ajalign.c

Function ajAlignDefine

Defines a sequence set as an alignment. The sequences are stored internally and may be edited by alignment processing.

Synopsis

Prototype

AjBool ajAlignDefine (
      AjPAlign thys,
      AjPSeqset seqset
);

Input & Output

thys:(Modify)Alignment object
seqset:(Modify)Sequence set object

Returns

AjBool:ajTrue on success

Description

Defines a sequence set as an alignment. The sequences are stored internally and may be edited by alignment processing.

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 ajAlignDefineSS

Defines a sequence pair as an alignment. The sequences are stored internally and may be edited by alignment processing.

Synopsis

Prototype

AjBool ajAlignDefineSS (
      AjPAlign thys,
      AjPSeq seqa,
      AjPSeq seqb
);

Input & Output

thys:(Modify)Alignment object
seqa:(Modify)Sequence object
seqb:(Modify)Second sequence object

Returns

AjBool:ajTrue on success

Description

Defines a sequence pair as an alignment. The sequences are stored internally and may be edited by alignment processing.

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 ajAlignDefineCC

Defines a pair of char* strings as an alignment

Synopsis

Prototype

AjBool ajAlignDefineCC (
      AjPAlign thys,
      const char* seqa,
      const char* seqb,
      const char* namea,
      const char* nameb
);

Input

seqa:(Input)First sequence
seqb:(Input)Second sequence
namea:(Input)Name of first sequence
nameb:(Input)Name of second sequence

Input & Output

thys:(Modify)Alignment object

Returns

AjBool:ajTrue on success

Description

Defines a pair of char* strings as an alignment

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 ajAlignDel

Destructor for Alignment objects

Synopsis

Prototype

void ajAlignDel (
      AjPAlign* pthys
);

Output

pthys:(Delete)Alignment object reference

Returns

void:No return value

Description

Destructor for Alignment objects

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 ajAlignReset

Reset for Alignment objects

Synopsis

Prototype

void ajAlignReset (
      AjPAlign thys
);

Output

thys:(Output)Alignment object reference

Returns

void:No return value

Description

Reset for Alignment objects

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 ajAlignOpen

Opens a new align file

Synopsis

Prototype

AjBool ajAlignOpen (
      AjPAlign thys,
      const AjPStr name
);

Input

name:(Input)File name

Input & Output

thys:(Modify)Alignment object

Returns

AjBool:ajTrue on success

Description

Opens a new align file

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 ajAlignFormatDefault

Sets the default format for an alignment

Synopsis

Prototype

AjBool ajAlignFormatDefault (
      AjPStr* pformat
);

Output

pformat:(Output)Default format returned

Returns

AjBool:ajTrue is format was returned

Description

Sets the default format for an alignment

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 ajAlignGetFilename

Returns the filename for an alignment.

Synopsis

Prototype

const char* ajAlignGetFilename (
      const AjPAlign thys
);

Input

thys:(Input)Alignment object.

Returns

const char*:Filename.

Description

Returns the filename for an alignment.

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 ajAlignGetFormat

Returns the sequence format for an alignment.

Synopsis

Prototype

const AjPStr ajAlignGetFormat (
      const AjPAlign thys
);

Input

thys:(Input)Alignment object.

Returns

const AjPStr:Alignment format

Description

Returns the sequence format for an alignment.

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 ajAlignFindFormat

Looks for the specified align format in the internal definitions and returns the index.

Synopsis

Prototype

AjBool ajAlignFindFormat (
      const AjPStr format,
      ajint* iformat
);

Input

format:(Input)Format required.

Output

iformat:(Output)Index

Returns

AjBool:ajTrue on success.

Description

Looks for the specified align format in the internal definitions and returns the index.

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 ajAlignValid

Test for an alignment object.

Checks the format works with the number of sequences. Checks the format works with the type (protein or nucleotide).

Synopsis

Prototype

AjBool ajAlignValid (
      AjPAlign thys
);

Input & Output

thys:(Modify)Alignment object

Returns

AjBool:ajTrue on success

Description

Test for an alignment object.

Checks the format works with the number of sequences. Checks the format works with the type (protein or nucleotide).

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 ajAlignNew

Constructor for an alignment object

Synopsis

Prototype

AjPAlign ajAlignNew (
      void
);

Returns

AjPAlign:New Alignment object

Description

Constructor for an alignment 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

Function ajAlignWrite

Writes an alignment file

Synopsis

Prototype

void ajAlignWrite (
      AjPAlign thys
);

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Writes an alignment file

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 ajAlignClose

Closes an alignment

Synopsis

Prototype

void ajAlignClose (
      AjPAlign thys
);

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Closes an alignment

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 ajAlignWriteHeader

Writes an alignment header.

Synopsis

Prototype

void ajAlignWriteHeader (
      AjPAlign thys
);

Input & Output

thys:(Modify)Alignment object. Internal count is updated to avoid duplicate headers

Returns

void:No return value

Description

Writes an alignment header.

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 ajAlignWriteTail

Writes an alignment tail

Synopsis

Prototype

void ajAlignWriteTail (
      AjPAlign thys
);

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Writes an alignment tail

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 ajAlignSetHeader

Defines an alignment header

Synopsis

Prototype

void ajAlignSetHeader (
      AjPAlign thys,
      const AjPStr header
);

Input

header:(Input)Align header with embedded newlines

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Defines an alignment header

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 ajAlignSetHeaderC

Defines an alignment header

Synopsis

Prototype

void ajAlignSetHeaderC (
      AjPAlign thys,
      const char* header
);

Input

header:(Input)Align header with embedded newlines

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Defines an alignment header

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 ajAlignSetHeaderApp

Appends to an alignment header

Synopsis

Prototype

void ajAlignSetHeaderApp (
      AjPAlign thys,
      const AjPStr header
);

Input

header:(Input)Align header with embedded newlines

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Appends to an alignment header

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 ajAlignSetTail

Defines an alignment tail

Synopsis

Prototype

void ajAlignSetTail (
      AjPAlign thys,
      const AjPStr tail
);

Input

tail:(Input)Align tail with embedded newlines

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Defines an alignment tail

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 ajAlignSetTailC

Defines an alignment tail

Synopsis

Prototype

void ajAlignSetTailC (
      AjPAlign thys,
      const char* tail
);

Input

tail:(Input)Align tail with embedded newlines

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Defines an alignment tail

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 ajAlignSetTailApp

Apopends to an alignment tail

Synopsis

Prototype

void ajAlignSetTailApp (
      AjPAlign thys,
      const AjPStr tail
);

Input

tail:(Input)Align tail with embedded newlines

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Apopends to an alignment tail

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 ajAlignSetSubTail

Defines an alignment tail

Synopsis

Prototype

void ajAlignSetSubTail (
      AjPAlign thys,
      const AjPStr tail
);

Input

tail:(Input)Align tail with embedded newlines

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Defines an alignment tail

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 ajAlignSetSubTailC

Defines an alignment tail

Synopsis

Prototype

void ajAlignSetSubTailC (
      AjPAlign thys,
      const char* tail
);

Input

tail:(Input)Align tail with embedded newlines

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Defines an alignment tail

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 ajAlignSetSubTailApp

Apopends to an alignment tail

Synopsis

Prototype

void ajAlignSetSubTailApp (
      AjPAlign thys,
      const AjPStr tail
);

Input

tail:(Input)Align tail with embedded newlines

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Apopends to an alignment tail

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 ajAlignSetSubHeader

Defines an alignment subheader (cleared after printing so it can be set again for the next alignment)

Synopsis

Prototype

void ajAlignSetSubHeader (
      AjPAlign thys,
      const AjPStr subheader
);

Input

subheader:(Input)Align subheader with embedded newlines

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Defines an alignment subheader (cleared after printing so it can be set again for the next alignment)

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 ajAlignSetSubHeaderC

Defines an alignment header (cleared after printing so it can be set again for the next alignment)

Synopsis

Prototype

void ajAlignSetSubHeaderC (
      AjPAlign thys,
      const char* subheader
);

Input

subheader:(Input)Align subheader with embedded newlines

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Defines an alignment header (cleared after printing so it can be set again for the next alignment)

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 ajAlignSetSubHeaderApp

Appends to an alignment subheader (cleared after printing so it can be set again for the next alignment)

Synopsis

Prototype

void ajAlignSetSubHeaderApp (
      AjPAlign thys,
      const AjPStr subheader
);

Input

subheader:(Input)Align subheader with embedded newlines

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Appends to an alignment subheader (cleared after printing so it can be set again for the next alignment)

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 ajAlignSetSubHeaderPre

Prepends to an alignment subheader (cleared after printing so it can be set again for the next alignment)

Synopsis

Prototype

void ajAlignSetSubHeaderPre (
      AjPAlign thys,
      const AjPStr subheader
);

Input

subheader:(Input)Align subheader with embedded newlines

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Prepends to an alignment subheader (cleared after printing so it can be set again for the next alignment)

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 ajAlignSetMatrixName

Defines an alignment matrix

Synopsis

Prototype

void ajAlignSetMatrixName (
      AjPAlign thys,
      const AjPStr matrix
);

Input

matrix:(Input)Matrix name

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Defines an alignment matrix

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 ajAlignSetMatrixNameC

Defines an alignment matrix

Synopsis

Prototype

void ajAlignSetMatrixNameC (
      AjPAlign thys,
      const char* matrix
);

Input

matrix:(Input)Matrix name

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Defines an alignment matrix

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 ajAlignSetMatrixInt

Defines an alignment matrix

Synopsis

Prototype

void ajAlignSetMatrixInt (
      AjPAlign thys,
      const AjPMatrix matrix
);

Input

matrix:(Input)Matrix object

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Defines an alignment matrix

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 ajAlignSetMatrixFloat

Defines an alignment matrix

Synopsis

Prototype

void ajAlignSetMatrixFloat (
      AjPAlign thys,
      const AjPMatrixf matrix
);

Input

matrix:(Input)Matrix (floating point version) object

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Defines an alignment matrix

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 ajAlignSetGapI

Defines alignment gap penalties

Synopsis

Prototype

void ajAlignSetGapI (
      AjPAlign thys,
      ajint gappen,
      ajint extpen
);

Input

gappen:(Input)Gap penalty
extpen:(Input)Gap extension penalty

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Defines alignment gap penalties

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 ajAlignSetGapR

Defines alignment gap penalties

Synopsis

Prototype

void ajAlignSetGapR (
      AjPAlign thys,
      float gappen,
      float extpen
);

Input

gappen:(Input)Gap penalty
extpen:(Input)Gap extension penalty

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Defines alignment gap penalties

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 ajAlignSetScoreI

Defines alignment score

Synopsis

Prototype

void ajAlignSetScoreI (
      AjPAlign thys,
      ajint score
);

Input

score:(Input)score

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Defines alignment score

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 ajAlignSetScoreL

Defines alignment score

Synopsis

Prototype

void ajAlignSetScoreL (
      AjPAlign thys,
      ajlong score
);

Input

score:(Input)score

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Defines alignment score

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 ajAlignSetScoreR

Defines alignment score

Synopsis

Prototype

void ajAlignSetScoreR (
      AjPAlign thys,
      float score
);

Input

score:(Input)score

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Defines alignment score

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 ajAlignSetStats

Sets standard properties for an alignment subheader. These are: Length, Identity, Gaps, Similarity, Score

Synopsis

Prototype

void ajAlignSetStats (
      AjPAlign thys,
      ajint iali,
      ajint len,
      ajint ident,
      ajint sim,
      ajint gaps,
      const AjPStr score
);

Input

iali:(Input)Alignment number
len:(Input)Alignment length
ident:(Input)Number of identities
sim:(Input)Number of similarities
gaps:(Input)Number of gaps
score:(Input)Alignment score (as saved by ajAlignSetScoreI or ajAlignSetScoreR)

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Sets standard properties for an alignment subheader. These are: Length, Identity, Gaps, Similarity, Score

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 ajAlignSetSubStandard

Sets standard subheader using the properties for an alignment. These are: Length, Identity, Gaps, Similarity, Score

Synopsis

Prototype

void ajAlignSetSubStandard (
      AjPAlign thys,
      ajint iali
);

Input

iali:(Input)Alignment number (or -1 for the latest)

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Sets standard subheader using the properties for an alignment. These are: Length, Identity, Gaps, Similarity, Score

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 ajAlignSetType

Sets the align type (if it is not set already)

Synopsis

Prototype

void ajAlignSetType (
      AjPAlign thys
);

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Sets the align type (if it is not set already)

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 ajAlignSetExternal

Sets the align object to use external sequence references, which are to be copied pointers rather than clones of the whole sequence.

Intended for alignments of large sequences where there is no need to keep many copies. An example is the EMBOSS application wordmatch.

Synopsis

Prototype

void ajAlignSetExternal (
      AjPAlign thys,
      AjBool external
);

Input

external:(Input)If true, do not make copies of sequence data and do not delete internal sequence data

Input & Output

thys:(Modify)Alignment object

Returns

void:No return value

Description

Sets the align object to use external sequence references, which are to be copied pointers rather than clones of the whole sequence.

Intended for alignments of large sequences where there is no need to keep many copies. An example is the EMBOSS application wordmatch.

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 ajAlignSetRange

Sets the alignment range in each sequence, but only for a pairwise alignment

Synopsis

Prototype

AjBool ajAlignSetRange (
      AjPAlign thys,
      ajint start1,
      ajint end1,
      ajint len1,
      ajint off1,
      ajint start2,
      ajint end2,
      ajint len2,
      ajint off2
);

Input

start1:(Input)Start in sequence 1
end1:(Input)End in sequence 1
len1:(Input)Length of sequence 1
off1:(Input)Offset of sequence 1
start2:(Input)Start in sequence 2
end2:(Input)End in sequence 2
len2:(Input)Length of sequence 2
off2:(Input)Offset of sequence 2

Input & Output

thys:(Modify)Alignment object

Returns

AjBool:ajTrue on success. Failure also writes an error message.

Description

Sets the alignment range in each sequence, but only for a pairwise alignment

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 ajAlignSetSubRange

Sets the alignment sub range in each sequence, but only for a pairwise alignment.

This sets the SubOffset in addition to the Start and End values, for use where the alignment has a large sequence, but only part of it is to be reported.

The usual example is where there are many matches in a long sequence, defined with SeqExternal so we use pointers to one original to avoid making multiple copies in memory while builing the AjPAlign and AlignPData structure.

Synopsis

Prototype

AjBool ajAlignSetSubRange (
      AjPAlign thys,
      ajint substart1,
      ajint start1,
      ajint end1,
      AjBool rev1,
      ajint len1,
      ajint substart2,
      ajint start2,
      ajint end2,
      AjBool rev2,
      ajint len2
);

Input

substart1:(Input)Subsequence offset in sequence 1
start1:(Input)Subsequence start in sequence 1
end1:(Input)Subsequence end in sequence 1
rev1:(Input)ajTrue if sequence 1 is reversed
len1:(Input)Length of sequence 1
substart2:(Input)Subsequence offset in sequence 2
start2:(Input)Subsequence start in sequence 2
end2:(Input)Subsequence end in sequence 2
rev2:(Input)ajTrue if sequence 2 is reversed
len2:(Input)Length of sequence 2

Input & Output

thys:(Modify)Alignment object

Returns

AjBool:ajTrue on success. Failure also writes an error message.

Description

Sets the alignment sub range in each sequence, but only for a pairwise alignment.

This sets the SubOffset in addition to the Start and End values, for use where the alignment has a large sequence, but only part of it is to be reported.

The usual example is where there are many matches in a long sequence, defined with SeqExternal so we use pointers to one original to avoid making multiple copies in memory while builing the AjPAlign and AlignPData structure.

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 ajAlignTraceT

Reports an AjPAlign object to debug output

Synopsis

Prototype

void ajAlignTraceT (
      const AjPAlign thys,
      const char* title
);

Input

thys:(Input)alignment object
title:(Input)Trace report title

Returns

void:No return value

Description

Reports an AjPAlign object to debug output

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 ajAlignTrace

Reports an AjPAlign object to debug output

Synopsis

Prototype

void ajAlignTrace (
      const AjPAlign thys
);

Input

thys:(Input)alignment object

Returns

void:No return value

Description

Reports an AjPAlign object to debug output

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 ajAlignPrintFormat

Reports the internal data structures

Synopsis

Prototype

void ajAlignPrintFormat (
      AjPFile outf,
      AjBool full
);

Input

full:(Input)Full report (usually ajFalse)

Input & Output

outf:(Modify)Output file

Returns

void:No return value

Description

Reports the internal data structures

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 ajAlignConsStats

Calculates alignment statistics (and a consensus) from a sequence set.

Synopsis

Prototype

AjBool ajAlignConsStats (
      const AjPSeqset thys,
      AjPMatrix mymatrix,
      AjPStr* cons,
      ajint* retident,
      ajint* retsim,
      ajint* retgap,
      ajint* retlen
);

Input

thys:(Input)Sequence set.

Output

mymatrix:(Output)User-defined matrix, or NULL for the default
cons:(Output)the created consensus sequence
retident:(Output)number of residues identical in all sequences
retsim:(Output)number of residues similar in all sequences
retgap:(Output)number of residues with a gap in 1 sequence
retlen:(Output)length of the alignment

Returns

AjBool:ajTrue on success

Description

Calculates alignment statistics (and a consensus) from a sequence set.

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 ajAlignExit

Cleans up report processing internal memory

Synopsis

Prototype

void ajAlignExit (
      void
);

Returns

void:No return value

Description

Cleans up report processing internal memory

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