embshow

Data type EmbPShow

Attributes

Name	Type	Description
list	list of EmbPShowInfo structures

Attributes

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

Attributes

Name	Type	Description
width	width of sequence to display on each line
length	length of a page (0 = indefinite)
margin	margin for numbers
html	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	Information descriptor (set of available descriptors)
type	Type of information (enumerated list)
Padding	Padding to alignment boundary

Data type EmbPShowSeq

Attributes

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

Data type EmbPShowBlank

Attributes

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

Data type EmbPShowComp

Attributes

Name	Type	Description
number	ajTrue = number the complement

Data type EmbPShowRE

Attributes

Name	Type	Description
sense	1 or -1 = sense to display
flat	ajTrue = display in flat format with recognition sites
matches	list of AjPMatmatch matches
plasmid	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	number of hits in list
sitelist	list of EmbSShowREsite

Data type EmbPShowFT

Attributes

Name	Type	Description
feat	Feature table

Data type EmbPShowNote

Attributes

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

Data type EmbPShowREsite

Attributes

Name	Type	Description
name	name of Restriction Enzyme
pos	cut site position
Padding	Padding to alignment boundary