Message_AMOS.hh File Reference

Header for Message_t and IMessagable_t. More...

#include "utility_AMOS.hh"
#include <string>
#include <vector>
#include <iostream>

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Namespaces
namespace	AMOS
Classes
class	AMOS::Message_t
	A generic AMOS message object for reading and writing data. More...
class	AMOS::IMessagable_t
	Interface for classes that can interpret messages. More...
Defines
#define	__Message_AMOS_HH   1
Variables
const char	E_ADD = 'A'
const char	E_DELETE = 'D'
const char	E_REPLACE = 'R'
const NCode_t	F_NULL = Encode ("nul")
const NCode_t	F_AHANG = Encode ("ahg")
const NCode_t	F_ACTION = Encode ("act")
const NCode_t	F_ADJACENCY = Encode ("adj")
const NCode_t	F_BASEPOSITION = Encode ("bcp")
const NCode_t	F_BHANG = Encode ("bhg")
const NCode_t	F_BID = Encode ("bid")
const NCode_t	F_CLEAR = Encode ("clr")
const NCode_t	F_COMMENT = Encode ("com")
const NCode_t	F_COUNT = Encode ("cnt")
const NCode_t	F_EID = Encode ("eid")
const NCode_t	F_EDGE = Encode ("edg")
const NCode_t	F_FLAG = Encode ("flg")
const NCode_t	F_FRAGMENT = Encode ("frg")
const NCode_t	F_GAPS = Encode ("gap")
const NCode_t	F_IID = Encode ("iid")
const NCode_t	F_LIBRARY = Encode ("lib")
const NCode_t	F_LINK = Encode ("lnk")
const NCode_t	F_MAP = Encode ("map")
const NCode_t	F_MEAN = Encode ("mea")
const NCode_t	F_MEMBER = Encode ("mbr")
const NCode_t	F_NODES = Encode ("nds")
const NCode_t	F_OBJECT = Encode ("obj")
const NCode_t	F_OFFSET = Encode ("off")
const NCode_t	F_POSITION = Encode ("pos")
const NCode_t	F_QUALITY = Encode ("qlt")
const NCode_t	F_QUALITYCLEAR = Encode ("qcr")
const NCode_t	F_READS = Encode ("rds")
const NCode_t	F_SCORE = Encode ("scr")
const NCode_t	F_SEQUENCE = Encode ("seq")
const NCode_t	F_SD = Encode ("std")
const NCode_t	F_SIZE = Encode ("sze")
const NCode_t	F_SOURCE = Encode ("src")
const NCode_t	F_STATUS = Encode ("sts")
const NCode_t	F_TYPE = Encode ("typ")
const NCode_t	F_VECTORCLEAR = Encode ("vcr")
const NCode_t	M_NULL = Encode ("NUL")
const NCode_t	M_UNIVERSAL = Encode ("UNV")
const NCode_t	M_CONTIG = Encode ("CTG")
const NCode_t	M_CONTIGEDGE = Encode ("CTE")
const NCode_t	M_CONTIGLINK = Encode ("CTL")
const NCode_t	M_DISTRIBUTION = Encode ("DST")
const NCode_t	M_EDGE = Encode ("EDG")
const NCode_t	M_FEATURE = Encode ("FEA")
const NCode_t	M_FRAGMENT = Encode ("FRG")
const NCode_t	M_GROUP = Encode ("GRP")
const NCode_t	M_KMER = Encode ("KMR")
const NCode_t	M_LAYOUT = Encode ("LAY")
const NCode_t	M_LIBRARY = Encode ("LIB")
const NCode_t	M_LINK = Encode ("LNK")
const NCode_t	M_IDMAP = Encode ("MAP")
const NCode_t	M_INDEX = Encode ("IDX")
const NCode_t	M_OVERLAP = Encode ("OVL")
const NCode_t	M_READ = Encode ("RED")
const NCode_t	M_SCAFFOLD = Encode ("SCF")
const NCode_t	M_SCAFFOLDEDGE = Encode ("SCE")
const NCode_t	M_SCAFFOLDLINK = Encode ("SCL")
const NCode_t	M_SEQUENCE = Encode ("SEQ")
const NCode_t	M_TILE = Encode ("TLE")

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Detailed Description

Header for Message_t and IMessagable_t.

Author:

Adam M Phillippy

Date:

11/12/2003

Todo:

Validity checking for Message and Field codes

Definition in file Message_AMOS.hh.

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Define Documentation

#define __Message_AMOS_HH   1

Definition at line 12 of file Message_AMOS.hh.

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Variable Documentation

const char AMOS::E_ADD = 'A'

Definition at line 23 of file Message_AMOS.hh.

const char AMOS::E_DELETE = 'D'

Definition at line 24 of file Message_AMOS.hh.

const char AMOS::E_REPLACE = 'R'

Definition at line 25 of file Message_AMOS.hh.

const NCode_t AMOS::F_ACTION = Encode ("act")

Definition at line 28 of file Message_AMOS.hh.

const NCode_t AMOS::F_ADJACENCY = Encode ("adj")

Definition at line 29 of file Message_AMOS.hh. Referenced by AMOS::Overlap_t::readMessage(), AMOS::Link_t::readMessage(), AMOS::Overlap_t::writeMessage(), and AMOS::Link_t::writeMessage().

const NCode_t AMOS::F_AHANG = Encode ("ahg")

Definition at line 27 of file Message_AMOS.hh. Referenced by AMOS::Overlap_t::readMessage(), and AMOS::Overlap_t::writeMessage().

const NCode_t AMOS::F_BASEPOSITION = Encode ("bcp")

Definition at line 30 of file Message_AMOS.hh. Referenced by AMOS::Read_t::readMessage(), and AMOS::Read_t::writeMessage().

const NCode_t AMOS::F_BHANG = Encode ("bhg")

Definition at line 31 of file Message_AMOS.hh. Referenced by AMOS::Overlap_t::readMessage(), and AMOS::Overlap_t::writeMessage().

const NCode_t AMOS::F_BID = Encode ("bid")

Definition at line 32 of file Message_AMOS.hh.

const NCode_t AMOS::F_CLEAR = Encode ("clr")

Definition at line 33 of file Message_AMOS.hh. Referenced by AMOS::Read_t::readMessage(), AMOS::Feature_t::readMessage(), AMOS::Tile_t::readMessage(), AMOS::Read_t::writeMessage(), AMOS::Feature_t::writeMessage(), and AMOS::Tile_t::writeMessage().

const NCode_t AMOS::F_COMMENT = Encode ("com")

Definition at line 34 of file Message_AMOS.hh. Referenced by AMOS::Universal_t::readMessage(), and AMOS::Universal_t::writeMessage().

const NCode_t AMOS::F_COUNT = Encode ("cnt")

Definition at line 35 of file Message_AMOS.hh. Referenced by AMOS::Kmer_t::readMessage(), and AMOS::Kmer_t::writeMessage().

const NCode_t AMOS::F_EDGE = Encode ("edg")

Definition at line 37 of file Message_AMOS.hh. Referenced by AMOS::Scaffold_t::readMessage(), and AMOS::Scaffold_t::writeMessage().

const NCode_t AMOS::F_EID = Encode ("eid")

Definition at line 36 of file Message_AMOS.hh. Referenced by AMOS::Universal_t::readMessage(), and AMOS::Universal_t::writeMessage().

const NCode_t AMOS::F_FLAG = Encode ("flg")

Definition at line 38 of file Message_AMOS.hh. Referenced by AMOS::Universal_t::readMessage(), AMOS::Overlap_t::readMessage(), AMOS::Universal_t::writeMessage(), and AMOS::Overlap_t::writeMessage().

const NCode_t AMOS::F_FRAGMENT = Encode ("frg")

Definition at line 39 of file Message_AMOS.hh. Referenced by AMOS::Read_t::readMessage(), and AMOS::Read_t::writeMessage().

const NCode_t AMOS::F_GAPS = Encode ("gap")

Definition at line 40 of file Message_AMOS.hh. Referenced by AMOS::Tile_t::readMessage(), and AMOS::Tile_t::writeMessage().

const NCode_t AMOS::F_IID = Encode ("iid")

Definition at line 41 of file Message_AMOS.hh. Referenced by AMOS::Universal_t::readMessage(), and AMOS::Universal_t::writeMessage().

const NCode_t AMOS::F_LIBRARY = Encode ("lib")

Definition at line 42 of file Message_AMOS.hh. Referenced by AMOS::Fragment_t::readMessage(), and AMOS::Fragment_t::writeMessage().

const NCode_t AMOS::F_LINK = Encode ("lnk")

Definition at line 43 of file Message_AMOS.hh. Referenced by AMOS::IEdge_t::readMessage(), and AMOS::IEdge_t::writeMessage().

const NCode_t AMOS::F_MAP = Encode ("map")

Definition at line 44 of file Message_AMOS.hh. Referenced by AMOS::Index_t::readMessage(), AMOS::IDMap_t::readMessage(), AMOS::Index_t::writeMessage(), and AMOS::IDMap_t::writeMessage().

const NCode_t AMOS::F_MEAN = Encode ("mea")

Definition at line 45 of file Message_AMOS.hh. Referenced by AMOS::Distribution_t::readMessage(), and AMOS::Distribution_t::writeMessage().

const NCode_t AMOS::F_MEMBER = Encode ("mbr")

Definition at line 46 of file Message_AMOS.hh. Referenced by AMOS::Group_t::readMessage(), and AMOS::Group_t::writeMessage().

const NCode_t AMOS::F_NODES = Encode ("nds")

Definition at line 47 of file Message_AMOS.hh. Referenced by AMOS::Link_t::readMessage(), and AMOS::Link_t::writeMessage().

const NCode_t AMOS::F_NULL = Encode ("nul")

Definition at line 26 of file Message_AMOS.hh.

const NCode_t AMOS::F_OBJECT = Encode ("obj")

Definition at line 48 of file Message_AMOS.hh. Referenced by AMOS::Link_t::readMessage(), AMOS::Index_t::readMessage(), AMOS::IDMap_t::readMessage(), AMOS::Group_t::readMessage(), AMOS::Link_t::writeMessage(), AMOS::Index_t::writeMessage(), AMOS::IDMap_t::writeMessage(), and AMOS::Group_t::writeMessage().

const NCode_t AMOS::F_OFFSET = Encode ("off")

Definition at line 49 of file Message_AMOS.hh. Referenced by AMOS::Tile_t::readMessage(), and AMOS::Tile_t::writeMessage().

const NCode_t AMOS::F_POSITION = Encode ("pos")

Definition at line 50 of file Message_AMOS.hh. Referenced by AMOS::Read_t::readMessage(), and AMOS::Read_t::writeMessage().

const NCode_t AMOS::F_QUALITY = Encode ("qlt")

Definition at line 51 of file Message_AMOS.hh. Referenced by AMOS::Sequence_t::readMessage(), and AMOS::Sequence_t::writeMessage().

const NCode_t AMOS::F_QUALITYCLEAR = Encode ("qcr")

Definition at line 52 of file Message_AMOS.hh. Referenced by AMOS::Read_t::readMessage(), and AMOS::Read_t::writeMessage().

const NCode_t AMOS::F_READS = Encode ("rds")

Definition at line 53 of file Message_AMOS.hh. Referenced by AMOS::Overlap_t::readMessage(), AMOS::Kmer_t::readMessage(), AMOS::Fragment_t::readMessage(), AMOS::Overlap_t::writeMessage(), AMOS::Kmer_t::writeMessage(), and AMOS::Fragment_t::writeMessage().

const NCode_t AMOS::F_SCORE = Encode ("scr")

Definition at line 54 of file Message_AMOS.hh. Referenced by AMOS::Overlap_t::readMessage(), and AMOS::Overlap_t::writeMessage().

const NCode_t AMOS::F_SD = Encode ("std")

Definition at line 56 of file Message_AMOS.hh. Referenced by AMOS::Link_t::readMessage(), AMOS::Distribution_t::readMessage(), AMOS::Link_t::writeMessage(), and AMOS::Distribution_t::writeMessage().

const NCode_t AMOS::F_SEQUENCE = Encode ("seq")

Definition at line 55 of file Message_AMOS.hh. Referenced by AMOS::Sequence_t::readMessage(), AMOS::Kmer_t::readMessage(), AMOS::Sequence_t::writeMessage(), and AMOS::Kmer_t::writeMessage().

const NCode_t AMOS::F_SIZE = Encode ("sze")

Definition at line 57 of file Message_AMOS.hh. Referenced by AMOS::Link_t::readMessage(), AMOS::Index_t::readMessage(), AMOS::IDMap_t::readMessage(), AMOS::Fragment_t::readMessage(), AMOS::Link_t::writeMessage(), AMOS::Index_t::writeMessage(), AMOS::IDMap_t::writeMessage(), and AMOS::Fragment_t::writeMessage().

const NCode_t AMOS::F_SOURCE = Encode ("src")

Definition at line 58 of file Message_AMOS.hh. Referenced by AMOS::Link_t::readMessage(), AMOS::Fragment_t::readMessage(), AMOS::Feature_t::readMessage(), AMOS::Tile_t::readMessage(), AMOS::Link_t::writeMessage(), AMOS::Fragment_t::writeMessage(), AMOS::Feature_t::writeMessage(), and AMOS::Tile_t::writeMessage().

const NCode_t AMOS::F_STATUS = Encode ("sts")

Definition at line 59 of file Message_AMOS.hh. Referenced by AMOS::Universal_t::readMessage(), and AMOS::Universal_t::writeMessage().

const NCode_t AMOS::F_TYPE = Encode ("typ")

Definition at line 60 of file Message_AMOS.hh. Referenced by AMOS::Read_t::readMessage(), AMOS::Link_t::readMessage(), AMOS::Fragment_t::readMessage(), AMOS::Feature_t::readMessage(), AMOS::Read_t::writeMessage(), AMOS::Link_t::writeMessage(), AMOS::Fragment_t::writeMessage(), and AMOS::Feature_t::writeMessage().

const NCode_t AMOS::F_VECTORCLEAR = Encode ("vcr")

Definition at line 61 of file Message_AMOS.hh. Referenced by AMOS::Read_t::readMessage(), and AMOS::Read_t::writeMessage().

const NCode_t AMOS::M_CONTIG = Encode ("CTG")

Definition at line 64 of file Message_AMOS.hh.

const NCode_t AMOS::M_CONTIGEDGE = Encode ("CTE")

Definition at line 65 of file Message_AMOS.hh.

const NCode_t AMOS::M_CONTIGLINK = Encode ("CTL")

Definition at line 66 of file Message_AMOS.hh.

const NCode_t AMOS::M_DISTRIBUTION = Encode ("DST")

Definition at line 67 of file Message_AMOS.hh. Referenced by AMOS::Library_t::readMessage().

const NCode_t AMOS::M_EDGE = Encode ("EDG")

Definition at line 68 of file Message_AMOS.hh.

const NCode_t AMOS::M_FEATURE = Encode ("FEA")

Definition at line 69 of file Message_AMOS.hh.

const NCode_t AMOS::M_FRAGMENT = Encode ("FRG")

Definition at line 70 of file Message_AMOS.hh.

const NCode_t AMOS::M_GROUP = Encode ("GRP")

Definition at line 71 of file Message_AMOS.hh.

const NCode_t AMOS::M_IDMAP = Encode ("MAP")

Definition at line 76 of file Message_AMOS.hh.

const NCode_t AMOS::M_INDEX = Encode ("IDX")

Definition at line 77 of file Message_AMOS.hh.

const NCode_t AMOS::M_KMER = Encode ("KMR")

Definition at line 72 of file Message_AMOS.hh.

const NCode_t AMOS::M_LAYOUT = Encode ("LAY")

Definition at line 73 of file Message_AMOS.hh.

const NCode_t AMOS::M_LIBRARY = Encode ("LIB")

Definition at line 74 of file Message_AMOS.hh.

const NCode_t AMOS::M_LINK = Encode ("LNK")

Definition at line 75 of file Message_AMOS.hh.

const NCode_t AMOS::M_NULL = Encode ("NUL")

Definition at line 62 of file Message_AMOS.hh. Referenced by AMOS::Message_t::clear(), and AMOS::Message_t::Message_t().

const NCode_t AMOS::M_OVERLAP = Encode ("OVL")

Definition at line 78 of file Message_AMOS.hh.

const NCode_t AMOS::M_READ = Encode ("RED")

Definition at line 79 of file Message_AMOS.hh.

const NCode_t AMOS::M_SCAFFOLD = Encode ("SCF")

Definition at line 80 of file Message_AMOS.hh.

const NCode_t AMOS::M_SCAFFOLDEDGE = Encode ("SCE")

Definition at line 81 of file Message_AMOS.hh.

const NCode_t AMOS::M_SCAFFOLDLINK = Encode ("SCL")

Definition at line 82 of file Message_AMOS.hh.

const NCode_t AMOS::M_SEQUENCE = Encode ("SEQ")

Definition at line 83 of file Message_AMOS.hh.

const NCode_t AMOS::M_TILE = Encode ("TLE")

Definition at line 84 of file Message_AMOS.hh. Referenced by AMOS::Scaffold_t::readMessage(), AMOS::Layout_t::readMessage(), and AMOS::Contig_t::readMessage().

const NCode_t AMOS::M_UNIVERSAL = Encode ("UNV")

Definition at line 63 of file Message_AMOS.hh.

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