embshow

Enum ShowEValtype

Enumerated value(s)

Name
SH_SEQ	Sequence
SH_BLANK	Blank line
SH_TICK	Tick marks
SH_TICKNUM	Tick numbers
SH_COMP	Complementary strand
SH_TRAN	Protein translation
SH_RE	Restriction enzyme cut sites
SH_FT	Features
SH_NOTE	Notes

Data type EmbPShow

Attributes

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

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

Data type EmbPShowInfo

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: ----------------------------

EmbPShowInfo->type=SH_BLANK | ->info=EmbPShowBlank | EmbPShowInfo->type=SH_TICKS | ->info=EmbPShowTicks | EmbPShowInfo->type=SH_SEQ | ->info=EmbPShowSeq | EmbPShowInfo->type=SH_COMP | ->info=EmbPShowComp | EmbPShowInfo->type=etc. | ->info=etc. | etc.

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

Data type EmbPShowSeq

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

Data type EmbPShowBlank

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

Data type EmbPShowTicks

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

Data type EmbPShowTicknum

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

Data type EmbPShowTran

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

Data type EmbPShowComp

Attributes

Name	Type	Description
number	AjBool	ajTrue = number the complement

Data type EmbPShowRE

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

Data type EmbPShowFT

Attributes

Name	Type	Description
feat	AjPFeattable	Feature table

Data type EmbPShowNote

Attributes

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

Data type EmbPShowREsite

Attributes

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