#include <Overlap_AMOS.hh>
Inheritance diagram for AMOS::Overlap_t:
Public Member Functions | |
| Overlap_t () | |
| Constructs an empty Overlap_t object. | |
| Overlap_t (const Overlap_t &source) | |
| Copy constructor. | |
| ~Overlap_t () | |
| Destroys a Overlap_t object. | |
| virtual void | clear () |
| Clears all object data, reinitializes the object. | |
| void | flip () |
| Flip the orientation of the overlap. | |
| OverlapAdjacency_t | getAdjacency () const |
| Get the overlapping ends of the reads. | |
| Size_t | getAhang () const |
| Get the A-hang overlap value. | |
| Size_t | getBhang () const |
| Get the B-hang overlap value. | |
| virtual NCode_t | getNCode () const |
| Get the AMOS NCode type identifier. | |
| std::pair< ID_t, ID_t > | getReads () const |
| Get the pair of contig IIDs joined by this overlap. | |
| uint32_t | getScore () const |
| Get the overlap score. | |
| bool | isFlagC () const |
| Check the value of flag C. | |
| virtual void | readMessage (const Message_t &msg) |
| Reads in data from a Message object. | |
| void | setAdjacency (OverlapAdjacency_t adj) |
| Set the overlapping ends of the reads. | |
| void | setAhang (Size_t aHang) |
| Set the A-hang overlap value. | |
| void | setBhang (Size_t bHang) |
| Set the B-hang overlap value. | |
| void | setFlagC (bool flag) |
| Set the value of flag C. | |
| void | setReads (std::pair< ID_t, ID_t > reads) |
| Set the read IID pair for this overlap. | |
| void | setScore (uint32_t score) |
| Set the overlap score. | |
| 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_OVERLAP |
| The NCode type identifier for this object. | |
| static const OverlapAdjacency_t | NULL_ADJACENCY = 0 |
| static const OverlapAdjacency_t | NORMAL = 'N' |
| E,B. | |
| static const OverlapAdjacency_t | ANTINORMAL = 'A' |
| B,E. | |
| static const OverlapAdjacency_t | INNIE = 'I' |
| E,E. | |
| static const OverlapAdjacency_t | OUTIE = 'O' |
| B,B. | |
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. | |
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 | NORMAL_BITS = 0x1 |
| static const uint8_t | ANTINORMAL_BITS = 0x2 |
| static const uint8_t | INNIE_BITS = 0x3 |
| static const uint8_t | OUTIE_BITS = 0x0 |
| static const uint8_t | ADJACENCY_BITS = 0x3 |
| adjacency info mask | |
| static const uint8_t | ADJACENCY_BIT = 0x4 |
| adjacency exists flag | |
| static const uint8_t | FLAGC_BIT = 0x8 |
| C flag. | |
A similarity based overlap between two Read_t that suggests their relative location (to one another) in the original sequence. If storing a large number of overlaps in an AMOS bank, it is wise to omit the IID and EID fields from the objects as these values will only be written to the bank if they are non-NULL. Also, an extra bit flag (FlagC) is provided in addition to FlagA and FlagB which are inherited.
Definition at line 33 of file Overlap_AMOS.hh.
| AMOS::Overlap_t::Overlap_t | ( | ) | [inline] |
Constructs an empty Overlap_t object.
Sets all members to 0
Definition at line 83 of file Overlap_AMOS.hh.
References AMOS::NULL_ID.
| AMOS::Overlap_t::Overlap_t | ( | const Overlap_t & | source | ) | [inline] |
| AMOS::Overlap_t::~Overlap_t | ( | ) | [inline] |
| virtual void AMOS::Overlap_t::clear | ( | ) | [inline, virtual] |
Clears all object data, reinitializes the object.
Reimplemented from AMOS::Universal_t.
Definition at line 110 of file Overlap_AMOS.hh.
References AMOS::Universal_t::clear(), and AMOS::NULL_ID.
Referenced by readMessage(), and writeMessage().
| void Overlap_t::flip | ( | ) |
Flip the orientation of the overlap.
Reverses the order of the read IIDs and changes the overlap adjacency as altered by the new orientation of the reads. Does not alter adjacency if it is currently a NULL_ADJACENCY. Also, swaps the a/bHang values. After flip, NORMAL becomes ANTINORMAL, ANTINORMAL becomes NORMAL, and INNIE and OUTIE remain the same.
Definition at line 22 of file Overlap_AMOS.cc.
References ANTINORMAL, getAdjacency(), NORMAL, and setAdjacency().
| OverlapAdjacency_t Overlap_t::getAdjacency | ( | ) | const |
Get the overlapping ends of the reads.
Get the overlap information for the reads, i.e. [N]ORMAL (EB), [A]NTINORMAL (BE), [I]NNIE (EE) or [O]UTIE (BB). Where B is the beginning of the read and E is the end of the read and [N]ORMAL means the end of read1 overlaps the beginning of read2.
Definition at line 39 of file Overlap_AMOS.cc.
References ADJACENCY_BIT, ADJACENCY_BITS, ANTINORMAL, ANTINORMAL_BITS, AMOS::IBankable_t::flags_m, INNIE, INNIE_BITS, NORMAL, NORMAL_BITS, NULL_ADJACENCY, OUTIE, and OUTIE_BITS.
Referenced by flip(), and writeMessage().
| Size_t AMOS::Overlap_t::getAhang | ( | ) | const [inline] |
Get the A-hang overlap value.
Get the length of the non-overlapping portion of the first read.
Definition at line 153 of file Overlap_AMOS.hh.
| Size_t AMOS::Overlap_t::getBhang | ( | ) | const [inline] |
Get the B-hang overlap value.
Get the length of the non-overlapping portion of the second read.
Definition at line 166 of file Overlap_AMOS.hh.
| const std::string& AMOS::Universal_t::getComment | ( | ) | const [inline, inherited] |
Get 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.
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.
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<<().
| virtual NCode_t AMOS::Overlap_t::getNCode | ( | ) | const [inline, virtual] |
Get the AMOS NCode type identifier.
Reimplemented from AMOS::Universal_t.
Definition at line 173 of file Overlap_AMOS.hh.
References NCODE.
Get the pair of contig IIDs joined by this overlap.
Definition at line 184 of file Overlap_AMOS.hh.
| uint32_t AMOS::Overlap_t::getScore | ( | ) | const [inline] |
Get the overlap score.
Definition at line 195 of file Overlap_AMOS.hh.
| const Status_t AMOS::Universal_t::getStatus | ( | ) | const [inline, inherited] |
| bool AMOS::IBankable_t::isFlagA | ( | ) | const [inline, inherited] |
Check 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 writeMessage().
| bool AMOS::IBankable_t::isFlagB | ( | ) | const [inline, inherited] |
Check 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 writeMessage().
| bool AMOS::Overlap_t::isFlagC | ( | ) | const [inline] |
Check the value of flag C.
Definition at line 206 of file Overlap_AMOS.hh.
References FLAGC_BIT, and AMOS::IBankable_t::flags_m.
Referenced by writeMessage().
| bool AMOS::IBankable_t::isModified | ( | ) | const [inline, inherited] |
Check if the object has been modified.
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.
Definition at line 206 of file Bank_AMOS.hh.
References AMOS::IBankable_t::flags_m.
| void Overlap_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.
| msg | The Message to read from |
| ArgumentException_t |
Reimplemented from AMOS::Universal_t.
Definition at line 56 of file Overlap_AMOS.cc.
References AMOS_THROW_ARGUMENT, clear(), AMOS::F_ADJACENCY, AMOS::F_AHANG, AMOS::F_BHANG, AMOS::F_FLAG, AMOS::F_READS, AMOS::F_SCORE, AMOS::Universal_t::readMessage(), setAdjacency(), AMOS::IBankable_t::setFlagA(), AMOS::IBankable_t::setFlagB(), and setFlagC().
| virtual void AMOS::Overlap_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.
| fix | The fixed length stream (stores all fixed length members) | |
| var | The variable length stream (stores all var length members) |
The get pointer of var is at the beginning of the record
Reimplemented from AMOS::Universal_t.
| virtual void AMOS::Overlap_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.
| fix | The fixed length stream (stores all fixed length members) |
Reimplemented from AMOS::Universal_t.
| void Overlap_t::setAdjacency | ( | OverlapAdjacency_t | adj | ) |
Set the overlapping ends of the reads.
Set the overlap information for the reads, i.e. [N]ORMAL (EB), [A]NTINORMAL (BE), [I]NNIE (EE) or [O]UTIE (BB). Where B is the beginning of the read and E is the end of the read and EB would mean the end of read1 overlaps the beginning of read2.
| adj | The new adjacency of the reads |
| ArgumentException_t |
Definition at line 156 of file Overlap_AMOS.cc.
References ADJACENCY_BIT, ADJACENCY_BITS, AMOS_THROW_ARGUMENT, ANTINORMAL, ANTINORMAL_BITS, AMOS::IBankable_t::flags_m, INNIE, INNIE_BITS, NORMAL, NORMAL_BITS, NULL_ADJACENCY, OUTIE, and OUTIE_BITS.
Referenced by flip(), and readMessage().
| void AMOS::Overlap_t::setAhang | ( | Size_t | aHang | ) | [inline] |
Set the A-hang overlap value.
Set the length of the non-overlapping portion of the first read.
| aHang | The new A-hang overlap value |
Definition at line 242 of file Overlap_AMOS.hh.
| void AMOS::Overlap_t::setBhang | ( | Size_t | bHang | ) | [inline] |
Set the B-hang overlap value.
Set the length of the non-overlapping portion of the second read.
| bHang | The new B-hang overlap value |
Definition at line 256 of file Overlap_AMOS.hh.
| void AMOS::Universal_t::setComment | ( | const std::string & | comment | ) | [inline, inherited] |
Set the comment string.
| comment | The new comment string |
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.
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.
| flag | The new flag A value |
Definition at line 272 of file Bank_AMOS.hh.
References AMOS::IBankable_t::flags_m.
Referenced by AMOS::Universal_t::readMessage(), and 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.
| flag | The new flag B value |
Definition at line 288 of file Bank_AMOS.hh.
References AMOS::IBankable_t::flags_m.
Referenced by AMOS::Universal_t::readMessage(), and readMessage().
| void AMOS::Overlap_t::setFlagC | ( | bool | flag | ) | [inline] |
Set the value of flag C.
| flag | The new flag C value |
Definition at line 268 of file Overlap_AMOS.hh.
References FLAGC_BIT, and AMOS::IBankable_t::flags_m.
Referenced by readMessage().
| void AMOS::IBankable_t::setIID | ( | ID_t | iid | ) | [inline, inherited] |
Set the internal ID.
| iid | The new internal ID |
Definition at line 300 of file Bank_AMOS.hh.
References AMOS::IBankable_t::iid_m.
Set the read IID pair for this overlap.
| reads | The new pair of read IIDs |
Definition at line 282 of file Overlap_AMOS.hh.
| void AMOS::Overlap_t::setScore | ( | uint32_t | score | ) | [inline] |
Set the overlap score.
| score | A 32-bit unsigned integer representing the overlap score |
Definition at line 294 of file Overlap_AMOS.hh.
| void AMOS::Universal_t::setStatus | ( | Status_t | status | ) | [inline, inherited] |
Set the status value.
| status | The new status value |
Definition at line 162 of file Universal_AMOS.hh.
Referenced by AMOS::Universal_t::readMessage().
| void Overlap_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.
| msg | The Message to write to |
Reimplemented from AMOS::Universal_t.
Definition at line 179 of file Overlap_AMOS.cc.
References clear(), AMOS::F_ADJACENCY, AMOS::F_AHANG, AMOS::F_BHANG, AMOS::F_FLAG, AMOS::F_READS, AMOS::F_SCORE, getAdjacency(), AMOS::IBankable_t::isFlagA(), AMOS::IBankable_t::isFlagB(), isFlagC(), NCODE, NULL_ADJACENCY, AMOS::NULL_ID, AMOS::NULL_STRING, and AMOS::Universal_t::writeMessage().
| virtual void AMOS::Overlap_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.
| fix | The fixed length stream (stores all fixed length members) | |
| var | The variable length stream (stores all var length members) |
Reimplemented from AMOS::Universal_t.
const uint8_t AMOS::Overlap_t::ADJACENCY_BIT = 0x4 [static, protected] |
adjacency exists flag
Definition at line 51 of file Overlap_AMOS.hh.
Referenced by getAdjacency(), and setAdjacency().
const uint8_t AMOS::Overlap_t::ADJACENCY_BITS = 0x3 [static, protected] |
adjacency info mask
Definition at line 50 of file Overlap_AMOS.hh.
Referenced by getAdjacency(), and setAdjacency().
const OverlapAdjacency_t AMOS::Overlap_t::ANTINORMAL = 'A' [static] |
B,E.
Definition at line 73 of file Overlap_AMOS.hh.
Referenced by flip(), getAdjacency(), and setAdjacency().
const uint8_t AMOS::Overlap_t::ANTINORMAL_BITS = 0x2 [static, protected] |
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().
const uint8_t AMOS::Overlap_t::FLAGC_BIT = 0x8 [static, protected] |
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(), getAdjacency(), AMOS::Link_t::getAdjacency(), AMOS::Sequence_t::isCompressed(), AMOS::IBankable_t::isFlagA(), AMOS::IBankable_t::isFlagB(), isFlagC(), AMOS::IBankable_t::isModified(), AMOS::IBankable_t::isRemoved(), AMOS::BankStream_t::operator<<(), AMOS::BankStream_t::operator>>(), AMOS::Bank_t::replaceBID(), setAdjacency(), AMOS::Link_t::setAdjacency(), AMOS::IBankable_t::setFlagA(), AMOS::IBankable_t::setFlagB(), setFlagC(), 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::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 OverlapAdjacency_t AMOS::Overlap_t::INNIE = 'I' [static] |
E,E.
Definition at line 74 of file Overlap_AMOS.hh.
Referenced by getAdjacency(), and setAdjacency().
const uint8_t AMOS::Overlap_t::INNIE_BITS = 0x3 [static, protected] |
const NCode_t Overlap_t::NCODE = M_OVERLAP [static] |
The NCode type identifier for this object.
Reimplemented from AMOS::Universal_t.
Definition at line 69 of file Overlap_AMOS.hh.
Referenced by getNCode(), and writeMessage().
const OverlapAdjacency_t AMOS::Overlap_t::NORMAL = 'N' [static] |
E,B.
Definition at line 72 of file Overlap_AMOS.hh.
Referenced by flip(), getAdjacency(), and setAdjacency().
const uint8_t AMOS::Overlap_t::NORMAL_BITS = 0x1 [static, protected] |
const OverlapAdjacency_t AMOS::Overlap_t::NULL_ADJACENCY = 0 [static] |
Definition at line 71 of file Overlap_AMOS.hh.
Referenced by getAdjacency(), setAdjacency(), and writeMessage().
const OverlapAdjacency_t AMOS::Overlap_t::OUTIE = 'O' [static] |
B,B.
Definition at line 75 of file Overlap_AMOS.hh.
Referenced by getAdjacency(), and setAdjacency().
const uint8_t AMOS::Overlap_t::OUTIE_BITS = 0x0 [static, protected] |
1.4.7