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
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
AjPSeqsetseqsetModifySequence set object
AjBool RETURNajTrue on success

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.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignDefineSS

Defines a sequence pair as an alignment. Either new copies of the sequences or direct references to them are made depending on the value of the SeqExternal attribute of the alignment object.

Synopsis

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

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
const AjPSeqseqaInputSequence object
const AjPSeqseqbInputSecond sequence object
AjBool RETURNajTrue on success

Input
seqa:(Input)Sequence object
seqb:(Input)Second sequence object
Input & Output
thys:(Modify)Alignment object
Returns
AjBool:ajTrue on success

Description

Defines a sequence pair as an alignment. Either new copies of the sequences or direct references to them are made depending on the value of the SeqExternal attribute of the alignment object.

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
const char*seqaInputFirst sequence
const char*seqbInputSecond sequence
const char*nameaInputName of first sequence
const char*namebInputName of second sequence
AjBool RETURNajTrue on success

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignDel

Destructor for Alignment objects

Synopsis

Prototype
void ajAlignDel (
      AjPAlign* pthys
);

TypeNameRead/WriteDescription
AjPAlign*pthysDeleteAlignment object reference
void RETURN

Output
pthys:(Delete)Alignment object reference
Returns
void:No return value

Description

Destructor for Alignment objects

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignReset

Reset for Alignment objects

Synopsis

Prototype
void ajAlignReset (
      AjPAlign thys
);

TypeNameRead/WriteDescription
AjPAlignthysOutputAlignment object reference
void RETURN

Output
thys:(Output)Alignment object reference
Returns
void:No return value

Description

Reset for Alignment objects

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignOpen

Opens a new align file

Synopsis

Prototype
AjBool ajAlignOpen (
      AjPAlign thys,
      const AjPStr name
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
const AjPStrnameInputFile name
AjBool RETURNajTrue on success

Input
name:(Input)File name
Input & Output
thys:(Modify)Alignment object
Returns
AjBool:ajTrue on success

Description

Opens a new align file

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignFormatDefault

Sets the default format for an alignment

Synopsis

Prototype
AjBool ajAlignFormatDefault (
      AjPStr* pformat
);

TypeNameRead/WriteDescription
AjPStr*pformatOutputDefault format returned
AjBool RETURNajTrue if format was returned

Output
pformat:(Output)Default format returned
Returns
AjBool:ajTrue if format was returned

Description

Sets the default format for an alignment

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignGetLen

Returns the filename for an alignment. If the alignment has more than one sub-alignment, returns the total.

Synopsis

Prototype
ajint ajAlignGetLen (
      const AjPAlign thys
);

TypeNameRead/WriteDescription
const AjPAlignthysInputAlignment object.
ajint RETURNAlignment length.

Input
thys:(Input)Alignment object.
Returns
ajint:Alignment length.

Description

Returns the filename for an alignment. If the alignment has more than one sub-alignment, returns the total.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignGetFilename

Returns the filename for an alignment.

Synopsis

Prototype
const char* ajAlignGetFilename (
      const AjPAlign thys
);

TypeNameRead/WriteDescription
const AjPAlignthysInputAlignment object.
const char* RETURNFilename.

Input
thys:(Input)Alignment object.
Returns
const char*:Filename.

Description

Returns the filename for an alignment.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignGetFormat

Returns the sequence format for an alignment.

Synopsis

Prototype
const AjPStr ajAlignGetFormat (
      const AjPAlign thys
);

TypeNameRead/WriteDescription
const AjPAlignthysInputAlignment object.
const AjPStr RETURNAlignment format

Input
thys:(Input)Alignment object.
Returns
const AjPStr:Alignment format

Description

Returns the sequence format for an alignment.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignFormatShowsSequences

Returns whether current alignment format includes sequences in output

Synopsis

Prototype
AjBool ajAlignFormatShowsSequences (
      const AjPAlign thys
);

TypeNameRead/WriteDescription
const AjPAlignthysInputAlignment object
AjBool RETURNtrue if sequences appear in output

Input
thys:(Input)Alignment object
Returns
AjBool:true if sequences appear in output

Description

Returns whether current alignment format includes sequences in output

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
const AjPStrformatInputFormat required.
ajint*iformatOutputIndex
AjBool RETURNajTrue on success.

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.

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
AjBool RETURNajTrue on success

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).

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignNew

Constructor for an alignment object

Synopsis

Prototype
AjPAlign ajAlignNew (
      void
);

TypeNameRead/WriteDescription
AjPAlign RETURNNew Alignment object

Returns
AjPAlign:New Alignment object

Description

Constructor for an alignment object

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignWrite

Writes an alignment file

Synopsis

Prototype
void ajAlignWrite (
      AjPAlign thys
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
void RETURN

Input & Output
thys:(Modify)Alignment object
Returns
void:No return value

Description

Writes an alignment file

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignClose

Closes an alignment

Synopsis

Prototype
void ajAlignClose (
      AjPAlign thys
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
void RETURN

Input & Output
thys:(Modify)Alignment object
Returns
void:No return value

Description

Closes an alignment

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignWriteHeader

Writes an alignment header.

Synopsis

Prototype
void ajAlignWriteHeader (
      AjPAlign thys
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object. Internal count is updated to avoid duplicate headers
void RETURN

Input & Output
thys:(Modify)Alignment object. Internal count is updated to avoid duplicate headers
Returns
void:No return value

Description

Writes an alignment header.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignWriteTail

Writes an alignment tail

Synopsis

Prototype
void ajAlignWriteTail (
      AjPAlign thys
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
void RETURN

Input & Output
thys:(Modify)Alignment object
Returns
void:No return value

Description

Writes an alignment tail

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignSetHeader

Defines an alignment header

Synopsis

Prototype
void ajAlignSetHeader (
      AjPAlign thys,
      const AjPStr header
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
const AjPStrheaderInputAlign header with embedded newlines
void RETURN

Input
header:(Input)Align header with embedded newlines
Input & Output
thys:(Modify)Alignment object
Returns
void:No return value

Description

Defines an alignment header

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignSetHeaderC

Defines an alignment header

Synopsis

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

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
const char*headerInputAlign header with embedded newlines
void RETURN

Input
header:(Input)Align header with embedded newlines
Input & Output
thys:(Modify)Alignment object
Returns
void:No return value

Description

Defines an alignment header

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignSetHeaderApp

Appends to an alignment header

Synopsis

Prototype
void ajAlignSetHeaderApp (
      AjPAlign thys,
      const AjPStr header
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
const AjPStrheaderInputAlign header with embedded newlines
void RETURN

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignSetTail

Defines an alignment tail

Synopsis

Prototype
void ajAlignSetTail (
      AjPAlign thys,
      const AjPStr tail
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
const AjPStrtailInputAlign tail with embedded newlines
void RETURN

Input
tail:(Input)Align tail with embedded newlines
Input & Output
thys:(Modify)Alignment object
Returns
void:No return value

Description

Defines an alignment tail

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignSetTailC

Defines an alignment tail

Synopsis

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

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
const char*tailInputAlign tail with embedded newlines
void RETURN

Input
tail:(Input)Align tail with embedded newlines
Input & Output
thys:(Modify)Alignment object
Returns
void:No return value

Description

Defines an alignment tail

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignSetTailApp

Appends to an alignment tail

Synopsis

Prototype
void ajAlignSetTailApp (
      AjPAlign thys,
      const AjPStr tail
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
const AjPStrtailInputAlign tail with embedded newlines
void RETURN

Input
tail:(Input)Align tail with embedded newlines
Input & Output
thys:(Modify)Alignment object
Returns
void:No return value

Description

Appends to an alignment tail

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignSetSubTail

Defines an alignment tail

Synopsis

Prototype
void ajAlignSetSubTail (
      AjPAlign thys,
      const AjPStr tail
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
const AjPStrtailInputAlign tail with embedded newlines
void RETURN

Input
tail:(Input)Align tail with embedded newlines
Input & Output
thys:(Modify)Alignment object
Returns
void:No return value

Description

Defines an alignment tail

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignSetSubTailC

Defines an alignment tail

Synopsis

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

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
const char*tailInputAlign tail with embedded newlines
void RETURN

Input
tail:(Input)Align tail with embedded newlines
Input & Output
thys:(Modify)Alignment object
Returns
void:No return value

Description

Defines an alignment tail

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignSetSubTailApp

Appends to an alignment tail

Synopsis

Prototype
void ajAlignSetSubTailApp (
      AjPAlign thys,
      const AjPStr tail
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
const AjPStrtailInputAlign tail with embedded newlines
void RETURN

Input
tail:(Input)Align tail with embedded newlines
Input & Output
thys:(Modify)Alignment object
Returns
void:No return value

Description

Appends to an alignment tail

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
const AjPStrsubheaderInputAlign subheader with embedded newlines
void RETURN

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)

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
const char*subheaderInputAlign subheader with embedded newlines
void RETURN

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)

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
const AjPStrsubheaderInputAlign subheader with embedded newlines
void RETURN

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)

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
const AjPStrsubheaderInputAlign subheader with embedded newlines
void RETURN

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)

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignSetMatrixName

Defines an alignment matrix

Synopsis

Prototype
void ajAlignSetMatrixName (
      AjPAlign thys,
      const AjPStr matrix
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
const AjPStrmatrixInputMatrix name
void RETURN

Input
matrix:(Input)Matrix name
Input & Output
thys:(Modify)Alignment object
Returns
void:No return value

Description

Defines an alignment matrix

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignSetMatrixNameC

Defines an alignment matrix

Synopsis

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

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
const char*matrixInputMatrix name
void RETURN

Input
matrix:(Input)Matrix name
Input & Output
thys:(Modify)Alignment object
Returns
void:No return value

Description

Defines an alignment matrix

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignSetMatrixInt

Defines an alignment matrix

Synopsis

Prototype
void ajAlignSetMatrixInt (
      AjPAlign thys,
      AjPMatrix matrix
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
AjPMatrixmatrixModifyMatrix object
void RETURN

Input & Output
thys:(Modify)Alignment object
matrix:(Modify)Matrix object
Returns
void:No return value

Description

Defines an alignment matrix

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignSetMatrixFloat

Defines an alignment matrix

Synopsis

Prototype
void ajAlignSetMatrixFloat (
      AjPAlign thys,
      AjPMatrixf matrix
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
AjPMatrixfmatrixModifyMatrix (floating point version) object
void RETURN

Input & Output
thys:(Modify)Alignment object
matrix:(Modify)Matrix (floating point version) object
Returns
void:No return value

Description

Defines an alignment matrix

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignSetGapI

Defines alignment gap penalties

Synopsis

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

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
ajintgappenInputGap penalty
ajintextpenInputGap extension penalty
void RETURN

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignSetGapR

Defines alignment gap penalties

Synopsis

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

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
floatgappenInputGap penalty
floatextpenInputGap extension penalty
void RETURN

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignSetScoreI

Defines alignment score

Synopsis

Prototype
void ajAlignSetScoreI (
      AjPAlign thys,
      ajint score
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
ajintscoreInputscore
void RETURN

Input
score:(Input)score
Input & Output
thys:(Modify)Alignment object
Returns
void:No return value

Description

Defines alignment score

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignSetScoreL

Defines alignment score

Synopsis

Prototype
void ajAlignSetScoreL (
      AjPAlign thys,
      ajlong score
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
ajlongscoreInputscore
void RETURN

Input
score:(Input)score
Input & Output
thys:(Modify)Alignment object
Returns
void:No return value

Description

Defines alignment score

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignSetScoreR

Defines alignment score

Synopsis

Prototype
void ajAlignSetScoreR (
      AjPAlign thys,
      float score
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
floatscoreInputscore
void RETURN

Input
score:(Input)score
Input & Output
thys:(Modify)Alignment object
Returns
void:No return value

Description

Defines alignment score

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
ajintialiInputAlignment number
ajintlenInputAlignment length
ajintidentInputNumber of identities
ajintsimInputNumber of similarities
ajintgapsInputNumber of gaps
const AjPStrscoreInputAlignment score (as saved by ajAlignSetScoreI or ajAlignSetScoreR)
void RETURN

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

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
ajintialiInputAlignment number (or -1 for the latest)
void RETURN

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignSetType

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

Synopsis

Prototype
void ajAlignSetType (
      AjPAlign thys
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
void RETURN

Input & Output
thys:(Modify)Alignment object
Returns
void:No return value

Description

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

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
AjBoolexternalInputIf true, do not make copies of sequence data and do not delete internal sequence data
void RETURN

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.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignSetRefSeqIndx

Sets the index of the reference sequence.

Synopsis

Prototype
void ajAlignSetRefSeqIndx (
      AjPAlign thys,
      ajint refseq
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
ajintrefseqInputindex of the reference sequence
void RETURN

Input
refseq:(Input)index of the reference sequence
Input & Output
thys:(Modify)Alignment object
Returns
void:No return value

Description

Sets the index of the reference sequence.

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
ajintstart1InputStart in sequence 1
ajintend1InputEnd in sequence 1
ajintlen1InputLength of sequence 1
ajintoff1InputOffset of sequence 1
ajintstart2InputStart in sequence 2
ajintend2InputEnd in sequence 2
ajintlen2InputLength of sequence 2
ajintoff2InputOffset of sequence 2
AjBool RETURNajTrue on success. Failure also writes an error message.

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

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignSetSubRange

Sets the local 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 building the AjPAlign and AlignPData structure.

Resets the alignment length to be the length of the longest subsequence

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
);

TypeNameRead/WriteDescription
AjPAlignthysModifyAlignment object
ajintsubstart1InputSubsequence offset in sequence 1
ajintstart1InputSubsequence start in sequence 1
ajintend1InputSubsequence end in sequence 1
AjBoolrev1InputajTrue if sequence 1 is reversed
ajintlen1InputLength of sequence 1
ajintsubstart2InputSubsequence offset in sequence 2
ajintstart2InputSubsequence start in sequence 2
ajintend2InputSubsequence end in sequence 2
AjBoolrev2InputajTrue if sequence 2 is reversed
ajintlen2InputLength of sequence 2
AjBool RETURNajTrue on success. Failure also writes an error message.

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 local 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 building the AjPAlign and AlignPData structure.

Resets the alignment length to be the length of the longest subsequence

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignTraceT

Reports an AjPAlign object to debug output

Synopsis

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

TypeNameRead/WriteDescription
const AjPAlignthysInputalignment object
const char*titleInputTrace report title
void RETURN

Input
thys:(Input)alignment object
title:(Input)Trace report title
Returns
void:No return value

Description

Reports an AjPAlign object to debug output

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignTrace

Reports an AjPAlign object to debug output

Synopsis

Prototype
void ajAlignTrace (
      const AjPAlign thys
);

TypeNameRead/WriteDescription
const AjPAlignthysInputalignment object
void RETURN

Input
thys:(Input)alignment object
Returns
void:No return value

Description

Reports an AjPAlign object to debug output

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignPrintFormat

Reports the internal data structures

Synopsis

Prototype
void ajAlignPrintFormat (
      AjPFile outf,
      AjBool full
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
AjBoolfullInputFull report (usually ajFalse)
void RETURN

Input
full:(Input)Full report (usually ajFalse)
Input & Output
outf:(Modify)Output file
Returns
void:No return value

Description

Reports the internal data structures

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignPrintbookFormat

Reports the alignment format internals as Docbook text

Synopsis

Prototype
void ajAlignPrintbookFormat (
      AjPFile outf
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
void RETURN

Input & Output
outf:(Modify)Output file
Returns
void:No return value

Description

Reports the alignment format internals as Docbook text

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignPrinthtmlFormat

Reports the internal data structures

Synopsis

Prototype
void ajAlignPrinthtmlFormat (
      AjPFile outf
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
void RETURN

Input & Output
outf:(Modify)Output file
Returns
void:No return value

Description

Reports the internal data structures

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignPrintwikiFormat

Reports the alignment format internals as wikitext

Synopsis

Prototype
void ajAlignPrintwikiFormat (
      AjPFile outf
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
void RETURN

Input & Output
outf:(Modify)Output file
Returns
void:No return value

Description

Reports the alignment format internals as wikitext

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignConsAmbig

Calculates alignment consensus of ambiguity characters from a sequence set.

Synopsis

Prototype
AjBool ajAlignConsAmbig (
      const AjPSeqset thys,
      AjPStr* cons
);

TypeNameRead/WriteDescription
const AjPSeqsetthysInputSequence set.
AjPStr*consOutputthe created consensus sequence
AjBool RETURNajTrue on success

Input
thys:(Input)Sequence set.
Output
cons:(Output)the created consensus sequence
Returns
AjBool:ajTrue on success

Description

Calculates alignment consensus of ambiguity characters from a sequence set.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignConsAmbigNuc

Calculates alignment consensus of ambiguity characters from a sequence set.

Synopsis

Prototype
AjBool ajAlignConsAmbigNuc (
      const AjPSeqset thys,
      AjPStr* cons
);

TypeNameRead/WriteDescription
const AjPSeqsetthysInputSequence set.
AjPStr*consOutputthe created consensus sequence
AjBool RETURNajTrue on success

Input
thys:(Input)Sequence set.
Output
cons:(Output)the created consensus sequence
Returns
AjBool:ajTrue on success

Description

Calculates alignment consensus of ambiguity characters from a sequence set.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignConsAmbigProt

Calculates alignment consensus of ambiguity characters from a sequence set.

Synopsis

Prototype
AjBool ajAlignConsAmbigProt (
      const AjPSeqset thys,
      AjPStr* cons
);

TypeNameRead/WriteDescription
const AjPSeqsetthysInputSequence set.
AjPStr*consOutputthe created consensus sequence
AjBool RETURNajTrue on success

Input
thys:(Input)Sequence set.
Output
cons:(Output)the created consensus sequence
Returns
AjBool:ajTrue on success

Description

Calculates alignment consensus of ambiguity characters from a sequence set.

See Also

See other functions in this section

Availability

In release 6.4.0

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
);

TypeNameRead/WriteDescription
const AjPSeqsetthysInputSequence set.
AjPMatrixmymatrixOutputUser-defined matrix, or NULL for the default
AjPStr*consOutputthe created consensus sequence
ajint*retidentOutputnumber of residues identical in all sequences
ajint*retsimOutputnumber of residues similar in all sequences
ajint*retgapOutputnumber of residues with a gap in 1 sequence
ajint*retlenOutputlength of the alignment
AjBool RETURNajTrue on success

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.

See Also

See other functions in this section

Availability

In release 6.4.0

Function ajAlignExit

Cleans up report processing internal memory

Synopsis

Prototype
void ajAlignExit (
      void
);

TypeNameRead/WriteDescription
void RETURN

Returns
void:No return value

Description

Cleans up report processing internal memory

See Also

See other functions in this section

Availability

In release 6.4.0