AMOS::Kmer_t

AMOS::Kmer_t Class Reference

String of K bases present in the assembly. More...

#include <Kmer_AMOS.hh>

Inheritance diagram for AMOS::Kmer_t:

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Collaboration diagram for AMOS::Kmer_t:
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List of all members.

Public Member Functions

 Kmer_t ()
 Constructs an empty Kmer_t object.
 Kmer_t (const Kmer_t &source)
 Copy constructor.
 ~Kmer_t ()
 Destroys a Kmer_t object.
virtual void clear ()
 Clears all object data, reinitializes the object.
char getBase (Pos_t index) const
 Get a single sequence base from the kmer.
uint32_t getCount () const
 Get the number of this Kmer's occurrences.
uint8_t getLength () const
 Gets the length of the Kmer.
virtual NCode_t getNCode () const
 Get the AMOS NCode type identifier.
const std::vector< ID_t > & getReads () const
 Get the containing read IIDs.
std::vector< ID_t > & getReads ()
 Get the containing read IIDs.
std::string getSeqString () const
 Get the Kmer sequence string.
virtual void readMessage (const Message_t &msg)
 Reads in data from a Message object.
void setBase (char seqchar, Pos_t index)
 Set a single sequence base for the kmer.
void setCount (uint32_t count)
 Set the number of this Kmer's occurrences.
void setReads (const std::vector< ID_t > &reads)
 Set the list of containing read IIDs.
void setSeqString (const std::string &seq)
 Set the Kmer sequence string.
Kmer_t & operator++ (int)
 Increments kmer count by 1 (postfix).
virtual void writeMessage (Message_t &msg) const
 Writes data to a Message object.
Kmer_t & operator= (const Kmer_t &source)
 Assignment (copy) operator.
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_KMER
 The NCode type identifier for this object.
static const uint8_t MAX_LENGTH = 255
 Maximum Kmer length.

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)
 Compresses a sequence char into two bits.
static char uncompress (uint8_t byte)
 Uncompresses two bits into a sequence char.

Protected Attributes

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 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

Detailed Description

String of K bases present in the assembly.

A string of K bases that is present in one or more occurrences throught a set of sequencing reads.

Definition at line 29 of file Kmer_AMOS.hh.

Constructor & Destructor Documentation

AMOS::Kmer_t::Kmer_t (  )  [inline]

Constructs an empty Kmer_t object.

Sets all members to 0 or NULL

Definition at line 122 of file Kmer_AMOS.hh.

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

Copy constructor.

Definition at line 132 of file Kmer_AMOS.hh.

AMOS::Kmer_t::~Kmer_t (  )  [inline]

Destroys a Kmer_t object.

Frees the memory used for the compressed sequence

Definition at line 144 of file Kmer_AMOS.hh.

Member Function Documentation

void Kmer_t::clear (  )  [virtual]

Clears all object data, reinitializes the object.

Reimplemented from AMOS::Universal_t.

Definition at line 23 of file Kmer_AMOS.cc.

References AMOS::Universal_t::clear().

Referenced by readMessage(), and writeMessage().

static uint8_t AMOS::Kmer_t::compress ( char  seqchar  )  [inline, static, protected]

Compresses a sequence char into two bits.

Note:
Must work with uncompress(uint8_t) method
Parameters:
seqchar The sequence base character
Precondition:
seqchar is A,C,G,T (case insensitive)
Exceptions:
ArgumentException_t 
Returns:
The compressed 2 bits (in the highest two bit positions)

Definition at line 59 of file Kmer_AMOS.hh.

References ADENINE_BITS, AMOS_THROW_ARGUMENT, CYTOSINE_BITS, GUANINE_BITS, and THYMINE_BITS.

Referenced by setBase().

char AMOS::Kmer_t::getBase ( Pos_t  index  )  const [inline]

Get a single sequence base from the kmer.

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

Definition at line 175 of file Kmer_AMOS.hh.

References AMOS_THROW_ARGUMENT, and uncompress().

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<<().

uint32_t AMOS::Kmer_t::getCount (  )  const [inline]

Get the number of this Kmer's occurrences.

Returns:
The number of occurrrences

Definition at line 188 of file Kmer_AMOS.hh.

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().

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<<().

uint8_t AMOS::Kmer_t::getLength (  )  const [inline]

Gets the length of the Kmer.

Returns:
The Kmer length

Definition at line 199 of file Kmer_AMOS.hh.

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

Get the AMOS NCode type identifier.

Returns:
The AMOS NCode type identifier

Reimplemented from AMOS::Universal_t.

Definition at line 206 of file Kmer_AMOS.hh.

References NCODE.

std::vector<ID_t>& AMOS::Kmer_t::getReads (  )  [inline]

Get the containing read IIDs.

Returns:
The vector of read IIDs that contain this Kmer

Definition at line 228 of file Kmer_AMOS.hh.

const std::vector<ID_t>& AMOS::Kmer_t::getReads (  )  const [inline]

Get the containing read IIDs.

Returns:
The vector of read IIDs that contain this Kmer

Definition at line 217 of file Kmer_AMOS.hh.

string Kmer_t::getSeqString (  )  const

Get the Kmer sequence string.

Uncompresses the Kmer sequence and returns a string representation.

Returns:
The Kmer sequence string

Definition at line 34 of file Kmer_AMOS.cc.

References AMOS::NULL_CHAR, and uncompress().

Referenced by writeMessage().

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::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.

Kmer_t& AMOS::Kmer_t::operator++ ( int   )  [inline]

Increments kmer count by 1 (postfix).

Increment the kmer count by 1 using postfix notation, i.e. mykmer ++;

Returns:
This kmer, after incrementation

Definition at line 334 of file Kmer_AMOS.hh.

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

Assignment (copy) operator.

Efficiently copies the compressed data from the another Kmer_t.

Parameters:
source The Kmer_t object to copy
Returns:
The resulting Kmer_t object

Definition at line 231 of file Kmer_AMOS.cc.

References AMOS::SafeRealloc().

void Kmer_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.

Definition at line 55 of file Kmer_AMOS.cc.

References AMOS_THROW_ARGUMENT, clear(), AMOS::F_COUNT, AMOS::F_READS, AMOS::F_SEQUENCE, AMOS::Universal_t::readMessage(), and setSeqString().

virtual void AMOS::Kmer_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.

virtual void AMOS::Kmer_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.

void AMOS::Kmer_t::setBase ( char  seqchar,
Pos_t  index 
) [inline]

Set a single sequence base for the kmer.

Only the characters A,C,G,T are allowed, all other characters will throw an exception.

Parameters:
seqchar The sequence base character
index The index to assign this character
Precondition:
index >= 0 && index < length

seqchar is A,C,G,T (case insensitive)

Exceptions:
ArgumentException_t 
Returns:
void

Definition at line 272 of file Kmer_AMOS.hh.

References AMOS_THROW_ARGUMENT, compress(), and SEQ_BITS.

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::Kmer_t::setCount ( uint32_t  count  )  [inline]

Set the number of this Kmer's occurrences.

Parameters:
count The new number of occurrences
Returns:
void

Definition at line 292 of file Kmer_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::Kmer_t::setReads ( const std::vector< ID_t > &  reads  )  [inline]

Set the list of containing read IIDs.

Parameters:
reads The new vector of read IIDs that contain this Kmer
Returns:
void

Definition at line 304 of file Kmer_AMOS.hh.

void AMOS::Kmer_t::setSeqString ( const std::string &  seq  ) 

Set the Kmer sequence string.

Compresses the string and updates the Kmer sequence. Does not alter Kmer count or read list, these must be reset manually. Only the characters A,C,G,T are allowed, all other characters will throw an exception (except for newlines, which will be discarded).

Parameters:
seq The new Kmer sequence string
Precondition:
seq can be longer than MAX_LENGTH (255) bases

seqchar is A,C,G,T (case insensitive)

Exceptions:
ArgumentException_t 
Returns:
void

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 162 of file Universal_AMOS.hh.

Referenced by AMOS::Universal_t::readMessage().

static char AMOS::Kmer_t::uncompress ( uint8_t  byte  )  [inline, static, protected]

Uncompresses two bits into a sequence char.

Note:
Must work with compress(char)
Parameters:
byte The compressed sequence bits (in highest two bit positions)
Exceptions:
Exception_t 
Returns:
The sequence char

Definition at line 82 of file Kmer_AMOS.hh.

References ADENINE_BITS, AMOS_THROW_ARGUMENT, CYTOSINE_BITS, GUANINE_BITS, SEQ_BITS, and THYMINE_BITS.

Referenced by getBase(), and getSeqString().

void Kmer_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.

Definition at line 177 of file Kmer_AMOS.cc.

References clear(), AMOS::F_COUNT, AMOS::F_READS, AMOS::F_SEQUENCE, getSeqString(), NCODE, AMOS::NULL_STRING, and AMOS::Universal_t::writeMessage().

virtual void AMOS::Kmer_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.

Member Data Documentation

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

'A' bit

Definition at line 42 of file Kmer_AMOS.hh.

Referenced by compress(), and uncompress().

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

'C' bit

Definition at line 43 of file Kmer_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(), AMOS::Sequence_t::clear(), AMOS::IBankable_t::clear(), AMOS::Sequence_t::compress(), AMOS::Bank_t::fetchBID(), AMOS::Bank_t::fetchBIDFix(), AMOS::Overlap_t::getAdjacency(), AMOS::Link_t::getAdjacency(), AMOS::Sequence_t::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 AMOS::Sequence_t::uncompress().

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

'G' bit

Definition at line 44 of file Kmer_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().

const uint8_t Kmer_t::MAX_LENGTH = 255 [static]

Maximum Kmer length.

Definition at line 114 of file Kmer_AMOS.hh.

const NCode_t Kmer_t::NCODE = M_KMER [static]

The NCode type identifier for this object.

Reimplemented from AMOS::Universal_t.

Definition at line 111 of file Kmer_AMOS.hh.

Referenced by getNCode(), and writeMessage().

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

sequence bit mask

Definition at line 46 of file Kmer_AMOS.hh.

Referenced by setBase(), and uncompress().

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

'T' bit

Definition at line 45 of file Kmer_AMOS.hh.

Referenced by compress(), and uncompress().

The documentation for this class was generated from the following files:
Generated on Mon Feb 22 17:36:37 2010 for libAMOS by  doxygen 1.4.7