embshow.c

Section: 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.

Functions: embShowNew

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
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence to describe
ajintbeginInputstart position in sequence
ajintendInputend position in sequence
ajintwidthInputwidth of displayed sequence on a line
ajintlengthInputlength of a page in lines (0=no length)
ajintmarginInputmargin for numbers etc.
AjBoolhtmlInputformat output for HTML
ajintoffsetInputnumber to start display of position numbering at
EmbPShow RETURNNew sequence show object.

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 6.4.0

Section: Show Sequence Destructors

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

Functions: embShowDel

Function embShowDel

Deletes a show sequence object.

Synopsis

Prototype
void embShowDel (
      EmbPShow* pthis
);

TypeNameRead/WriteDescription
EmbPShow*pthisDeleteShow sequence object
void RETURN

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 6.4.0

Section: Show Sequence Assignments

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

Functions: embShowAddSeq embShowAddBlank embShowAddTicks embShowAddTicknum embShowAddComp embShowAddTran embShowAddRE embShowAddFT embShowAddNote

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
);

TypeNameRead/WriteDescription
EmbPShowthysModifyShow sequence object
AjBoolnumberInputNumber the sequence
AjBoolthreeletterInputUse three letter protein code
const AjPRangeupperrangeInputRange of sequence to uppercase
const AjPRangecolourInputRange of sequence to colour in HTML
void RETURN

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 6.4.0

Function embShowAddBlank

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

Synopsis

Prototype
void embShowAddBlank (
      EmbPShow thys
);

TypeNameRead/WriteDescription
EmbPShowthysModifyShow sequence object
void RETURN

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 6.4.0

Function embShowAddTicks

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

Synopsis

Prototype
void embShowAddTicks (
      EmbPShow thys
);

TypeNameRead/WriteDescription
EmbPShowthysModifyShow sequence object
void RETURN

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 6.4.0

Function embShowAddTicknum

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

Synopsis

Prototype
void embShowAddTicknum (
      EmbPShow thys
);

TypeNameRead/WriteDescription
EmbPShowthysModifyShow sequence object
void RETURN

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 6.4.0

Function embShowAddComp

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

Synopsis

Prototype
void embShowAddComp (
      EmbPShow thys,
      AjBool number
);

TypeNameRead/WriteDescription
EmbPShowthysModifyShow sequence object
AjBoolnumberInputajTrue = number the complement
void RETURN

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 6.4.0

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
);

TypeNameRead/WriteDescription
EmbPShowthysModifyShow sequence object
const AjPTrntrnTableInputTranslation table
ajintframeInputReading frame to translate
AjBoolthreeletterInputajTrue for 3 letter code
AjBoolnumberInputajTrue for numbering
const AjPRangeregionsInputSequence range(s)
ajintorfminsizeInputMinimum length of ORF to be shown
AjBoollcinterorfInputajTrue to put inter-orf regions in lowercase
AjBoolfirstorfInputajTrue beginning of the seq is a possible ORF
AjBoollastorfInputajTrue end of the seq is a possible ORF
AjBoolshowframeInputajTrue write the frame number
void RETURN

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 6.4.0

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
);

TypeNameRead/WriteDescription
EmbPShowthysModifyShow sequence object
ajintsenseInputsense to translate (+1 or -1)
const AjPListrestrictlistInputrestriction enzyme cut site list
AjBoolplasmidInputCircular (plasmid) sequence
AjBoolflatInputshow in flat format with recognition sites
void RETURN

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 6.4.0

Function embShowAddFT

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

Synopsis

Prototype
void embShowAddFT (
      EmbPShow thys,
      const AjPFeattable feat
);

TypeNameRead/WriteDescription
EmbPShowthysModifyShow sequence object
const AjPFeattablefeatInputfeatures
void RETURN

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 6.4.0

Function embShowAddNote

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

Synopsis

Prototype
void embShowAddNote (
      EmbPShow thys,
      const AjPRange regions
);

TypeNameRead/WriteDescription
EmbPShowthysModifyShow sequence object
const AjPRangeregionsInputSequence range(s)
void RETURN

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 6.4.0

Section: Show Sequence Operators

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

Functions: embShowPrint

Function embShowPrint

Prints a Show object

Synopsis

Prototype
void embShowPrint (
      AjPFile out,
      const EmbPShow thys
);

TypeNameRead/WriteDescription
AjPFileoutModifyOutput file handle
const EmbPShowthysInputShow sequence object
void RETURN

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 6.4.0

Section: Show Fill Assignments

These functions fill out the sequence and features lines according to the descriptor data.

Functions: embShowUpperRange embShowColourRange

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,
      ajuint pos
);

TypeNameRead/WriteDescription
AjPStr*lineModifyline to uppercase if it is in the ranges
const AjPRangeupperrangeInputrange of original sequence to uppercase
ajuintposInputposition in sequence that line starts at
void RETURN

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 6.4.0

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,
      ajuint pos
);

TypeNameRead/WriteDescription
AjPStr*lineModifyline to colour if it is in the ranges
const AjPRangecolourInputrange of original sequence to colour
ajuintposInputposition in sequence that line starts at
void RETURN

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 6.4.0