embword.c

Function embWordLength

Sets the word length for all functions. Must be called first. Creates the word length list if not yet done. Pushes the latest word length value on the list.

Synopsis

Prototype

void embWordLength (
      ajint wordlen
);

Type Name Read/Write Description

ajint wordlen Input Word length

void RETURN

Type	Name	Read/Write	Description
ajint	wordlen	Input	Word length
void		RETURN

Input

wordlen:

(Input)

Word length

Returns

void:

No return value

Description

Sets the word length for all functions. Must be called first. Creates the word length list if not yet done. Pushes the latest word length value on the list.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embWordClear

Clears the word length for all functions. To be called when all is done. Pops the last word length from the list and frees it. If there is nothing else on the list, it frees the list.

Synopsis

Prototype

void embWordClear (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
void		RETURN

Returns

void:

No return value

Description

Clears the word length for all functions. To be called when all is done. Pops the last word length from the list and frees it. If there is nothing else on the list, it frees the list.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embWordPrintTable

Print the words found with their frequencies.

Synopsis

Prototype

void embWordPrintTable (
      const AjPTable table
);

Type Name Read/Write Description

const AjPTable table Input table to be printed

void RETURN

Type	Name	Read/Write	Description
const AjPTable	table	Input	table to be printed
void		RETURN

Input

table:

(Input)

table to be printed

Returns

void:

No return value

Description

Print the words found with their frequencies.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embWordPrintTableFI

Print the words found with their frequencies.

Synopsis

Prototype

void embWordPrintTableFI (
      const AjPTable table,
      ajint mincount,
      AjPFile outf
);

Type Name Read/Write Description

const AjPTable table Input table to be printed

ajint mincount Input Minimum frequency to report

AjPFile outf Modify Output file.

void RETURN

Type	Name	Read/Write	Description
const AjPTable	table	Input	table to be printed
ajint	mincount	Input	Minimum frequency to report
AjPFile	outf	Modify	Output file.
void		RETURN

Input

table:	(Input)	table to be printed
mincount:	(Input)	Minimum frequency to report

Input & Output

outf:

(Modify)

Output file.

Returns

void:

No return value

Description

Print the words found with their frequencies.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embWordPrintTableF

Print the words found with their frequencies.

Synopsis

Prototype

void embWordPrintTableF (
      const AjPTable table,
      AjPFile outf
);

Type Name Read/Write Description

const AjPTable table Input table to be printed

AjPFile outf Modify Output file.

void RETURN

Type	Name	Read/Write	Description
const AjPTable	table	Input	table to be printed
AjPFile	outf	Modify	Output file.
void		RETURN

Input

table:

(Input)

table to be printed

Input & Output

outf:

(Modify)

Output file.

Returns

void:

No return value

Description

Print the words found with their frequencies.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embWordFreeTable

delete the word table and free the memory.

Synopsis

Prototype

void embWordFreeTable (
      AjPTable* table
);

Type Name Read/Write Description

AjPTable* table Delete table to be deleted

void RETURN

Type	Name	Read/Write	Description
AjPTable*	table	Delete	table to be deleted
void		RETURN

Output

table:

(Delete)

table to be deleted

Returns

void:

No return value

Description

delete the word table and free the memory.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embWordMatchListDelete

delete the word table.

Synopsis

Prototype

void embWordMatchListDelete (
      AjPList* plist
);

Type Name Read/Write Description

AjPList* plist Modify list to be deleted.

void RETURN

Type	Name	Read/Write	Description
AjPList*	plist	Modify	list to be deleted.
void		RETURN

Input & Output

plist:

(Modify)

list to be deleted.

Returns

void:

No return value

Description

delete the word table.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embWordMatchListPrint

print the word table.

Synopsis

Prototype

void embWordMatchListPrint (
      AjPFile file,
      const AjPList list
);

Type Name Read/Write Description

AjPFile file Modify Output file

const AjPList list Input list to be printed.

void RETURN

Type	Name	Read/Write	Description
AjPFile	file	Modify	Output file
const AjPList	list	Input	list to be printed.
void		RETURN

Input

list:

(Input)

list to be printed.

Input & Output

file:

(Modify)

Output file

Returns

void:

No return value

Description

print the word table.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embWordMatchListConvToFeat

convert the word table to feature tables.

Synopsis

Prototype

void embWordMatchListConvToFeat (
      const AjPList list,
      AjPFeattable* tab1,
      AjPFeattable* tab2,
      const AjPSeq seq1,
      const AjPSeq seq2
);

Type Name Read/Write Description

const AjPList list Input list to be printed.

AjPFeattable* tab1 Modify feature table for sequence 1

AjPFeattable* tab2 Modify feature table for sequence 2

const AjPSeq seq1 Input sequence

const AjPSeq seq2 Input second sequence

void RETURN

Type	Name	Read/Write	Description
const AjPList	list	Input	list to be printed.
AjPFeattable*	tab1	Modify	feature table for sequence 1
AjPFeattable*	tab2	Modify	feature table for sequence 2
const AjPSeq	seq1	Input	sequence
const AjPSeq	seq2	Input	second sequence
void		RETURN

Input

list:	(Input)	list to be printed.
seq1:	(Input)	sequence
seq2:	(Input)	second sequence

Input & Output

tab1:	(Modify)	feature table for sequence 1
tab2:	(Modify)	feature table for sequence 2

Returns

void:

No return value

Description

convert the word table to feature tables.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embWordGetTable

Builds a table of all words in a sequence.

The word length must be defined by a call to embWordLength.

Synopsis

Prototype

AjBool embWordGetTable (
      AjPTable* table,
      const AjPSeq seq
);

Type Name Read/Write Description

AjPTable* table Modify table to be created or updated.

const AjPSeq seq Input Sequence to be "worded"

AjBool RETURN ajTrue if successful

Type	Name	Read/Write	Description
AjPTable*	table	Modify	table to be created or updated.
const AjPSeq	seq	Input	Sequence to be "worded"
AjBool		RETURN	ajTrue if successful

Input

seq:

(Input)

Sequence to be "worded"

Input & Output

table:

(Modify)

table to be created or updated.

Returns

AjBool:

ajTrue if successful

Description

Builds a table of all words in a sequence.

The word length must be defined by a call to embWordLength.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embWordBuildMatchTable

Create a linked list of all the matches and order them by the second sequence.

We need three lists: (a) all hits, added in positional order (b) ongoing hits, where we have not reached the end yet which is a list of items in "all hits" being updated (c) new hits, found in the word table from the other sequence.

Synopsis

Prototype

AjPList embWordBuildMatchTable (
      const AjPTable seq1MatchTable,
      const AjPSeq seq2,
      ajint orderit
);

Type Name Read/Write Description

const AjPTable seq1MatchTable Input Match table

const AjPSeq seq2 Input Second sequence

ajint orderit Input 1 to sort results at end, else 0.

AjPList RETURN List of matches.

Type	Name	Read/Write	Description
const AjPTable	seq1MatchTable	Input	Match table
const AjPSeq	seq2	Input	Second sequence
ajint	orderit	Input	1 to sort results at end, else 0.
AjPList		RETURN	List of matches.

Input

seq1MatchTable:	(Input)	Match table
seq2:	(Input)	Second sequence
orderit:	(Input)	1 to sort results at end, else 0.

Returns

AjPList:

List of matches.

Description

Create a linked list of all the matches and order them by the second sequence.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embWordMatchNew

Creates and initialises a word match object

Synopsis

Prototype

EmbPWordMatch embWordMatchNew (
      const AjPSeq seq,
      ajuint seq1start,
      ajuint seq2start,
      ajint length
);

Type Name Read/Write Description

const AjPSeq seq Input Query sequence, match has been found

ajuint seq1start Input Start position in target sequence

ajuint seq2start Input Start position in query sequence

ajint length Input length of the word match

EmbPWordMatch RETURN New word match object.

Type	Name	Read/Write	Description
const AjPSeq	seq	Input	Query sequence, match has been found
ajuint	seq1start	Input	Start position in target sequence
ajuint	seq2start	Input	Start position in query sequence
ajint	length	Input	length of the word match
EmbPWordMatch		RETURN	New word match object.

Input

seq:	(Input)	Query sequence, match has been found
seq1start:	(Input)	Start position in target sequence
seq2start:	(Input)	Start position in query sequence
length:	(Input)	length of the word match

Returns

EmbPWordMatch:

New word match object.

Description

Creates and initialises a word match object

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embWordMatchMin

Given a list of matches, reduce it to the minimal set of best non-overlapping matches.

Synopsis

Prototype

void embWordMatchMin (
      AjPList matchlist
);

Type Name Read/Write Description

AjPList matchlist Modify list of matches to reduce to non-overlapping set

void RETURN

Type	Name	Read/Write	Description
AjPList	matchlist	Modify	list of matches to reduce to non-overlapping set
void		RETURN

Input & Output

matchlist:

(Modify)

list of matches to reduce to non-overlapping set

Returns

void:

No return value

Description

Given a list of matches, reduce it to the minimal set of best non-overlapping matches.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embWordMatchFirstMax

Given list of matches returns the first match with maximum similarity/score.

Synopsis

Prototype

EmbPWordMatch embWordMatchFirstMax (
      const AjPList matchlist
);

Type Name Read/Write Description

const AjPList matchlist Input list of matches

EmbPWordMatch RETURN maximum match

Type	Name	Read/Write	Description
const AjPList	matchlist	Input	list of matches
EmbPWordMatch		RETURN	maximum match

Input

matchlist:

(Input)

list of matches

Returns

EmbPWordMatch:

maximum match

Description

Given list of matches returns the first match with maximum similarity/score.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embWordRabinKarpInit

Scans word/pattern table and repackages the words in EmbPWordRK objects to improve access efficiency by Rabin-Karp search. Computes hash values for each word/pattern.

Synopsis

Prototype

ajuint embWordRabinKarpInit (
      const AjPTable table,
      EmbPWordRK** ewords,
      ajuint wordlen,
      const AjPSeqset seqset
);

Type Name Read/Write Description

const AjPTable table Input Table of patterns

EmbPWordRK** ewords Modify Extended word objects to be used in Rabin-Karp search

ajuint wordlen Input Length of words/patterns, kmer size

const AjPSeqset seqset Input Sequence set, input patterns were derived from

ajuint RETURN number of words

Type	Name	Read/Write	Description
const AjPTable	table	Input	Table of patterns
EmbPWordRK**	ewords	Modify	Extended word objects to be used in Rabin-Karp search
ajuint	wordlen	Input	Length of words/patterns, kmer size
const AjPSeqset	seqset	Input	Sequence set, input patterns were derived from
ajuint		RETURN	number of words

Input

table:	(Input)	Table of patterns
wordlen:	(Input)	Length of words/patterns, kmer size
seqset:	(Input)	Sequence set, input patterns were derived from

Input & Output

ewords:

(Modify)

Extended word objects to be used in Rabin-Karp search

Returns

ajuint:

number of words

Description

Scans word/pattern table and repackages the words in EmbPWordRK objects to improve access efficiency by Rabin-Karp search. Computes hash values for each word/pattern.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embWordRabinKarpSearch

Rabin Karp search for multiple patterns.

Synopsis

Prototype

ajuint embWordRabinKarpSearch (
      const AjPStr sseq,
      const AjPSeqset seqset,
      EmbPWordRK const* patterns,
      ajuint plen,
      ajuint npatterns,
      AjPList* matchlist,
      ajuint* lastlocation,
      AjBool checkmode
);

Type Name Read/Write Description

const AjPStr sseq Input Sequence to be scanned for multiple patterns

const AjPSeqset seqset Input Sequence-set, where search patterns coming from

EmbPWordRK const* patterns Input Patterns to be searched

ajuint plen Input Length of patterns

ajuint npatterns Input Number of patterns

AjPList* matchlist Modify List of matches for each sequence in the sequence set

ajuint* lastlocation Modify Position of the search for each sequence in the sequence set

AjBool checkmode Input If true, not writing features or alignments but running to produce match statistics only

ajuint RETURN total number of matches

Input

sseq:	(Input)	Sequence to be scanned for multiple patterns
seqset:	(Input)	Sequence-set, where search patterns coming from
patterns:	(Input)	Patterns to be searched
plen:	(Input)	Length of patterns
npatterns:	(Input)	Number of patterns
checkmode:	(Input)	If true, not writing features or alignments but running to produce match statistics only

Input & Output

matchlist:	(Modify)	List of matches for each sequence in the sequence set
lastlocation:	(Modify)	Position of the search for each sequence in the sequence set

Returns

ajuint:

total number of matches

Description

Rabin Karp search for multiple patterns.

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embWordMatchIter

Return the start positions and length for the next match. The caller iterates over the list, which is a standard AjPList

Synopsis

Prototype

AjBool embWordMatchIter (
      AjIList iter,
      ajint* start1,
      ajint* start2,
      ajint* len,
      const AjPSeq* seq
);

Type Name Read/Write Description

AjIList iter Modify List iterator

ajint* start1 Output Start in first sequence

ajint* start2 Output Start in second sequence

ajint* len Output Length of match

const AjPSeq* seq Output Pointer to sequence

AjBool RETURN ajFalse if the iterator was exhausted

Output

start1:	(Output)	Start in first sequence
start2:	(Output)	Start in second sequence
len:	(Output)	Length of match
seq:	(Output)	Pointer to sequence

Input & Output

iter:

(Modify)

List iterator

Returns

AjBool:

ajFalse if the iterator was exhausted

Description

Return the start positions and length for the next match. The caller iterates over the list, which is a standard AjPList

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embWordUnused

Unused functions. Here to keep compiler warnings away

Synopsis

Prototype

void embWordUnused (
      void
);

Type Name Read/Write Description

void RETURN

Returns

void:

No return value

Description

Unused functions. Here to keep compiler warnings away

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Function embWordExit

Cleanup word matching indexing internals on exit

Synopsis

Prototype

void embWordExit (
      void
);

Type Name Read/Write Description

void RETURN

Returns

void:

No return value

Description

Cleanup word matching indexing internals on exit

Usage

See source code

Example

In preparation

Errors

See source code

Dependencies

See source code

Availability

In release 6.4.0

Type	Name	Read/Write	Description
const AjPStr	sseq	Input	Sequence to be scanned for multiple patterns
const AjPSeqset	seqset	Input	Sequence-set, where search patterns coming from
EmbPWordRK const*	patterns	Input	Patterns to be searched
ajuint	plen	Input	Length of patterns
ajuint	npatterns	Input	Number of patterns
AjPList*	matchlist	Modify	List of matches for each sequence in the sequence set
ajuint*	lastlocation	Modify	Position of the search for each sequence in the sequence set
AjBool	checkmode	Input	If true, not writing features or alignments but running to produce match statistics only
ajuint		RETURN	total number of matches

Type	Name	Read/Write	Description
AjIList	iter	Modify	List iterator
ajint*	start1	Output	Start in first sequence
ajint*	start2	Output	Start in second sequence
ajint*	len	Output	Length of match
const AjPSeq*	seq	Output	Pointer to sequence
AjBool		RETURN	ajFalse if the iterator was exhausted

embword.c

Synopsis

Prototype

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Synopsis

Prototype

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Synopsis

Prototype

Input

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Synopsis

Prototype

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Synopsis

Prototype

Input

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Synopsis

Prototype

Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Synopsis

Prototype

Input & Output

Returns

Description

Usage

Example

Errors

Dependencies

See Also

Availability

Synopsis