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.

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

From EMBOSS 1.0.0

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.

Prototype

void embWordClear (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
`void`		RETURN

From EMBOSS 1.0.0

Function embWordPrintTable

Print the words found with their frequencies.

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

From EMBOSS 1.0.0

Function embWordPrintTableFI

Print the words found with their frequencies.

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

From EMBOSS 4.0.0

Function embWordPrintTableF

Print the words found with their frequencies.

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

From EMBOSS 1.0.0

Function embWordFreeTable

delete the word table and free the memory.

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

From EMBOSS 1.0.0

Function embWordMatchListDelete

delete the word table.

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

From EMBOSS 1.0.0

Function embWordMatchListPrint

print the word table.

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

From EMBOSS 1.0.0

Function embWordMatchListConvToFeat

convert the word table to feature tables.

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

From EMBOSS 1.0.0

Function embWordGetTable

Builds a table of all words in a sequence.

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

From EMBOSS 1.0.0

Function embWordBuildMatchTable

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

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.

From EMBOSS 1.0.0

Function embWordMatchNew

Creates and initialises a word match object

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.

From EMBOSS 6.3.0

Function embWordMatchMin

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

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

From EMBOSS 2.0.0

Function embWordMatchFirstMax

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

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

From EMBOSS 6.3.0

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.

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

From EMBOSS 6.3.0

Function embWordRabinKarpSearch

Rabin Karp search for multiple patterns.

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

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

From EMBOSS 6.3.0

Function embWordMatchIter

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

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

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

From EMBOSS 2.4.0

Function embWordUnused

Unused functions. Here to keep compiler warnings away

Prototype

void embWordUnused (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
`void`		RETURN

From EMBOSS 2.0.0

Function embWordExit

Cleanup word matching indexing internals on exit

Prototype

void embWordExit (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
`void`		RETURN

From EMBOSS 4.0.0