AMOS::Sequence_t

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.
virtual double getGCContent (const Range_t &rng) const
 Get the gc content of the sequence.
virtual double getGCContent () const
 Get the gc content of the sequence.
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

static 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 readRecordFix (std::istream &fix)
 Read selected class members from a fixed store only.
virtual void writeRecord (std::ostream &fix, std::ostream &var) const
 Write selected class members to a biserial record.

Static Protected Member Functions

static uint8_t compress (char seqchar, char qualchar)
 Compresses a sequence char and quality char into a single byte.
static 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

static const uint8_t COMPRESS_BIT = 0x1
 compressed sequence flag
static const uint8_t ADENINE_BITS = 0x0
 'A' bit
static const uint8_t CYTOSINE_BITS = 0x40
 'C' bit
static const uint8_t GUANINE_BITS = 0x80
 'G' bit
static const uint8_t THYMINE_BITS = 0xC0
 'T' bit
static const uint8_t SEQ_BITS = 0xC0
 sequence bit mask
static 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 136 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 146 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 158 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, AMOS::IBankable_t::flags_m, 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, AMOS::IBankable_t::flags_m, isCompressed(), length_m, qual_m, and seq_m.

Referenced by clear(), and setBase().

static 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.

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 205 of file Sequence_AMOS.hh.

References AMOS_THROW_ARGUMENT, isCompressed(), length_m, qual_m, seq_m, and uncompress().

Referenced by getGCContent(), getQualString(), getSeqString(), AMOS::Contig_t::getUngappedLength(), 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 116 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 174 of file Bank_AMOS.hh.

References AMOS::IBankable_t::eid_m.

Referenced by AMOS::TiledRead_t::TiledRead_t().

virtual double AMOS::Sequence_t::getGCContent (  )  const [inline, virtual]

Get the gc content of the sequence.

Returns:
The gc content of the full range of the sequence

Reimplemented in AMOS::Contig_t.

Definition at line 260 of file Sequence_AMOS.hh.

References length_m.

virtual double AMOS::Sequence_t::getGCContent ( const Range_t &  rng  )  const [inline, virtual]

Get the gc content of the sequence.

Returns:
The gc content for the specified range of the sequence

Reimplemented in AMOS::Contig_t.

Definition at line 226 of file Sequence_AMOS.hh.

References getBase(), AMOS::Range_t::getHi(), and AMOS::Range_t::getLo().

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

Get the internal ID.

Returns:
The internal ID

Definition at line 185 of file Bank_AMOS.hh.

References 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 272 of file Sequence_AMOS.hh.

References length_m.

Referenced by AMOS::Contig_t::getAvgRho(), 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 279 of file Sequence_AMOS.hh.

References NCODE.

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 59 of file Sequence_AMOS.cc.

References AMOS_THROW_ARGUMENT, getBase(), length_m, AMOS::NULL_CHAR, 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 290 of file Sequence_AMOS.hh.

References length_m.

Referenced by AMOS::ContigIterator_t::ContigIterator_t(), AMOS::Contig_t::insertGapColumn(), AMOS::operator<<(), and AMOS::Contig_t::reverseComplement().

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 83 of file Sequence_AMOS.cc.

References AMOS_THROW_ARGUMENT, getBase(), length_m, AMOS::NULL_CHAR, 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 315 of file Sequence_AMOS.hh.

References length_m.

Referenced by AMOS::ContigIterator_t::ContigIterator_t(), AMOS::Contig_t::insertGapColumn(), AMOS::operator<<(), and AMOS::Contig_t::reverseComplement().

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

Get the status value.

Returns:
The status value

Definition at line 127 of file Universal_AMOS.hh.

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 343 of file Sequence_AMOS.hh.

References COMPRESS_BIT, and AMOS::IBankable_t::flags_m.

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

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

Check the value of flag A.

Returns:
The value of flag A

Definition at line 228 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 239 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 217 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 206 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 314 of file Sequence_AMOS.cc.

References isCompressed(), length_m, and AMOS::SafeRealloc().

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 107 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().

virtual void AMOS::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.

virtual void AMOS::Sequence_t::readRecordFix ( std::istream &  fix  )  [protected, virtual]

Read selected class members from a fixed store only.

Reads the fixed stream and initializes the class members to the values stored within. Used to fetch the fixed portion of 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)
Precondition:
The get pointer of fix is at the beginning of the record
Returns:
void

Reimplemented from AMOS::Universal_t.

Reimplemented in AMOS::Contig_t, and AMOS::Read_t.

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 373 of file Sequence_AMOS.hh.

References AMOS_THROW_ARGUMENT, compress(), isCompressed(), length_m, 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 150 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 252 of file Bank_AMOS.hh.

References AMOS::IBankable_t::eid_m, and AMOS::NL_CHAR.

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 272 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 288 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 300 of file Bank_AMOS.hh.

References AMOS::IBankable_t::iid_m.

void AMOS::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

Reimplemented in AMOS::Contig_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

Reimplemented in AMOS::Contig_t.

Definition at line 163 of file Sequence_AMOS.cc.

References AMOS_THROW_ARGUMENT, isCompressed(), length_m, AMOS::NL_CHAR, qual_m, AMOS::SafeRealloc(), and setBase().

Referenced by readMessage(), and AMOS::Contig_t::setSequence().

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 162 of file Universal_AMOS.hh.

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 231 of file Sequence_AMOS.cc.

References COMPRESS_BIT, AMOS::IBankable_t::flags_m, isCompressed(), length_m, and AMOS::SafeRealloc().

Referenced by getBase().

static 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 255 of file Sequence_AMOS.cc.

References CHARS_PER_LINE, clear(), AMOS::F_QUALITY, AMOS::F_SEQUENCE, getBase(), length_m, NCODE, AMOS::NL_CHAR, and AMOS::Universal_t::writeMessage().

Referenced by AMOS::Read_t::writeMessage(), and AMOS::Contig_t::writeMessage().

virtual void AMOS::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.

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::Bank_t::append(), AMOS::IBankable_t::clear(), AMOS::IBankable_t::getEID(), AMOS::BankStream_t::operator<<(), AMOS::BankStream_t::operator>>(), AMOS::Universal_t::readMessage(), AMOS::BankStream_t::replace(), AMOS::Bank_t::replace(), AMOS::BankStream_t::replaceByBID(), AMOS::IBankable_t::setEID(), and AMOS::Universal_t::writeMessage().

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::Bank_t::appendBID(), clear(), AMOS::IBankable_t::clear(), compress(), AMOS::Bank_t::fetchBID(), AMOS::Bank_t::fetchBIDFix(), AMOS::Overlap_t::getAdjacency(), AMOS::Link_t::getAdjacency(), isCompressed(), AMOS::IBankable_t::isFlagA(), AMOS::IBankable_t::isFlagB(), AMOS::Overlap_t::isFlagC(), AMOS::IBankable_t::isModified(), AMOS::IBankable_t::isRemoved(), AMOS::BankStream_t::operator<<(), AMOS::BankStream_t::operator>>(), AMOS::Bank_t::replaceBID(), AMOS::Overlap_t::setAdjacency(), AMOS::Link_t::setAdjacency(), AMOS::IBankable_t::setFlagA(), AMOS::IBankable_t::setFlagB(), AMOS::Overlap_t::setFlagC(), and uncompress().

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::Bank_t::append(), AMOS::IBankable_t::clear(), AMOS::IBankable_t::getIID(), AMOS::IBankable_t::IBankable_t(), AMOS::BankStream_t::operator<<(), AMOS::BankStream_t::operator>>(), AMOS::Universal_t::readMessage(), AMOS::BankStream_t::replace(), AMOS::Bank_t::replace(), AMOS::BankStream_t::replaceByBID(), AMOS::IBankable_t::setIID(), and AMOS::Universal_t::writeMessage().

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(), getGCContent(), AMOS::Contig_t::getGCContent(), getLength(), getQualString(), getSeqString(), AMOS::Contig_t::getUngappedLength(), operator=(), Sequence_t(), setBase(), setSequence(), uncompress(), and writeMessage().

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 128 of file Sequence_AMOS.hh.

Referenced by getNCode(), and writeMessage().

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(), Sequence_t(), setBase(), setSequence(), 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(), AMOS::Contig_t::getGCContent(), Sequence_t(), setBase(), 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 Mon Feb 22 17:36:38 2010 for libAMOS by  doxygen 1.4.7