMOS_THROW_ARGUMENT, AMOS::Sequence_t::isCompressed(), AMOS::Sequence_t::length_m, AMOS::Pos_t, AMOS::Sequence_t::qual_m, AMOS::Sequence_t::seq_m, and AMOS::Sequence_t::uncompress().
Referenced by AMOS::Sequence_t::getQualString(), AMOS::Sequence_t::getSeqString(), getUngappedQualString(), getUngappedSeqString(), and AMOS::Sequence_t::writeMessage().

const std::string& AMOS::Universal_t::getComment ( ) const [inline, inherited]

Get the comment string.

Returns:
The comment string
Definition at line 110 of file Universal_AMOS.hh.
Referenced by AMOS::operator<<().

const std::string& AMOS::IBankable_t::getEID ( ) const [inline, inherited]

Get the external ID.

Returns:
The external ID
Definition at line 156 of file Bank_AMOS.hh.
References AMOS::IBankable_t::eid_m.
Referenced by writeUMD().

ID_t AMOS::IBankable_t::getIID ( ) const [inline, inherited]

Get the internal ID.

Returns:
The internal ID
Definition at line 167 of file Bank_AMOS.hh.
References AMOS::ID_t, and AMOS::IBankable_t::iid_m.
Referenced by AMOS::Index_t::buildContigFeature(), AMOS::Index_t::buildContigScaffold(), AMOS::Index_t::buildReadContig(), AMOS::Index_t::buildReadLibrary(), AMOS::Index_t::buildScaffoldFeature(), and AMOS::operator<<().

Size_t AMOS::Sequence_t::getLength ( ) const [inline, inherited]

Get the length of the sequence.

Returns:
The length of the sequence
Definition at line 220 of file Sequence_AMOS.hh.
References AMOS::Sequence_t::length_m, and AMOS::Size_t.
Referenced by getSpan(), getUngappedQualString(), getUngappedSeqString(), and AMOS::Read_t::writeMessage().

virtual NCode_t AMOS::Contig_t::getNCode ( ) const [inline, virtual]

Get the AMOS NCode type identifier.

Returns:
The AMOS NCode type identifier

Reimplemented from AMOS::Sequence_t.
Definition at line 135 of file Contig_AMOS.hh.
References AMOS::NCode_t.

string Sequence_t::getQualString ( Range_t range ) const [inherited]

Get a quality score substring.
Returns a subrange of quality scores [begin, end) or (end, begin]. The reversed range will pull the reverse string of quality scores.

Parameters:

range The range of quality scores to get

Precondition:
range lo >= 0 && hi <= length

Exceptions:

ArgumentException_t

Returns:
A subrange quality scores
Definition at line 56 of file Sequence_AMOS.cc.
References AMOS_THROW_ARGUMENT, AMOS::Sequence_t::getBase(), AMOS::Sequence_t::length_m, AMOS::NULL_CHAR, AMOS::Pos_t, and AMOS::Reverse().

std::string AMOS::Sequence_t::getQualString ( ) const [inline, inherited]

Get the quality score string.

Returns:
The full string of quality scores
Definition at line 238 of file Sequence_AMOS.hh.
References AMOS::Sequence_t::length_m.
Referenced by AMOS::operator<<().

std::vector<Tile_t>& AMOS::Contig_t::getReadTiling ( ) [inline]

Definition at line 153 of file Contig_AMOS.hh.

const std::vector<Tile_t>& AMOS::Contig_t::getReadTiling ( ) const [inline]

Get the tiling of underlying reads.

Returns:
The vector of underlying reads
Definition at line 146 of file Contig_AMOS.hh.
Referenced by readUMD().

string Sequence_t::getSeqString ( Range_t range ) const [inherited]

Get a sequence base substring.
Returns a subrange of sequence bases [begin, end) or (end, being]. The reversed range will pull the reverse complement string of sequences bases.

Parameters:

range The range of sequence bases to get

Precondition:
range lo >= 0 && hi <= length

Exceptions:

ArgumentException_t

Returns:
A subrange of sequence bases
Definition at line 80 of file Sequence_AMOS.cc.
References AMOS_THROW_ARGUMENT, AMOS::Sequence_t::getBase(), AMOS::Sequence_t::length_m, AMOS::NULL_CHAR, AMOS::Pos_t, and AMOS::ReverseComplement().

std::string AMOS::Sequence_t::getSeqString ( ) const [inline, inherited]

Get the sequence base string.

Returns:
The full string of sequence bases
Definition at line 263 of file Sequence_AMOS.hh.
References AMOS::Sequence_t::length_m.
Referenced by AMOS::operator<<().

Size_t Contig_t::getSpan ( ) const

Get the span of the read layout.
Returns the difference between min(offset) and max(offset+len). Since the layout is not necessarily sorted, this method requires linear time.

Returns:
The span of the layout
Definition at line 49 of file Contig_AMOS.cc.
References AMOS::Sequence_t::getLength(), AMOS::Pos_t, and AMOS::Size_t.

const Status_t AMOS::Universal_t::getStatus ( ) const [inline, inherited]

Get the status value.

Returns:
The status value
Definition at line 121 of file Universal_AMOS.hh.
References AMOS::Status_t.

Size_t Contig_t::getUngappedLength ( ) const

Get the ungapped consensus length.
Unlike getLength( ) which is constant time, this method requires linear time.

Returns:
The ungapped length of the consensus sequence
Definition at line 79 of file Contig_AMOS.cc.
References AMOS::Pos_t, and AMOS::Size_t.

string Contig_t::getUngappedQualString ( Range_t range ) const

Get an ungapped quality score substring.
Returns a subrange of quality scores [begin, end) or (end, begin] with all the gap scores removed. The range bounds are relative to the gapped consensus sequence, and a reversed range will pull the reverse string of quality scores.

Parameters:

range The range of quality scores to get

Precondition:
range lo >= 0 && hi <= length

Exceptions:

ArgumentException

Returns:
A subrange of ungapped quality scores
Definition at line 92 of file Contig_AMOS.cc.
References AMOS_THROW_ARGUMENT, AMOS::Sequence_t::getBase(), AMOS::Sequence_t::getLength(), AMOS::Pos_t, and AMOS::Reverse().

std::string AMOS::Contig_t::getUngappedQualString ( ) const [inline]

Get the ungapped quality score string.
Returns the quality string with all the gap scores removed.

Returns:
The full string of ungapped quality scores
Definition at line 188 of file Contig_AMOS.hh.
References AMOS::Sequence_t::getLength().

string Contig_t::getUngappedSeqString ( Range_t range ) const

Get an ungapped sequence base substring.
Returns a subrange of ungapped sequence bases [begin, end) or (end, begin] with all the gaps (non-alphas) removed. The range bounds are relative to the gapped consensus sequence, and reversed range will pull the reverse complement string of sequence bases.

Parameters:

range The range of sequence bases to get

Precondition:
range lo >= 0 && hi <= length

Exceptions:

ArgumentException

Returns:
A subrange of ungapped sequence bases
Definition at line 121 of file Contig_AMOS.cc.
References AMOS_THROW_ARGUMENT, AMOS::Sequence_t::getBase(), AMOS::Sequence_t::getLength(), AMOS::Pos_t, and AMOS::ReverseComplement().

std::string AMOS::Contig_t::getUngappedSeqString ( ) const [inline]

Get the ungapped sequence base string.

Returns:
The full string of ungapped sequence bases
Definition at line 215 of file Contig_AMOS.hh.
References AMOS::Sequence_t::getLength().

bool AMOS::Sequence_t::isCompressed ( ) const [inline, inherited]

Checks if the sequence data is compressed.
Returns true if the Sequence is currently operating in compressed mode, or false if under normal operation.

Returns:
True if compressed, false if not
Definition at line 291 of file Sequence_AMOS.hh.
References AMOS::Sequence_t::COMPRESS_BIT.
Referenced by AMOS::Sequence_t::compress(), AMOS::Sequence_t::getBase(), AMOS::Sequence_t::operator=(), AMOS::Sequence_t::readRecord(), AMOS::Sequence_t::setBase(), AMOS::Sequence_t::setSequence(), AMOS::Sequence_t::uncompress(), and AMOS::Sequence_t::writeRecord().

bool AMOS::IBankable_t::isFlagA ( ) const [inline, inherited]

Check the value of flag A.

Returns:
The value of flag A
Definition at line 210 of file Bank_AMOS.hh.
References AMOS::IBankable_t::flags_m.
Referenced by AMOS::Universal_t::writeMessage(), and AMOS::Overlap_t::writeMessage().

bool AMOS::IBankable_t::isFlagB ( ) const [inline, inherited]

Check the value of flag B.

Returns:
The value of flag B
Definition at line 221 of file Bank_AMOS.hh.
References AMOS::IBankable_t::flags_m.
Referenced by AMOS::Universal_t::writeMessage(), and AMOS::Overlap_t::writeMessage().

bool AMOS::IBankable_t::isModified ( ) const [inline, inherited]

Check if the object has been modified.

Returns:
true if modified, otherwise false
Definition at line 199 of file Bank_AMOS.hh.
References AMOS::IBankable_t::flags_m.

bool AMOS::IBankable_t::isRemoved ( ) const [inline, inherited]

Check if the object is waiting to be removed from the bank.

Note:
Useful for debugging only

Returns:
true if removed, otherwise false
Definition at line 188 of file Bank_AMOS.hh.
References AMOS::IBankable_t::flags_m.

void Contig_t::readMessage ( const Message_t & msg ) [virtual]

Reads in data from a Message object.
Reads the data contained in a Message object and stores it in the Messagable object. Will not complain if incoming message is of the wrong type, will only try and suck out the fields it recognizes. All previous data in the Messagable object will be cleared or overwritten.

Parameters:

msg The Message to read from

Precondition:
The expected fields are formatted properly

Exceptions:

ArgumentException_t

Returns:
void

Reimplemented from AMOS::Sequence_t.
Definition at line 150 of file Contig_AMOS.cc.
References clear(), AMOS::M_TILE, and AMOS::Sequence_t::readMessage().

void Contig_t::readRecord ( std::istream & fix,

std::istream & var

) [protected, virtual]

Read selected class members from a biserial record.
Reads the fixed and variable length streams from a biserial record and initializes the class members to the values stored within. Used in translating a biserial IBankable object, and needed to retrieve objects from a bank.

Note:
This method must be able to interpret the biserial record produced by its related function writeRecord.

Parameters:

fix The fixed length stream (stores all fixed length members)

var The variable length stream (stores all var length members)

Precondition:
The get pointer of fix is at the beginning of the record
The get pointer of var is at the beginning of the record

Returns:
void

Reimplemented from AMOS::Sequence_t.
Definition at line 177 of file Contig_AMOS.cc.
References AMOS::Pos_t, AMOS::readLE(), AMOS::Sequence_t::readRecord(), and AMOS::Size_t.

bool Contig_t::readUMD ( std::istream & in )

Read a UMD contig message from an input stream.
Reads a University of Maryland style contig message and populates the appropriate fields with the values read from the stream. Will throw an exception if a message is found, but is not properly formatted. All fields not included in the message will be reinitialized. Contig EID will be set, and each tile will be stored with Read IID, read offset, and read range. Read range will be flipped to represent reverse complement.

Parameters:

in The input stream to read from

Precondition:
The incoming message is properly formatted

Exceptions:

IOException_t

Returns:
true if a message was read, false if no message read (EOF)
Definition at line 191 of file Contig_AMOS.cc.
References AMOS_THROW_ARGUMENT, clear(), getReadTiling(), and AMOS::IBankable_t::setEID().

void AMOS::Sequence_t::setBase ( char seqchar,

char qualchar,

Pos_t index

) [inline, inherited]

Set a sequence base and its quality score.
Any characters may be used for seq and qualchar unless dealing with a compressed sequence. If compressed, the sequence should only contain A,C,G,T and Ns and quality scores in the range [MIN_QUALITY,MAX_QUALITY], if either of these conditions are not met the information will be lost when the data is compressed (see postconditions below).

Parameters:

seqchar The sequence base character

qualchar The quality score character

index The index to assign these values

Precondition:
index >= 0 && index < length

Postcondition:
If compressed:

All invalid quality scores will be cast to MIN_QUALITY
All N's will be assigned a MIN_QUALITY quality score
All MIN_QUALITY scores will be assigned a N seqchar

Exceptions:

ArgumentException_t

Returns:
void
Definition at line 321 of file Sequence_AMOS.hh.
References AMOS_THROW_ARGUMENT, AMOS::Sequence_t::compress(), AMOS::Sequence_t::isCompressed(), AMOS::Sequence_t::length_m, AMOS::Pos_t, AMOS::Sequence_t::qual_m, and AMOS::Sequence_t::seq_m.
Referenced by AMOS::Sequence_t::setSequence().

void AMOS::Universal_t::setComment ( const std::string & comment ) [inline, inherited]

Set the comment string.

Parameters:

comment The new comment string

Returns:
void
Definition at line 144 of file Universal_AMOS.hh.

void AMOS::IBankable_t::setEID ( const std::string & eid ) [inline, inherited]

Set the external ID.
Will only use the characters up to but not including the first newline.

Returns:
void
Definition at line 234 of file Bank_AMOS.hh.
References AMOS::IBankable_t::eid_m, and AMOS::NL_CHAR.
Referenced by readUMD().

void AMOS::IBankable_t::setFlagA ( bool flag ) [inline, inherited]

Set flag A.
Has no effect on the actual object in memory other than setting a flag. This is one of two user accessible flags to be used as needed, the other is flag B.

Parameters:

flag The new flag A value

Returns:
void
Definition at line 254 of file Bank_AMOS.hh.
References AMOS::IBankable_t::flags_m.
Referenced by AMOS::Universal_t::readMessage(), and AMOS::Overlap_t::readMessage().

void AMOS::IBankable_t::setFlagB ( bool flag ) [inline, inherited]

Set flag B.
Has no effect on the actual object in memory other than setting a flag. This is one of two user accessible flags to be used as needed, the other is flag A.

Parameters:

flag The new flag B value

Returns:
void
Definition at line 270 of file Bank_AMOS.hh.
References AMOS::IBankable_t::flags_m.
Referenced by AMOS::Universal_t::readMessage(), and AMOS::Overlap_t::readMessage().

void AMOS::IBankable_t::setIID ( ID_t iid ) [inline, inherited]

Set the internal ID.

Parameters:

iid The new internal ID

Returns:
void
Definition at line 282 of file Bank_AMOS.hh.
References AMOS::ID_t, and AMOS::IBankable_t::iid_m.

void AMOS::Contig_t::setReadTiling ( const Layout_t & layout ) [inline]

Set the tiling of underlying reads.

Parameters:

layout The new read layout

Returns:
void
Definition at line 277 of file Contig_AMOS.hh.

void AMOS::Contig_t::setReadTiling ( const std::vector< Tile_t > & reads ) [inline]

Set the tiling of underlying reads.

Parameters:

reads The new vector of underlying reads

Returns:
void
Definition at line 265 of file Contig_AMOS.hh.

void Sequence_t::setSequence ( const std::string & seq,

const std::string & qual

) [inherited]

Set the entire sequence.
Combines and compresses the sequence and quality data contained in the two STL strings. If current Sequence object is compressed, please refer to the postconditions for the setBase(char,char,Pos_t) operation. All newline characters will be discarded. but the newlines must be in the same location in both the sequence and quality files.

Parameters:

seq The sequence base string

qual The quality score string

Precondition:
seq . size( ) == qual . size( )

Exceptions:

ArgumentException_t

Returns:
void
Definition at line 179 of file Sequence_AMOS.cc.
References AMOS_THROW_ARGUMENT, AMOS::Sequence_t::isCompressed(), AMOS::Sequence_t::length_m, AMOS::NL_CHAR, AMOS::Pos_t, AMOS::Sequence_t::qual_m, AMOS::SafeRealloc(), AMOS::Sequence_t::seq_m, AMOS::Sequence_t::setBase(), and AMOS::Size_t.

void Sequence_t::setSequence ( const char * seq,

const char * qual

) [inherited]

Set the entire sequence.
Combines and compresses the sequence and quality data contained in the two C strings. If current Sequence object is compressed, please refer to the postconditions for the setBase(char,char,Pos_t) operation. All newline characters will be discarded, but the newlines must be in the same location in both the sequence and quality files.

Parameters:

seq The sequence base string

qual The quality score string

Precondition:
strlen(seq) == strlen(qual)

Exceptions:

ArgumentException_t

Returns:
void
Definition at line 145 of file Sequence_AMOS.cc.
References AMOS_THROW_ARGUMENT, AMOS::Sequence_t::isCompressed(), AMOS::Sequence_t::length_m, AMOS::NL_CHAR, AMOS::Pos_t, AMOS::Sequence_t::qual_m, AMOS::SafeRealloc(), AMOS::Sequence_t::seq_m, AMOS::Sequence_t::setBase(), and AMOS::Size_t.
Referenced by AMOS::Sequence_t::readMessage().

void AMOS::Universal_t::setStatus ( Status_t status ) [inline, inherited]

Set the status value.

Parameters:

status The new status value

Returns:
void
Definition at line 156 of file Universal_AMOS.hh.
References AMOS::Status_t.
Referenced by AMOS::Universal_t::readMessage().

std::pair<char, char> AMOS::Sequence_t::uncompress ( uint8_t byte ) [inline, static, protected, inherited]

Uncompresses a byte into a sequence and quality char.

Note:
Must work with compress(char,char)

Parameters:

byte The compressed sequence and quality byte

Returns:
The sequence and quality char respectively
Definition at line 93 of file Sequence_AMOS.hh.
References AMOS::Sequence_t::ADENINE_BITS, AMOS::Sequence_t::CYTOSINE_BITS, AMOS::Sequence_t::GUANINE_BITS, AMOS::Qual2Char(), AMOS::Sequence_t::QUAL_BITS, AMOS::Sequence_t::SEQ_BITS, and AMOS::Sequence_t::THYMINE_BITS.

Size_t Contig_t::ungap2gap ( Pos_t ungap ) const

Translates an ungapped position to a gapped position.
This method requires linear time.

Parameters:

The ungapped position

Precondition:
ungap < getUngappedLength( )

Returns:
The gapped position
Definition at line 36 of file Contig_AMOS.cc.
References AMOS::Pos_t, and AMOS::Size_t.

void Contig_t::writeMessage ( Message_t & msg ) const [virtual]

Writes data to a Message object.
Writes the data contained in a Messagable object to a Message object. All previous data in the Message will be cleared or overwritten.

Parameters:

msg The Message to write to

Returns:
void

Reimplemented from AMOS::Sequence_t.
Definition at line 250 of file Contig_AMOS.cc.
References clear(), AMOS::Pos_t, and AMOS::Sequence_t::writeMessage().

void Contig_t::writeRecord ( std::ostream & fix,

std::ostream & var

) const [protected, virtual]

Write selected class members to a biserial record.
Writes the fixed and variable length streams to a biserial record. Used in generating a biserial IBankable object, and needed to commit objects to a bank. Should not write the flags, EID, or IID of the object because the bank will handle the storage of these fields on its own.

Note:
This method must be able to produce a biserial record that can be read by its related funtion readRecord.

Parameters:

fix The fixed length stream (stores all fixed length members)

var The variable length stream (stores all var length members)

Returns:
void

Reimplemented from AMOS::Sequence_t.
Definition at line 276 of file Contig_AMOS.cc.
References AMOS::Pos_t, AMOS::Size_t, AMOS::writeLE(), and AMOS::Sequence_t::writeRecord().

void Contig_t::writeUMD ( std::ostream & out ) const

Write a UMD contig message to an output stream.
Writes a University of Maryland style contig message to the output stream. Will throw an exception if there was an error trying to write to the output stream.

Parameters:

out The output stream to write to

Precondition:
The ostream is open and writable

Exceptions:

IOException_t

Returns:
void
Definition at line 289 of file Contig_AMOS.cc.
References AMOS_THROW_IO, and AMOS::IBankable_t::getEID().

Member Data Documentation

const uint8_t AMOS::Sequence_t::ADENINE_BITS = 0x0 [static, protected, inherited]

'A' bit
Definition at line 47 of file Sequence_AMOS.hh.
Referenced by AMOS::Sequence_t::compress(), and AMOS::Sequence_t::uncompress().

const uint8_t AMOS::Sequence_t::COMPRESS_BIT = 0x1 [static, protected, inherited]

compressed sequence flag
Definition at line 46 of file Sequence_AMOS.hh.
Referenced by AMOS::Sequence_t::clear(), AMOS::Sequence_t::compress(), AMOS::Sequence_t::isCompressed(), and AMOS::Sequence_t::uncompress().

const uint8_t AMOS::Sequence_t::CYTOSINE_BITS = 0x40 [static, protected, inherited]

'C' bit
Definition at line 48 of file Sequence_AMOS.hh.
Referenced by AMOS::Sequence_t::compress(), and AMOS::Sequence_t::uncompress().

std::string AMOS::IBankable_t::eid_m [protected, inherited]

external ID (anything you want sans newlines)
Definition at line 66 of file Bank_AMOS.hh.
Referenced by AMOS::IBankable_t::clear(), AMOS::IBankable_t::getEID(), and AMOS::IBankable_t::setEID().

BankFlags_t AMOS::IBankable_t::flags_m [protected, inherited]

bank flags, derived classes may use "nibble"
Definition at line 68 of file Bank_AMOS.hh.
Referenced by AMOS::IBankable_t::clear(), AMOS::IBankable_t::isFlagA(), AMOS::IBankable_t::isFlagB(), AMOS::IBankable_t::isModified(), AMOS::IBankable_t::isRemoved(), AMOS::IBankable_t::setFlagA(), and AMOS::IBankable_t::setFlagB().

const uint8_t AMOS::Sequence_t::GUANINE_BITS = 0x80 [static, protected, inherited]

'G' bit
Definition at line 49 of file Sequence_AMOS.hh.
Referenced by AMOS::Sequence_t::compress(), and AMOS::Sequence_t::uncompress().

ID_t AMOS::IBankable_t::iid_m [protected, inherited]

internal ID (integer AMOS identifier)
Definition at line 64 of file Bank_AMOS.hh.
Referenced by AMOS::IBankable_t::clear(), AMOS::IBankable_t::getIID(), AMOS::IBankable_t::IBankable_t(), and AMOS::IBankable_t::setIID().

const NCode_t Contig_t::NCODE = M_CONTIG [static]

The NCode type identifier for this object.

Reimplemented from AMOS::Sequence_t.
Definition at line 19 of file Contig_AMOS.cc.

const uint8_t AMOS::Sequence_t::QUAL_BITS = 0x3F [static, protected, inherited]

quality bit mask
Definition at line 52 of file Sequence_AMOS.hh.
Referenced by AMOS::Sequence_t::uncompress().

uint8_t* AMOS::Sequence_t::qual_m [protected, inherited]

uncompressed qual data
Definition at line 42 of file Sequence_AMOS.hh.
Referenced by AMOS::Sequence_t::clear(), AMOS::Sequence_t::compress(), AMOS::Sequence_t::getBase(), AMOS::Sequence_t::operator=(), AMOS::Sequence_t::readRecord(), AMOS::Sequence_t::Sequence_t(), AMOS::Sequence_t::setBase(), AMOS::Sequence_t::setSequence(), AMOS::Sequence_t::uncompress(), AMOS::Sequence_t::writeRecord(), and AMOS::Sequence_t::~Sequence_t().

const uint8_t AMOS::Sequence_t::SEQ_BITS = 0xC0 [static, protected, inherited]

sequence bit mask
Definition at line 51 of file Sequence_AMOS.hh.
Referenced by AMOS::Sequence_t::compress(), and AMOS::Sequence_t::uncompress().

const uint8_t AMOS::Sequence_t::THYMINE_BITS = 0xC0 [static, protected, inherited]

'T' bit
Definition at line 50 of file Sequence_AMOS.hh.
Referenced by AMOS::Sequence_t::compress(), and AMOS::Sequence_t::uncompress().

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

Generated on Tue May 17 15:19:42 2005 for libAMOS by

1.3.8

AMOS::Contig_t Class Reference

Public Member Functions

Static Public Attributes

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation