embshow

Data type EmbPShow

NUCLEUS data structure for EmbPShow object for a sequence

Attributes

Name Type Description

list AjPList list of EmbPShowInfo structures

Name	Type	Description
list	AjPList	list of EmbPShowInfo structures

Attributes

Name Type Description

seq const AjPSeq the sequence

nucleic AjBool ajTrue = the sequence is nucleic

offset ajuint offset to start numbering at

start ajuint sequence position to start printing at

end ajuint sequence position to stop printing at

Name	Type	Description
seq	const AjPSeq	the sequence
nucleic	AjBool	ajTrue = the sequence is nucleic
offset	ajuint	offset to start numbering at
start	ajuint	sequence position to start printing at
end	ajuint	sequence position to stop printing at

Attributes

Name Type Description

width ajuint width of sequence to display on each line

length ajuint length of a page (0 = indefinite)

margin ajuint margin for numbers

html AjBool ajTrue = format page for HTML

Name	Type	Description
width	ajuint	width of sequence to display on each line
length	ajuint	length of a page (0 = indefinite)
margin	ajuint	margin for numbers
html	AjBool	ajTrue = format page for HTML

Data type EmbPShowInfo

The sequence and associated things to show are held in an ordered list of type EmbPShowInfo. This list is held in the structure EmbPShow.

The things to show are displayed around the sequence in the order that they are held on the list.

EmbPShowInfo holds the descriptor (one of EmbPShowBlank, EmbPShowTicks, EmbPShowSeq, EmbPShowComp, etc.) and the type of the descriptor (one of SH_BLANK, SH_TICKS, SH_SEQ, SH_COMP, etc. )

Each descriptor (EmbPShowSeq, EmbPShowBlank, EmbPShowTicks, etc.) holds information that could be useful in displaying its type of information.

So, for example:

EmbPShow could have a list of: ----------------------------

Attributes

Name Type Description

info void* Information descriptor (set of available descriptors)

type ajint Type of information (enumerated list)

Padding char[4] Padding to alignment boundary

Name	Type	Description
info	void*	Information descriptor (set of available descriptors)
type	ajint	Type of information (enumerated list)
Padding	char[4]	Padding to alignment boundary

Data type EmbPShowSeq

NUCLEUS data structure for sequence information, type = SH_SEQ

Attributes

Name Type Description

number AjBool ajTrue = number the sequence

threeletter AjBool ajTrue = display proteins in three letter code

upperrange const AjPRange range of sequence to uppercase

highlight const AjPRange range of sequence to colour in HTML

Name	Type	Description
number	AjBool	ajTrue = number the sequence
threeletter	AjBool	ajTrue = display proteins in three letter code
upperrange	const AjPRange	range of sequence to uppercase
highlight	const AjPRange	range of sequence to colour in HTML

Data type EmbPShowBlank

NUCLEUS data structure for blank line information, type = SH_BLANK

Attributes

Name Type Description

dummy AjBool Dummy attribute - no specific information needed AJNEW0() falls over if 0 bytes are allocated, so put in this dummy to pad the structure out

Name	Type	Description
dummy	AjBool	Dummy attribute - no specific information needed AJNEW0() falls over if 0 bytes are allocated, so put in this dummy to pad the structure out

Data type EmbPShowTicks

NUCLEUS data structure for tick line information, type = SH_TICK

Attributes

Name Type Description

dummy AjBool Dummy attribute - no specific information needed AJNEW0() falls over if 0 bytes are allocated, so put in this dummy to pad the structure out

Name	Type	Description
dummy	AjBool	Dummy attribute - no specific information needed AJNEW0() falls over if 0 bytes are allocated, so put in this dummy to pad the structure out

Data type EmbPShowTicknum

NUCLEUS data structure for tick number line information, type = SH_TICKNUM

Attributes

Name Type Description

dummy AjBool Dummy attribute - no specific information needed AJNEW0() falls over if 0 bytes are allocated, so put in this dummy to pad the structure out

Name	Type	Description
dummy	AjBool	Dummy attribute - no specific information needed AJNEW0() falls over if 0 bytes are allocated, so put in this dummy to pad the structure out

Data type EmbPShowTran

NUCLEUS data structure for translation information, type = SH_TRAN

Attributes

Name Type Description

transeq AjPSeq Copy of our stored translation

trnTable const AjPTrn translation table

frame ajint 1,2,3,-1,-2 or -3 = frame to translate

threeletter AjBool ajTrue = display in three letter code

number AjBool ajTrue = number the translation

tranpos ajuint store of translation position for numbering

regions const AjPRange only translate in these regions, NULL = do all

orfminsize ajuint minimum size of ORF to display

lcinterorf AjBool ajTrue = put the inter-orf regions in lower case

firstorf AjBool ajTrue = beginning of the seq is a possible ORF

lastorf AjBool ajTrue = end of the seq is a possible ORF

showframe AjBool ajTrue = write the frame number

Padding char[4] Padding to alignment boundary

Name	Type	Description
transeq	AjPSeq	Copy of our stored translation
trnTable	const AjPTrn	translation table
frame	ajint	1,2,3,-1,-2 or -3 = frame to translate
threeletter	AjBool	ajTrue = display in three letter code
number	AjBool	ajTrue = number the translation
tranpos	ajuint	store of translation position for numbering
regions	const AjPRange	only translate in these regions, NULL = do all
orfminsize	ajuint	minimum size of ORF to display
lcinterorf	AjBool	ajTrue = put the inter-orf regions in lower case
firstorf	AjBool	ajTrue = beginning of the seq is a possible ORF
lastorf	AjBool	ajTrue = end of the seq is a possible ORF
showframe	AjBool	ajTrue = write the frame number
Padding	char[4]	Padding to alignment boundary

Data type EmbPShowComp

NUCLEUS data structure for sequence complement information, type = SH_COMP

Attributes

Name Type Description

number AjBool ajTrue = number the complement

Name	Type	Description
number	AjBool	ajTrue = number the complement

Data type EmbPShowRE

NUCLEUS data structure for RE cut site information, type = SH_RE

Attributes

Name Type Description

sense ajint 1 or -1 = sense to display

flat AjBool ajTrue = display in flat format with recognition sites

matches AjPList list of AjPMatmatch matches

plasmid AjBool ajTrue = Circular (plasmid) sequence. Needed so that when we display sequences we can decide whether to show cuts that go past the origin in either direction

hits ajuint number of hits in list

sitelist AjPList list of EmbSShowREsite

Name	Type	Description
sense	ajint	1 or -1 = sense to display
flat	AjBool	ajTrue = display in flat format with recognition sites
matches	AjPList	list of AjPMatmatch matches
plasmid	AjBool	ajTrue = Circular (plasmid) sequence. Needed so that when we display sequences we can decide whether to show cuts that go past the origin in either direction
hits	ajuint	number of hits in list
sitelist	AjPList	list of EmbSShowREsite

Data type EmbPShowFT

NUCLEUS data structure for Feature information, type = SH_FT

Attributes

Name Type Description

feat AjPFeattable Feature table

Name	Type	Description
feat	AjPFeattable	Feature table

Data type EmbPShowNote

NUCLEUS data structure for annotation information, type = SH_NOTE

Attributes

Name Type Description

regions const AjPRange regions to annotate, NULL = no regions

Name	Type	Description
regions	const AjPRange	regions to annotate, NULL = no regions

Data type EmbPShowREsite

NUCLEUS data structure for Restriction Enzyme cut site position list node

Attributes

Name Type Description

name AjPStr name of Restriction Enzyme

pos ajint cut site position

Padding char[4] Padding to alignment boundary

Name	Type	Description
name	AjPStr	name of Restriction Enzyme
pos	ajint	cut site position
Padding	char[4]	Padding to alignment boundary