AMOS::Sequence_t Class Reference

Sequence bases with quality scores. More...

#include <Sequence_AMOS.hh>

Inheritance diagram for AMOS::Sequence_t:

[legend]Collaboration diagram for AMOS::Sequence_t:

[legend]List of all members.


Public Member Functions
	Sequence_t ()
	Constructs an empty Sequence_t object.
	Sequence_t (const Sequence_t &source)
	Copy constructor.
virtual	~Sequence_t ()
	Destroys a Sequence_t object.
virtual void	clear ()
	Clears all object data, reinitializes the object.
void	compress ()
	Compress the internal representation of this sequence.
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.
virtual NCode_t	getNCode () const
	Get the AMOS NCode type identifier.
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.
virtual void	readMessage (const Message_t &msg)
	Reads in data from a Message object.
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.
void	uncompress ()
	Uncompress the internal representation of this sequence.
Sequence_t &	operator= (const Sequence_t &source)
	Assignment (copy) operator.
virtual void	writeMessage (Message_t &msg) const
	Writes data to a Message object.
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_SEQUENCE
	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

Sequence bases with quality scores.

Stores both sequence and quality score data in a space efficient manner (when compressed). Can represent any type of sequence data, but must always be used with both sequence AND quality data. If just one of these two data types is required use a simple character array instead. Can be used in uncompressed mode where a base and its quality occupy 2 bytes, or a compressed mode where a base and its quality are packed into a single byte. In uncompressed mode, any characters are valid for bases and quality scores, however in compressed mode, acceptable sequence bases are A,C,G,T and N (case insensitive) and acceptable quality scores are between MIN_QUALITY and MAX_QUALITY.

Definition at line 36 of file Sequence_AMOS.hh.

Constructor & Destructor Documentation

AMOS::Sequence_t::Sequence_t ( ) [inline]

Constructs an empty Sequence_t object.
Sets all members to 0 or NULL Definition at line 134 of file Sequence_AMOS.hh.
References length_m, qual_m, and seq_m.

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

Copy constructor.
Definition at line 144 of file Sequence_AMOS.hh.
References qual_m, and seq_m.

virtual AMOS::Sequence_t::~Sequence_t ( ) [inline, virtual]

Destroys a Sequence_t object.
Frees the memory used for storing the sequence and quality data. Definition at line 156 of file Sequence_AMOS.hh.
References qual_m, and seq_m.

Member Function Documentation

void Sequence_t::clear ( ) [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::Universal_t.

Reimplemented in AMOS::Contig_t, and AMOS::Read_t.
Definition at line 23 of file Sequence_AMOS.cc.
References AMOS::Universal_t::clear(), compress(), COMPRESS_BIT, length_m, qual_m, and seq_m.
Referenced by AMOS::Read_t::clear(), AMOS::Contig_t::clear(), readMessage(), and writeMessage().

void Sequence_t::compress ( )

Compress the internal representation of this sequence.
After compression, this object will continue to compress incoming data until the uncompress method is called. Compression packs both a base and a quality score into a single byte, effectively halving the memory requirements for each object.
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).

Postcondition:
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

Returns:
void
Definition at line 37 of file Sequence_AMOS.cc.
References COMPRESS_BIT, isCompressed(), length_m, AMOS::Pos_t, qual_m, and seq_m.
Referenced by setBase().

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

char qualchar

) [inline, static, protected]

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 ADENINE_BITS, AMOS::Char2Qual(), CYTOSINE_BITS, GUANINE_BITS, SEQ_BITS, and THYMINE_BITS.
Referenced by clear().

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

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, isCompressed(), length_m, AMOS::Pos_t, qual_m, seq_m, and uncompress().
Referenced by getQualString(), getSeqString(), AMOS::Contig_t::getUngappedQualString(), AMOS::Contig_t::getUngappedSeqString(), and 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 AMOS::Contig_t::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]

Get the length of the sequence.

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

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

Get the AMOS NCode type identifier.

Returns:
The AMOS NCode type identifier

Reimplemented from AMOS::Universal_t.

Reimplemented in AMOS::Contig_t, and AMOS::Read_t.
Definition at line 227 of file Sequence_AMOS.hh.
References AMOS::NCode_t.

string Sequence_t::getQualString ( Range_t range ) const

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, getBase(), length_m, AMOS::NULL_CHAR, AMOS::Pos_t, and AMOS::Reverse().

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

Get the quality score string.

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

string Sequence_t::getSeqString ( Range_t range ) const

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, getBase(), length_m, AMOS::NULL_CHAR, AMOS::Pos_t, and AMOS::ReverseComplement().

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

Get the sequence base string.

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

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.

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

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 COMPRESS_BIT.
Referenced by compress(), getBase(), operator=(), readRecord(), setBase(), setSequence(), uncompress(), and 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.

Sequence_t & Sequence_t::operator= ( const Sequence_t & source )

Assignment (copy) operator.
Efficiently copies the compressed data from the other Sequence_t.

Parameters:

source The sequence to copy

Returns:
The resulting Sequence_t object
Definition at line 293 of file Sequence_AMOS.cc.
References isCompressed(), length_m, qual_m, AMOS::SafeRealloc(), and seq_m.

void Sequence_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::Universal_t.

Reimplemented in AMOS::Contig_t, and AMOS::Read_t.
Definition at line 104 of file Sequence_AMOS.cc.
References AMOS_THROW_ARGUMENT, clear(), AMOS::F_QUALITY, AMOS::F_SEQUENCE, AMOS::Universal_t::readMessage(), and setSequence().
Referenced by AMOS::Read_t::readMessage(), and AMOS::Contig_t::readMessage().

void Sequence_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::Universal_t.

Reimplemented in AMOS::Contig_t, and AMOS::Read_t.
Definition at line 127 of file Sequence_AMOS.cc.
References isCompressed(), length_m, qual_m, AMOS::readLE(), AMOS::Universal_t::readRecord(), AMOS::SafeRealloc(), and seq_m.
Referenced by AMOS::Read_t::readRecord(), and AMOS::Contig_t::readRecord().

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

char qualchar,

Pos_t index

) [inline]

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, compress(), isCompressed(), length_m, AMOS::Pos_t, qual_m, and seq_m.
Referenced by 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 AMOS::Contig_t::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 Sequence_t::setSequence ( const std::string & seq,

const std::string & qual

)

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, isCompressed(), length_m, AMOS::NL_CHAR, AMOS::Pos_t, qual_m, AMOS::SafeRealloc(), seq_m, setBase(), and AMOS::Size_t.

void Sequence_t::setSequence ( const char * seq,

const char * qual

)

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, isCompressed(), length_m, AMOS::NL_CHAR, AMOS::Pos_t, qual_m, AMOS::SafeRealloc(), seq_m, setBase(), and AMOS::Size_t.
Referenced by 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().

void Sequence_t::uncompress ( )

Uncompress the internal representation of this sequence.
After uncompression, this object will not compress incoming data until the compress method is called once again. The uncompressed version uses two bytes to store a base and quality score, thus doubling the memory requirements over a compressed version.

Returns:
void
Definition at line 213 of file Sequence_AMOS.cc.
References COMPRESS_BIT, isCompressed(), length_m, AMOS::Pos_t, qual_m, AMOS::SafeRealloc(), and seq_m.
Referenced by getBase().

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

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 ADENINE_BITS, CYTOSINE_BITS, GUANINE_BITS, AMOS::Qual2Char(), QUAL_BITS, SEQ_BITS, and THYMINE_BITS.

void Sequence_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::Universal_t.

Reimplemented in AMOS::Contig_t, and AMOS::Read_t.
Definition at line 234 of file Sequence_AMOS.cc.
References CHARS_PER_LINE, clear(), AMOS::F_QUALITY, AMOS::F_SEQUENCE, getBase(), length_m, AMOS::NL_CHAR, AMOS::Pos_t, AMOS::Size_t, and AMOS::Universal_t::writeMessage().
Referenced by AMOS::Read_t::writeMessage(), and AMOS::Contig_t::writeMessage().

void Sequence_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::Universal_t.

Reimplemented in AMOS::Contig_t, and AMOS::Read_t.
Definition at line 279 of file Sequence_AMOS.cc.
References isCompressed(), length_m, qual_m, seq_m, AMOS::writeLE(), and AMOS::Universal_t::writeRecord().
Referenced by AMOS::Read_t::writeRecord(), and AMOS::Contig_t::writeRecord().

Member Data Documentation

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

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

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

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

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

'C' bit
Definition at line 48 of file Sequence_AMOS.hh.
Referenced by compress(), and 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]

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

Size_t AMOS::Sequence_t::length_m [protected]

length of the sequence and quality data
Definition at line 43 of file Sequence_AMOS.hh.
Referenced by clear(), compress(), getBase(), getLength(), getQualString(), getSeqString(), operator=(), readRecord(), Sequence_t(), setBase(), setSequence(), uncompress(), writeMessage(), and writeRecord().

const NCode_t Sequence_t::NCODE = M_SEQUENCE [static]

The NCode type identifier for this object.

Reimplemented from AMOS::Universal_t.

Reimplemented in AMOS::Contig_t, and AMOS::Read_t.
Definition at line 19 of file Sequence_AMOS.cc.

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

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

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

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

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

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

uint8_t* AMOS::Sequence_t::seq_m [protected]

compressed seq and qual data or uncompressed seq
Definition at line 41 of file Sequence_AMOS.hh.
Referenced by clear(), compress(), getBase(), operator=(), readRecord(), Sequence_t(), setBase(), setSequence(), uncompress(), writeRecord(), and ~Sequence_t().

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

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

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

Generated on Tue May 17 15:19:51 2005 for libAMOS by

1.3.8

AMOS::Sequence_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