embshow.c

Show Sequence Constructors

All constructors return a new show sequence object by pointer. The target pointer does not need to be initialised to NULL, but it is good programming practice to do so anyway.

Function embShowNew

Creates a new sequence show object.

Synopsis

Prototype

EmbPShow embShowNew (
      const AjPSeq seq,
      ajint begin,
      ajint end,
      ajint width,
      ajint length,
      ajint margin,
      AjBool html,
      ajint offset
);

Input

seq:(Input)Sequence to describe
begin:(Input)start position in sequence
end:(Input)end position in sequence
width:(Input)width of displayed sequence on a line
length:(Input)length of a page in lines (0=no length)
margin:(Input)margin for numbers etc.
html:(Input)format output for HTML
offset:(Input)number to start display of position numbering at

Returns

EmbPShow:New sequence show object.

Description

Creates a new sequence show object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Show Sequence Destructors

Destruction destroys all internal data structures and frees the memory allocated for the show sequence object.

Function embShowDel

Deletes a show sequence object.

Synopsis

Prototype

void embShowDel (
      EmbPShow* pthis
);

Output

pthis:(Delete)Show sequence object

Returns

void:No return value

Description

Deletes a show sequence object.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Show Sequence Assignments

These functions add to the show sequence object provided as the first argument.

Function embShowAddSeq

Adds the sequence to be displayed to the list of things to show This must be done before the final printing is done as without a sequence to hang all the other features and things on, there can be no output to show.

Synopsis

Prototype

void embShowAddSeq (
      EmbPShow thys,
      AjBool number,
      AjBool threeletter,
      const AjPRange upperrange,
      const AjPRange colour
);

Input

number:(Input)Number the sequence
threeletter:(Input)Use three letter protein code
upperrange:(Input)Range of sequence to uppercase
colour:(Input)Range of sequence to colour in HTML

Input & Output

thys:(Modify)Show sequence object

Returns

void:No return value

Description

Adds the sequence to be displayed to the list of things to show This must be done before the final printing is done as without a sequence to hang all the other features and things on, there can be no output to show.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function embShowAddBlank

Adds a blank line to the list of things to show.

Synopsis

Prototype

void embShowAddBlank (
      EmbPShow thys
);

Input & Output

thys:(Modify)Show sequence object

Returns

void:No return value

Description

Adds a blank line to the list of things to show.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function embShowAddTicks

Adds a ticks line to the list of things to show.

Synopsis

Prototype

void embShowAddTicks (
      EmbPShow thys
);

Input & Output

thys:(Modify)Show sequence object

Returns

void:No return value

Description

Adds a ticks line to the list of things to show.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function embShowAddTicknum

Adds a ticks number line to the list of things to show.

Synopsis

Prototype

void embShowAddTicknum (
      EmbPShow thys
);

Input & Output

thys:(Modify)Show sequence object

Returns

void:No return value

Description

Adds a ticks number line to the list of things to show.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function embShowAddComp

Adds the sequence complement to be displayed to the list of things to show

Synopsis

Prototype

void embShowAddComp (
      EmbPShow thys,
      AjBool number
);

Input

number:(Input)ajTrue = number the complement

Input & Output

thys:(Modify)Show sequence object

Returns

void:No return value

Description

Adds the sequence complement to be displayed to the list of things to show

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function embShowAddTran

Adds the translation to be displayed to the list of things to show

Synopsis

Prototype

void embShowAddTran (
      EmbPShow thys,
      const AjPTrn trnTable,
      ajint frame,
      AjBool threeletter,
      AjBool number,
      const AjPRange regions,
      ajint orfminsize,
      AjBool lcinterorf,
      AjBool firstorf,
      AjBool lastorf,
      AjBool showframe
);

Input

trnTable:(Input)Translation table
frame:(Input)Reading frame to translate
threeletter:(Input)ajTrue for 3 letter code
number:(Input)ajTrue for numbering
regions:(Input)Sequence range(s)
orfminsize:(Input)Minimum length of ORF to be shown
lcinterorf:(Input)ajTrue to put inter-orf regions in lowercase
firstorf:(Input)ajTrue beginning of the seq is a possible ORF
lastorf:(Input)ajTrue end of the seq is a possible ORF
showframe:(Input)ajTrue write the frame number

Input & Output

thys:(Modify)Show sequence object

Returns

void:No return value

Description

Adds the translation to be displayed to the list of things to show

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function embShowAddRE

Adds the Restriction Enzymes to be displayed to the list of things to show

Synopsis

Prototype

void embShowAddRE (
      EmbPShow thys,
      ajint sense,
      const AjPList restrictlist,
      AjBool plasmid,
      AjBool flat
);

Input

sense:(Input)sense to translate (+1 or -1)
restrictlist:(Input)restriction enzyme cut site list
plasmid:(Input)Circular (plasmid) sequence
flat:(Input)show in flat format with recognition sites

Input & Output

thys:(Modify)Show sequence object

Returns

void:No return value

Description

Adds the Restriction Enzymes to be displayed to the list of things to show

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function embShowAddFT

Adds the Features to be displayed to the list of things to show

Synopsis

Prototype

void embShowAddFT (
      EmbPShow thys,
      const AjPFeattable feat
);

Input

feat:(Input)features

Input & Output

thys:(Modify)Show sequence object

Returns

void:No return value

Description

Adds the Features to be displayed to the list of things to show

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function embShowAddNote

Adds the annotations to be displayed to the list of things to show

Synopsis

Prototype

void embShowAddNote (
      EmbPShow thys,
      const AjPRange regions
);

Input

regions:(Input)Sequence range(s)

Input & Output

thys:(Modify)Show sequence object

Returns

void:No return value

Description

Adds the annotations to be displayed to the list of things to show

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Show Sequence Operators

These functions use the contents of a Show object but do not modify it.

Function embShowPrint

Prints a Show object

Synopsis

Prototype

void embShowPrint (
      AjPFile out,
      const EmbPShow thys
);

Input

thys:(Input)Show sequence object

Input & Output

out:(Modify)Output file handle

Returns

void:No return value

Description

Prints a Show object

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Show Fill Assignments

Add a set of space characters to the lines list to pad out an output line

Function embShowUpperRange

Uppercase a string from a sequence with a range I.e ranges of a sequence are to be uppercased. We have a small region of the original sequence in a string. We want to uppercase any bits of the string that are in the ranges.

Synopsis

Prototype

void embShowUpperRange (
      AjPStr* line,
      const AjPRange upperrange,
      ajint pos
);

Input

upperrange:(Input)range of original sequence to uppercase
pos:(Input)position in sequence that line starts at

Input & Output

line:(Modify)line to uppercase if it is in the ranges

Returns

void:No return value

Description

Uppercase a string from a sequence with a range I.e ranges of a sequence are to be uppercased. We have a small region of the original sequence in a string. We want to uppercase any bits of the string that are in the ranges.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0

Function embShowColourRange

colour a string from a sequence with a range I.e ranges of a sequence are to be coloured in HTML. We have a small region of the original sequence in a string. We want to colour any bits of the string that are in the ranges.

Synopsis

Prototype

void embShowColourRange (
      AjPStr* line,
      const AjPRange colour,
      ajint pos
);

Input

colour:(Input)range of original sequence to colour
pos:(Input)position in sequence that line starts at

Input & Output

line:(Modify)line to colour if it is in the ranges

Returns

void:No return value

Description

colour a string from a sequence with a range I.e ranges of a sequence are to be coloured in HTML. We have a small region of the original sequence in a string. We want to colour any bits of the string that are in the ranges.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

See Also

See other functions in this section

Availability

In release 3.0.0