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 Creates a new sequence show object.

Function embShowNew

Creates a new sequence show object.

Prototype

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

Type Name Read/Write Description

const AjPSeq seq Input Sequence to describe

ajint begin Input start position in sequence

ajint end Input end position in sequence

ajint width Input width of displayed sequence on a line

ajint length Input length of a page in lines (0=no length)

ajint margin Input margin for numbers etc.

AjBool html Input format output for HTML

ajint offset Input number to start display of position numbering at

EmbPShow RETURN New sequence show object.

Type	Name	Read/Write	Description
`const AjPSeq`	`seq`	Input	Sequence to describe
`ajint`	`begin`	Input	start position in sequence
`ajint`	`end`	Input	end position in sequence
`ajint`	`width`	Input	width of displayed sequence on a line
`ajint`	`length`	Input	length of a page in lines (0=no length)
`ajint`	`margin`	Input	margin for numbers etc.
`AjBool`	`html`	Input	format output for HTML
`ajint`	`offset`	Input	number to start display of position numbering at
`EmbPShow`		RETURN	New sequence show object.

From EMBOSS 1.0.0

Section: Show Sequence Destructors

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

Functions:

embShowDel Deletes a show sequence object.

Function embShowDel

Deletes a show sequence object.

Prototype

void embShowDel (
      EmbPShow* pthis
);

Type Name Read/Write Description

EmbPShow* pthis Delete Show sequence object

void RETURN

Type	Name	Read/Write	Description
`EmbPShow*`	`pthis`	Delete	Show sequence object
`void`		RETURN

From EMBOSS 1.0.0

Section: Show Sequence Assignments

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

Functions:

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.

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

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

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

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

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

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

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

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

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.

Prototype

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

Type Name Read/Write Description

EmbPShow thys Modify Show sequence object

AjBool number Input Number the sequence

AjBool threeletter Input Use three letter protein code

const AjPRange upperrange Input Range of sequence to uppercase

const AjPRange colour Input Range of sequence to colour in HTML

void RETURN

Type	Name	Read/Write	Description
`EmbPShow`	`thys`	Modify	Show sequence object
`AjBool`	`number`	Input	Number the sequence
`AjBool`	`threeletter`	Input	Use three letter protein code
`const AjPRange`	`upperrange`	Input	Range of sequence to uppercase
`const AjPRange`	`colour`	Input	Range of sequence to colour in HTML
`void`		RETURN

From EMBOSS 1.0.0

Function embShowAddBlank

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

Prototype

void embShowAddBlank (
      EmbPShow thys
);

Type Name Read/Write Description

EmbPShow thys Modify Show sequence object

void RETURN

Type	Name	Read/Write	Description
`EmbPShow`	`thys`	Modify	Show sequence object
`void`		RETURN

From EMBOSS 1.0.0

Function embShowAddTicks

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

Prototype

void embShowAddTicks (
      EmbPShow thys
);

Type Name Read/Write Description

EmbPShow thys Modify Show sequence object

void RETURN

Type	Name	Read/Write	Description
`EmbPShow`	`thys`	Modify	Show sequence object
`void`		RETURN

From EMBOSS 1.0.0

Function embShowAddTicknum

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

Prototype

void embShowAddTicknum (
      EmbPShow thys
);

Type Name Read/Write Description

EmbPShow thys Modify Show sequence object

void RETURN

Type	Name	Read/Write	Description
`EmbPShow`	`thys`	Modify	Show sequence object
`void`		RETURN

From EMBOSS 1.0.0

Function embShowAddComp

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

Prototype

void embShowAddComp (
      EmbPShow thys,
      AjBool number
);

Type Name Read/Write Description

EmbPShow thys Modify Show sequence object

AjBool number Input ajTrue = number the complement

void RETURN

Type	Name	Read/Write	Description
`EmbPShow`	`thys`	Modify	Show sequence object
`AjBool`	`number`	Input	ajTrue = number the complement
`void`		RETURN

From EMBOSS 1.0.0

Function embShowAddTran

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

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
);

Type Name Read/Write Description

EmbPShow thys Modify Show sequence object

const AjPTrn trnTable Input Translation table

ajint frame Input Reading frame to translate

AjBool threeletter Input ajTrue for 3 letter code

AjBool number Input ajTrue for numbering

const AjPRange regions Input Sequence range(s)

ajint orfminsize Input Minimum length of ORF to be shown

AjBool lcinterorf Input ajTrue to put inter-orf regions in lowercase

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

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

AjBool showframe Input ajTrue write the frame number

void RETURN

Type	Name	Read/Write	Description
`EmbPShow`	`thys`	Modify	Show sequence object
`const AjPTrn`	`trnTable`	Input	Translation table
`ajint`	`frame`	Input	Reading frame to translate
`AjBool`	`threeletter`	Input	ajTrue for 3 letter code
`AjBool`	`number`	Input	ajTrue for numbering
`const AjPRange`	`regions`	Input	Sequence range(s)
`ajint`	`orfminsize`	Input	Minimum length of ORF to be shown
`AjBool`	`lcinterorf`	Input	ajTrue to put inter-orf regions in lowercase
`AjBool`	`firstorf`	Input	ajTrue beginning of the seq is a possible ORF
`AjBool`	`lastorf`	Input	ajTrue end of the seq is a possible ORF
`AjBool`	`showframe`	Input	ajTrue write the frame number
`void`		RETURN

From EMBOSS 1.0.0

Function embShowAddRE

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

Prototype

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

Type Name Read/Write Description

EmbPShow thys Modify Show sequence object

ajint sense Input sense to translate (+1 or -1)

const AjPList restrictlist Input restriction enzyme cut site list

AjBool plasmid Input Circular (plasmid) sequence

AjBool flat Input show in flat format with recognition sites

void RETURN

Type	Name	Read/Write	Description
`EmbPShow`	`thys`	Modify	Show sequence object
`ajint`	`sense`	Input	sense to translate (+1 or -1)
`const AjPList`	`restrictlist`	Input	restriction enzyme cut site list
`AjBool`	`plasmid`	Input	Circular (plasmid) sequence
`AjBool`	`flat`	Input	show in flat format with recognition sites
`void`		RETURN

From EMBOSS 1.0.0

Function embShowAddFT

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

Prototype

void embShowAddFT (
      EmbPShow thys,
      const AjPFeattable feat
);

Type Name Read/Write Description

EmbPShow thys Modify Show sequence object

const AjPFeattable feat Input features

void RETURN

Type	Name	Read/Write	Description
`EmbPShow`	`thys`	Modify	Show sequence object
`const AjPFeattable`	`feat`	Input	features
`void`		RETURN

From EMBOSS 1.0.0

Function embShowAddNote

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

Prototype

void embShowAddNote (
      EmbPShow thys,
      const AjPRange regions
);

Type Name Read/Write Description

EmbPShow thys Modify Show sequence object

const AjPRange regions Input Sequence range(s)

void RETURN

Type	Name	Read/Write	Description
`EmbPShow`	`thys`	Modify	Show sequence object
`const AjPRange`	`regions`	Input	Sequence range(s)
`void`		RETURN

From EMBOSS 2.1.0

Section: Show Sequence Operators

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

Functions:

embShowPrint Prints a Show object

Function embShowPrint

Prints a Show object

Prototype

void embShowPrint (
      AjPFile out,
      const EmbPShow thys
);

Type Name Read/Write Description

AjPFile out Modify Output file handle

const EmbPShow thys Input Show sequence object

void RETURN

Type	Name	Read/Write	Description
`AjPFile`	`out`	Modify	Output file handle
`const EmbPShow`	`thys`	Input	Show sequence object
`void`		RETURN

From EMBOSS 1.0.0

Section: Show Fill Assignments

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

Functions:

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.

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.

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.

Prototype

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

Type Name Read/Write Description

AjPStr* line Modify line to uppercase if it is in the ranges

const AjPRange upperrange Input range of original sequence to uppercase

ajuint pos Input position in sequence that line starts at

void RETURN

Type	Name	Read/Write	Description
`AjPStr*`	`line`	Modify	line to uppercase if it is in the ranges
`const AjPRange`	`upperrange`	Input	range of original sequence to uppercase
`ajuint`	`pos`	Input	position in sequence that line starts at
`void`		RETURN

From EMBOSS 1.13.0

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.

Prototype

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

Type Name Read/Write Description

AjPStr* line Modify line to colour if it is in the ranges

const AjPRange colour Input range of original sequence to colour

ajuint pos Input position in sequence that line starts at

void RETURN

Type	Name	Read/Write	Description
`AjPStr*`	`line`	Modify	line to colour if it is in the ranges
`const AjPRange`	`colour`	Input	range of original sequence to colour
`ajuint`	`pos`	Input	position in sequence that line starts at
`void`		RETURN

From EMBOSS 1.13.0

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.
embShowAddBlank	Adds a blank line to the list of things to show.
embShowAddTicks	Adds a ticks line to the list of things to show.
embShowAddTicknum	Adds a ticks number line to the list of things to show.
embShowAddComp	Adds the sequence complement to be displayed to the list of things to show
embShowAddTran	Adds the translation to be displayed to the list of things to show
embShowAddRE	Adds the Restriction Enzymes to be displayed to the list of things to show
embShowAddFT	Adds the Features to be displayed to the list of things to show
embShowAddNote	Adds the annotations to be displayed to the list of things to show

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.
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.