embdmx.c

Section: Constructors

All constructors return a pointer to a new instance. It is the responsibility of the user to first destroy any previous instance. The target pointer does not need to be initialised to NULL, but it is good programming practice to do so anyway.

Functions:

embDmxNrseqNew Creates an empty non redundant sequence object

embDmxScophitsToHitlist Reads from a list of Scophit objects and writes a Hitlist object with the next block of hits with identical SCOP classification. If the iterator passed in is NULL it will read from the start of the list, otherwise it will read from the current position. Memory for the Hitlist will be allocated if necessary and must be freed by the user.

embDmxScophitToHit Copies the contents from a Scophit to a Hit object. Creates the Hit object if necessary.

embDmxScophitsAccToHitlist Reads from a list of Scophit objects and writes a Hitlist object with the next block of hits with identical SCOP classification. A Hit is only written to the Hitlist if an accession number is given. Also, only one of any pair of duplicate hits (overlapping hits with identical accession) will be written to the Hitlist. An 'overlap' is defined as a shared region of 10 or more residues. To check for these the list is first be sorted by Accession number.

embDmxHitsWrite Writes a list of AjOHit objects to an output file. This is intended for displaying the results from scans of a model against a protein sequence database. Output in a sigplot compatible format.

embDmxScopToScophit Writes a Scophit structure with the common information in a Scop structure. The swissprot sequence is taken in preference to the pdb sequence.

embDmxScopalgToScop Takes a Scopalg object (scop alignment) and an array of Scop objects taken from, e.g. a scop classification file. Extracts the scop domain codes from the alignment and compiles a list of corresponding Scop objects from the scop classification file.

embDmxScophitsOverlapAcc Checks for overlap and identical accession numbers between two hits.

embDmxScophitsOverlap Checks for overlap between two hits.

embDmxScophitMerge Creates a new Scophit object which corresponds to a merging of the two sequences from the Scophit objects hit1 and hit2.

embDmxScophitMergeInsertOther Creates a new Scophit object which corresponds to a merging of two Scophit objects hit1 and hit2. Appends the new Scophit onto a list. Target hit1 and hit2 for removal (set the Target element to ajTrue).

embDmxScophitMergeInsertOtherTarget Creates a new Scophit object which corresponds to a merging of two Scophit objects hit1 and hit2. Appends the new Scophit onto a list. Target hit1 and hit2 for removal (set the Target element to ajTrue).

embDmxScophitMergeInsertOtherTargetBoth Creates a new Scophit object which corresponds to a merging of two Scophit objects hit1 and hit2. Appends the new Scophit onto a list. Target hit1 and hit2 for removal (set the Target element to ajTrue).

embDmxScophitMergeInsertThis Creates a new Scophit object which corresponds to a merging of two Scophit objects hit1 and hit2. Insert the new Scophit immediately after hit2. Target hit1 and hit2 for removal (set the Target element to ajTrue).

embDmxScophitMergeInsertThisTarget Creates a new Scophit object which corresponds to a merging of two Scophit objects hit1 and hit2. Insert the new Scophit immediately after hit2. Target hit1, hit2 and the new Scophit for removal (set the Target element to ajTrue).

embDmxScophitMergeInsertThisTargetBoth Creates a new Scophit object which corresponds to a merging of two Scophit objects hit1 and hit2. Insert the new Scophit immediately after hit2. Target hit1, hit2 and the new Scophit for removal (both the Target and Target2 elements are set to ajTrue).

embDmxSeqNR Reads a list of AjPSeq's and writes an array describing the redundancy in the list. Elements in the array correspond to sequences in the list, i.e. the array[0] corresponds to the first sequence in the list.

embDmxSeqNRRange Reads a list of AjPSeq's and writes an array describing the redundancy in the list. Elements in the array correspond to sequences in the list, i.e. the array[0] corresponds to the first sequence in the list.

embDmxSeqCompall Reads a list of AjPSeq's and writes an array of sequence similarity values for an all-versus-all comparison of the sequences. The rows and columns in the array correspond to the order of the sequences in the list.

embDmxScophitReadAllFasta Reads a DHF file and returns a list of Scophit objects. Parsing routine is identical to embHitlistReadFasta.

embDmxHitlistToScophits Read from a list of Hitlist structures and writes a list of Scophit structures.

Function embDmxNrseqNew

Creates an empty non redundant sequence object

Prototype

EmbPDmxNrseq embDmxNrseqNew (
      const AjPSeq seq
);

Type Name Read/Write Description

const AjPSeq seq Input Sequence object

EmbPDmxNrseq RETURN New non-redundant sequence object

Type	Name	Read/Write	Description
`const AjPSeq`	`seq`	Input	Sequence object
`EmbPDmxNrseq`		RETURN	New non-redundant sequence object

From EMBOSS 6.1.0

Function embDmxScophitsToHitlist

Reads from a list of Scophit objects and writes a Hitlist object with the next block of hits with identical SCOP classification. If the iterator passed in is NULL it will read from the start of the list, otherwise it will read from the current position. Memory for the Hitlist will be allocated if necessary and must be freed by the user.

Prototype

AjBool embDmxScophitsToHitlist (
      const AjPList in,
      EmbPHitlist* out,
      AjIList* iter
);

Type Name Read/Write Description

const AjPList in Input List of pointers to Scophit objects

EmbPHitlist* out Output Pointer to Hitlist object

AjIList* iter Modify Pointer to iterator for list.

AjBool RETURN True on success (lists were processed ok)

Type	Name	Read/Write	Description
`const AjPList`	`in`	Input	List of pointers to Scophit objects
`EmbPHitlist*`	`out`	Output	Pointer to Hitlist object
`AjIList*`	`iter`	Modify	Pointer to iterator for list.
`AjBool`		RETURN	True on success (lists were processed ok)

From EMBOSS 2.9.0

Function embDmxScophitToHit

Copies the contents from a Scophit to a Hit object. Creates the Hit object if necessary.

Prototype

AjBool embDmxScophitToHit (
      EmbPHit* to,
      const AjPScophit from
);

Type Name Read/Write Description

EmbPHit* to Output Hit object pointer

const AjPScophit from Input Scophit object

AjBool RETURN True if copy was successful.

Type	Name	Read/Write	Description
`EmbPHit*`	`to`	Output	Hit object pointer
`const AjPScophit`	`from`	Input	Scophit object
`AjBool`		RETURN	True if copy was successful.

From EMBOSS 2.9.0

Function embDmxScophitsAccToHitlist

Reads from a list of Scophit objects and writes a Hitlist object with the next block of hits with identical SCOP classification. A Hit is only written to the Hitlist if an accession number is given. Also, only one of any pair of duplicate hits (overlapping hits with identical accession) will be written to the Hitlist. An 'overlap' is defined as a shared region of 10 or more residues. To check for these the list is first be sorted by Accession number.

Prototype

AjBool embDmxScophitsAccToHitlist (
      const AjPList in,
      EmbPHitlist* out,
      AjIList* iter
);

Type	Name	Read/Write	Description
`const AjPList`	`in`	Input	List of pointers to Scophit objects
`EmbPHitlist*`	`out`	Output	Pointer to Hitlist object
`AjIList*`	`iter`	Modify	Pointer to iterator for list.
`AjBool`		RETURN	True on success (lists were processed ok)

From EMBOSS 2.9.0

Function embDmxHitsWrite

Writes a list of AjOHit objects to an output file. This is intended for displaying the results from scans of a model against a protein sequence database. Output in a sigplot compatible format.

Prototype

AjBool embDmxHitsWrite (
      AjPFile outf,
      EmbPHitlist hits,
      ajint maxhits
);

Type Name Read/Write Description

AjPFile outf Modify Output file stream

EmbPHitlist hits Modify Hitlist objects with hits from scan

ajint maxhits Input Max. hits to write.

AjBool RETURN True if file was written

Type	Name	Read/Write	Description
`AjPFile`	`outf`	Modify	Output file stream
`EmbPHitlist`	`hits`	Modify	Hitlist objects with hits from scan
`ajint`	`maxhits`	Input	Max. hits to write.
`AjBool`		RETURN	True if file was written

From EMBOSS 2.9.0

Function embDmxScopToScophit

Writes a Scophit structure with the common information in a Scop structure. The swissprot sequence is taken in preference to the pdb sequence.

Prototype

AjBool embDmxScopToScophit (
      const AjPScop source,
      AjPScophit* target
);

Type Name Read/Write Description

const AjPScop source Input The Scop object to convert

AjPScophit* target Output Destination of the the scophit structure to write to.

AjBool RETURN ajTrue on the success of creating a Scophit structure.

Type	Name	Read/Write	Description
`const AjPScop`	`source`	Input	The Scop object to convert
`AjPScophit*`	`target`	Output	Destination of the the scophit structure to write to.
`AjBool`		RETURN	ajTrue on the success of creating a Scophit structure.

From EMBOSS 2.9.0

Function embDmxScopalgToScop

Takes a Scopalg object (scop alignment) and an array of Scop objects taken from, e.g. a scop classification file. Extracts the scop domain codes from the alignment and compiles a list of corresponding Scop objects from the scop classification file.

Prototype

AjBool embDmxScopalgToScop (
      const AjPScopalg align,
      AjPScop const* scop_arr,
      ajint scop_dim,
      AjPList* list
);

Type Name Read/Write Description

const AjPScopalg align Input Contains a seed alignment.

AjPScop const* scop_arr Input Array of AjPScop objects

ajint scop_dim Input Size of array

AjPList* list Output List of Scop objects.

AjBool RETURN A populated list has been returned (a file has been written)

Type	Name	Read/Write	Description
`const AjPScopalg`	`align`	Input	Contains a seed alignment.
`AjPScop const*`	`scop_arr`	Input	Array of AjPScop objects
`ajint`	`scop_dim`	Input	Size of array
`AjPList*`	`list`	Output	List of Scop objects.
`AjBool`		RETURN	A populated list has been returned (a file has been written)

From EMBOSS 2.9.0

Function embDmxScophitsOverlapAcc

Checks for overlap and identical accession numbers between two hits.

Prototype

AjBool embDmxScophitsOverlapAcc (
      const AjPScophit h1,
      const AjPScophit h2,
      ajuint n
);

Type Name Read/Write Description

const AjPScophit h1 Input Pointer to hit object 1

const AjPScophit h2 Input Pointer to hit object 2

ajuint n Input Threshold number of residues for overlap

AjBool RETURN True if the overlap between the sequences is at least as long as the threshold. False otherwise.

Type	Name	Read/Write	Description
`const AjPScophit`	`h1`	Input	Pointer to hit object 1
`const AjPScophit`	`h2`	Input	Pointer to hit object 2
`ajuint`	`n`	Input	Threshold number of residues for overlap
`AjBool`		RETURN	True if the overlap between the sequences is at least as long as the threshold. False otherwise.

From EMBOSS 2.9.0

Function embDmxScophitsOverlap

Checks for overlap between two hits.

Prototype

AjBool embDmxScophitsOverlap (
      const AjPScophit h1,
      const AjPScophit h2,
      ajuint n
);

Type	Name	Read/Write	Description
`const AjPScophit`	`h1`	Input	Pointer to hit object 1
`const AjPScophit`	`h2`	Input	Pointer to hit object 2
`ajuint`	`n`	Input	Threshold number of residues for overlap
`AjBool`		RETURN	True if the overlap between the sequences is at least as long as the threshold. False otherwise.

From EMBOSS 2.9.0

Function embDmxScophitMerge

Creates a new Scophit object which corresponds to a merging of the two sequences from the Scophit objects hit1 and hit2.

Prototype

AjPScophit embDmxScophitMerge (
      const AjPScophit hit1,
      const AjPScophit hit2
);

Type Name Read/Write Description

const AjPScophit hit1 Input Scophit 1

const AjPScophit hit2 Input Scophit 2

AjPScophit RETURN Pointer to Scophit object.

Type	Name	Read/Write	Description
`const AjPScophit`	`hit1`	Input	Scophit 1
`const AjPScophit`	`hit2`	Input	Scophit 2
`AjPScophit`		RETURN	Pointer to Scophit object.

From EMBOSS 2.9.0

Function embDmxScophitMergeInsertOther

Creates a new Scophit object which corresponds to a merging of two Scophit objects hit1 and hit2. Appends the new Scophit onto a list. Target hit1 and hit2 for removal (set the Target element to ajTrue).

Prototype

AjBool embDmxScophitMergeInsertOther (
      AjPList list,
      AjPScophit hit1,
      AjPScophit hit2
);

Type Name Read/Write Description

AjPList list Modify List of Scophit objects

AjPScophit hit1 Delete Scophit object 1

AjPScophit hit2 Delete Scophit object 2

AjBool RETURN True on success.

Type	Name	Read/Write	Description
`AjPList`	`list`	Modify	List of Scophit objects
`AjPScophit`	`hit1`	Delete	Scophit object 1
`AjPScophit`	`hit2`	Delete	Scophit object 2
`AjBool`		RETURN	True on success.

From EMBOSS 2.9.0

Function embDmxScophitMergeInsertOtherTarget

Prototype

AjBool embDmxScophitMergeInsertOtherTarget (
      AjPList list,
      AjPScophit hit1,
      AjPScophit hit2
);

Type	Name	Read/Write	Description
`AjPList`	`list`	Modify	List of Scophit objects
`AjPScophit`	`hit1`	Delete	Scophit object 1
`AjPScophit`	`hit2`	Delete	Scophit object 2
`AjBool`		RETURN	True on success.

From EMBOSS 2.9.0

Function embDmxScophitMergeInsertOtherTargetBoth

Prototype

AjBool embDmxScophitMergeInsertOtherTargetBoth (
      AjPList list,
      AjPScophit hit1,
      AjPScophit hit2
);

Type	Name	Read/Write	Description
`AjPList`	`list`	Modify	List of Scophit objects
`AjPScophit`	`hit1`	Delete	Scophit object 1
`AjPScophit`	`hit2`	Delete	Scophit object 2
`AjBool`		RETURN	True on success.

From EMBOSS 2.9.0

Function embDmxScophitMergeInsertThis

Creates a new Scophit object which corresponds to a merging of two Scophit objects hit1 and hit2. Insert the new Scophit immediately after hit2. Target hit1 and hit2 for removal (set the Target element to ajTrue).

Prototype

AjBool embDmxScophitMergeInsertThis (
      const AjPList list,
      AjPScophit hit1,
      AjPScophit hit2,
      AjIList iter
);

Type Name Read/Write Description

const AjPList list Input List of Scophit objects

AjPScophit hit1 Delete Scophit object 1

AjPScophit hit2 Delete Scophit object 2

AjIList iter Modify List iterator

AjBool RETURN True on success.

Type	Name	Read/Write	Description
`const AjPList`	`list`	Input	List of Scophit objects
`AjPScophit`	`hit1`	Delete	Scophit object 1
`AjPScophit`	`hit2`	Delete	Scophit object 2
`AjIList`	`iter`	Modify	List iterator
`AjBool`		RETURN	True on success.

From EMBOSS 2.9.0

Function embDmxScophitMergeInsertThisTarget

Creates a new Scophit object which corresponds to a merging of two Scophit objects hit1 and hit2. Insert the new Scophit immediately after hit2. Target hit1, hit2 and the new Scophit for removal (set the Target element to ajTrue).

Prototype

AjBool embDmxScophitMergeInsertThisTarget (
      const AjPList list,
      AjPScophit hit1,
      AjPScophit hit2,
      AjIList iter
);

Type	Name	Read/Write	Description
`const AjPList`	`list`	Input	List of Scophit objects
`AjPScophit`	`hit1`	Delete	Scophit object 1
`AjPScophit`	`hit2`	Delete	Scophit object 2
`AjIList`	`iter`	Modify	List iterator
`AjBool`		RETURN	True on success.

From EMBOSS 2.9.0

Function embDmxScophitMergeInsertThisTargetBoth

Prototype

AjBool embDmxScophitMergeInsertThisTargetBoth (
      const AjPList list,
      AjPScophit hit1,
      AjPScophit hit2,
      AjIList iter
);

Type	Name	Read/Write	Description
`const AjPList`	`list`	Input	List of Scophit objects
`AjPScophit`	`hit1`	Delete	Scophit object 1
`AjPScophit`	`hit2`	Delete	Scophit object 2
`AjIList`	`iter`	Modify	List iterator
`AjBool`		RETURN	True on success.

From EMBOSS 2.9.0

Function embDmxSeqNR

Reads a list of AjPSeq's and writes an array describing the redundancy in the list. Elements in the array correspond to sequences in the list, i.e. the array[0] corresponds to the first sequence in the list.

Prototype

AjBool embDmxSeqNR (
      const AjPList input,
      AjPUint* keep,
      ajint* nset,
      const AjPMatrixf matrix,
      float gapopen,
      float gapextend,
      float thresh,
      AjBool CheckGarbage
);

Type Name Read/Write Description

const AjPList input Input List of EmbPDmxNrseq objects

AjPUint* keep Output 0: rejected (redundant) sequence, 1: the sequence was retained

ajint* nset Output Number of non-garbage sequences in nr set

const AjPMatrixf matrix Input Residue substitution matrix

float gapopen Input Gap insertion penalty

float gapextend Input Gap extension penalty

float thresh Input Threshold residue id. for "redundancy"

AjBool CheckGarbage Input If True, when two sequences are compared and deemed redundant, then the Sequence that is *not* garbage is marked up as redundant. A sequence is "garbage" if the Garbage element of the data structure is set. If False, the shortest sequence is marked as redundant as normal.

AjBool RETURN ajTrue on success

Type	Name	Read/Write	Description
`const AjPList`	`input`	Input	List of EmbPDmxNrseq objects
`AjPUint*`	`keep`	Output	0: rejected (redundant) sequence, 1: the sequence was retained
`ajint*`	`nset`	Output	Number of non-garbage sequences in nr set
`const AjPMatrixf`	`matrix`	Input	Residue substitution matrix
`float`	`gapopen`	Input	Gap insertion penalty
`float`	`gapextend`	Input	Gap extension penalty
`float`	`thresh`	Input	Threshold residue id. for "redundancy"
`AjBool`	`CheckGarbage`	Input	If True, when two sequences are compared and deemed redundant, then the Sequence that is not garbage is marked up as redundant. A sequence is "garbage" if the Garbage element of the data structure is set. If False, the shortest sequence is marked as redundant as normal.
`AjBool`		RETURN	ajTrue on success

From EMBOSS 2.9.0

Function embDmxSeqNRRange

Prototype

AjBool embDmxSeqNRRange (
      const AjPList input,
      AjPUint* keep,
      ajint* nset,
      const AjPMatrixf matrix,
      float gapopen,
      float gapextend,
      float threshlow,
      float threshup,
      AjBool CheckGarbage
);

Type Name Read/Write Description

const AjPList input Input List of EmbPDmxNrseq objects

AjPUint* keep Output 0: rejected (redundant) sequence, 1: the sequence was retained

ajint* nset Output Number of non-garbage sequences in nr set.

const AjPMatrixf matrix Input Residue substitution matrix

float gapopen Input Gap insertion penalty

float gapextend Input Gap extension penalty

float threshlow Input Threshold lower limit

float threshup Input Threshold upper limit

AjBool CheckGarbage Input If True, when two sequences are compared and deemed redundant, then the Sequence that is *not* garbage is marked up as redundant. A sequence is "garbage" if the Garbage element of the data structure is set. If False, the shortest sequence is marked as redundant as normal.

AjBool RETURN ajTrue on success

Type	Name	Read/Write	Description
`const AjPList`	`input`	Input	List of EmbPDmxNrseq objects
`AjPUint*`	`keep`	Output	0: rejected (redundant) sequence, 1: the sequence was retained
`ajint*`	`nset`	Output	Number of non-garbage sequences in nr set.
`const AjPMatrixf`	`matrix`	Input	Residue substitution matrix
`float`	`gapopen`	Input	Gap insertion penalty
`float`	`gapextend`	Input	Gap extension penalty
`float`	`threshlow`	Input	Threshold lower limit
`float`	`threshup`	Input	Threshold upper limit
`AjBool`	`CheckGarbage`	Input	If True, when two sequences are compared and deemed redundant, then the Sequence that is not garbage is marked up as redundant. A sequence is "garbage" if the Garbage element of the data structure is set. If False, the shortest sequence is marked as redundant as normal.
`AjBool`		RETURN	ajTrue on success

From EMBOSS 2.9.0

Function embDmxSeqCompall

Reads a list of AjPSeq's and writes an array of sequence similarity values for an all-versus-all comparison of the sequences. The rows and columns in the array correspond to the order of the sequences in the list.

Prototype

AjBool embDmxSeqCompall (
      const AjPList input,
      AjPFloat2d* scores,
      const AjPMatrixf matrix,
      float gapopen,
      float gapextend
);

Type Name Read/Write Description

const AjPList input Input List of ajPSeq's

AjPFloat2d* scores Output Sequence similarity values

const AjPMatrixf matrix Input Residue substitution matrix

float gapopen Input Gap insertion penalty

float gapextend Input Gap extension penalty

AjBool RETURN ajTrue on success

Type	Name	Read/Write	Description
`const AjPList`	`input`	Input	List of ajPSeq's
`AjPFloat2d*`	`scores`	Output	Sequence similarity values
`const AjPMatrixf`	`matrix`	Input	Residue substitution matrix
`float`	`gapopen`	Input	Gap insertion penalty
`float`	`gapextend`	Input	Gap extension penalty
`AjBool`		RETURN	ajTrue on success

From EMBOSS 3.0.0

Function embDmxScophitReadAllFasta

Reads a DHF file and returns a list of Scophit objects. Parsing routine is identical to embHitlistReadFasta.

Prototype

AjPList embDmxScophitReadAllFasta (
      AjPFile inf
);

Type Name Read/Write Description

AjPFile inf Modify DHF file.

AjPList RETURN List of Scophit object pointers, or NULL (error).

Type	Name	Read/Write	Description
`AjPFile`	`inf`	Modify	DHF file.
`AjPList`		RETURN	List of Scophit object pointers, or NULL (error).

From EMBOSS 3.0.0

Function embDmxHitlistToScophits

Read from a list of Hitlist structures and writes a list of Scophit structures.

Prototype

AjBool embDmxHitlistToScophits (
      const AjPList in,
      AjPList out
);

Type Name Read/Write Description

const AjPList in Input List of pointers to Hitlist structures

AjPList out Output List of Scophit structures

AjBool RETURN True on success (lists were processed ok)

Type	Name	Read/Write	Description
`const AjPList`	`in`	Input	List of pointers to Hitlist structures
`AjPList`	`out`	Output	List of Scophit structures
`AjBool`		RETURN	True on success (lists were processed ok)

From EMBOSS 2.9.0

Section: Structure Destructors

All destructor functions receive the address of the instance to be deleted. The original pointer is set to NULL so is ready for re-use.

Functions:

embDmxNrseqDel Creates an empty non redundant sequence object

Function embDmxNrseqDel

Creates an empty non redundant sequence object

Prototype

void embDmxNrseqDel (
      EmbPDmxNrseq* Pnrseq
);

Type Name Read/Write Description

EmbPDmxNrseq* Pnrseq Delete Non-redundant sequence object

void RETURN

Type	Name	Read/Write	Description
`EmbPDmxNrseq*`	`Pnrseq`	Delete	Non-redundant sequence object
`void`		RETURN

From EMBOSS 6.1.0

embDmxNrseqNew	Creates an empty non redundant sequence object
embDmxScophitsToHitlist	Reads from a list of Scophit objects and writes a Hitlist object with the next block of hits with identical SCOP classification. If the iterator passed in is NULL it will read from the start of the list, otherwise it will read from the current position. Memory for the Hitlist will be allocated if necessary and must be freed by the user.
embDmxScophitToHit	Copies the contents from a Scophit to a Hit object. Creates the Hit object if necessary.
embDmxScophitsAccToHitlist	Reads from a list of Scophit objects and writes a Hitlist object with the next block of hits with identical SCOP classification. A Hit is only written to the Hitlist if an accession number is given. Also, only one of any pair of duplicate hits (overlapping hits with identical accession) will be written to the Hitlist. An 'overlap' is defined as a shared region of 10 or more residues. To check for these the list is first be sorted by Accession number.
embDmxHitsWrite	Writes a list of AjOHit objects to an output file. This is intended for displaying the results from scans of a model against a protein sequence database. Output in a sigplot compatible format.
embDmxScopToScophit	Writes a Scophit structure with the common information in a Scop structure. The swissprot sequence is taken in preference to the pdb sequence.
embDmxScopalgToScop	Takes a Scopalg object (scop alignment) and an array of Scop objects taken from, e.g. a scop classification file. Extracts the scop domain codes from the alignment and compiles a list of corresponding Scop objects from the scop classification file.
embDmxScophitsOverlapAcc	Checks for overlap and identical accession numbers between two hits.
embDmxScophitsOverlap	Checks for overlap between two hits.
embDmxScophitMerge	Creates a new Scophit object which corresponds to a merging of the two sequences from the Scophit objects hit1 and hit2.
embDmxScophitMergeInsertOther	Creates a new Scophit object which corresponds to a merging of two Scophit objects hit1 and hit2. Appends the new Scophit onto a list. Target hit1 and hit2 for removal (set the Target element to ajTrue).
embDmxScophitMergeInsertOtherTarget	Creates a new Scophit object which corresponds to a merging of two Scophit objects hit1 and hit2. Appends the new Scophit onto a list. Target hit1 and hit2 for removal (set the Target element to ajTrue).
embDmxScophitMergeInsertOtherTargetBoth	Creates a new Scophit object which corresponds to a merging of two Scophit objects hit1 and hit2. Appends the new Scophit onto a list. Target hit1 and hit2 for removal (set the Target element to ajTrue).
embDmxScophitMergeInsertThis	Creates a new Scophit object which corresponds to a merging of two Scophit objects hit1 and hit2. Insert the new Scophit immediately after hit2. Target hit1 and hit2 for removal (set the Target element to ajTrue).
embDmxScophitMergeInsertThisTarget	Creates a new Scophit object which corresponds to a merging of two Scophit objects hit1 and hit2. Insert the new Scophit immediately after hit2. Target hit1, hit2 and the new Scophit for removal (set the Target element to ajTrue).
embDmxScophitMergeInsertThisTargetBoth	Creates a new Scophit object which corresponds to a merging of two Scophit objects hit1 and hit2. Insert the new Scophit immediately after hit2. Target hit1, hit2 and the new Scophit for removal (both the Target and Target2 elements are set to ajTrue).
embDmxSeqNR	Reads a list of AjPSeq's and writes an array describing the redundancy in the list. Elements in the array correspond to sequences in the list, i.e. the array[0] corresponds to the first sequence in the list.
embDmxSeqNRRange	Reads a list of AjPSeq's and writes an array describing the redundancy in the list. Elements in the array correspond to sequences in the list, i.e. the array[0] corresponds to the first sequence in the list.
embDmxSeqCompall	Reads a list of AjPSeq's and writes an array of sequence similarity values for an all-versus-all comparison of the sequences. The rows and columns in the array correspond to the order of the sequences in the list.
embDmxScophitReadAllFasta	Reads a DHF file and returns a list of Scophit objects. Parsing routine is identical to embHitlistReadFasta.
embDmxHitlistToScophits	Read from a list of Hitlist structures and writes a list of Scophit structures.