ajseq.c

Datatypes:
AjPSeq Sequence
AjPSeqall Sequence stream
AjPSeqset Sequence set
AjPStr sequence strings
AjPSeqCvt sequence conversion
AjPSeqDate sequence dates
AjPSeqDesc sequence descriptions
AjPList Description list operations
AjPSeqSubdesc sequence sub-descriptions
AjPList Description list operations
AjPSeqGene gene names
AjPList Reference list operations
AjPSeqXref sequence citations
AjPList Cross-reference list operations
AjPSeqRef sequence citations
AjPList Reference list operations
AjPStr string tests


Datatype: AjPSeq

Function is for manipulating sequence objects

Sections:
constructorsConstructors
destructorsDestructors
modifiersModifiers
processModifiers
element retrievalGeneral use
testing propertiesGeneral use
conversionDerievd values
calculated propertiesGeneral use
exitMiscellaneous
debugMiscellaneous


AjPSeq: constructors

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

Functions:
ajSeqNewCreates and initialises a sequence object.
ajSeqNewNameCCreates and initialises a sequence object with a specified existing sequence as a char
ajSeqNewNameSCreates and initialises a sequence object with a specified existing sequence as a string
ajSeqNewRangeCCreates and initialises a sequence object with a specified existing sequence as a string,and provides offsets, and direction.
ajSeqNewRangeSCreates and initialises a sequence object with a specified existing sequence as a string,and provides offsets, and direction.
ajSeqNewResCreates and initialises a sequence object with a specified sequence length.
ajSeqNewSeqCreates and initialises a sequence object with a specified existing sequence.


Function ajSeqNew

Creates and initialises a sequence object.

Prototype

AjPSeq ajSeqNew (
      void
);

TypeNameRead/WriteDescription
AjPSeq RETURNNew sequence object.

From EMBOSS 1.0.0


Function ajSeqNewNameC

Creates and initialises a sequence object with a specified existing sequence as a char

Prototype

AjPSeq ajSeqNewNameC (
      const char* txt,
      const char* name
);

TypeNameRead/WriteDescription
const char*txtInputSequence string
const char*nameInputSequence name
AjPSeq RETURNNew sequence object.

From EMBOSS 4.0.0


Function ajSeqNewNameS

Creates and initialises a sequence object with a specified existing sequence as a string

Prototype

AjPSeq ajSeqNewNameS (
      const AjPStr str,
      const AjPStr name
);

TypeNameRead/WriteDescription
const AjPStrstrInputSequence string
const AjPStrnameInputSequence name
AjPSeq RETURNNew sequence object.

From EMBOSS 4.0.0


Function ajSeqNewRangeC

Creates and initialises a sequence object with a specified existing sequence as a string,and provides offsets, and direction.

Prototype

AjPSeq ajSeqNewRangeC (
      const char* txt,
      ajint offset,
      ajint offend,
      AjBool rev
);

TypeNameRead/WriteDescription
const char*txtInputSequence string
ajintoffsetInputOffset at start
ajintoffendInputOffset at end
AjBoolrevInputReversed if true (reverses offsets)
AjPSeq RETURNNew sequence object.

From EMBOSS 4.0.0


Function ajSeqNewRangeS

Creates and initialises a sequence object with a specified existing sequence as a string,and provides offsets, and direction.

Prototype

AjPSeq ajSeqNewRangeS (
      const AjPStr str,
      ajint offset,
      ajint offend,
      AjBool rev
);

TypeNameRead/WriteDescription
const AjPStrstrInputSequence string
ajintoffsetInputOffset at start
ajintoffendInputOffset at end
AjBoolrevInputReversed if true (reverses offsets)
AjPSeq RETURNNew sequence object.

From EMBOSS 4.0.0


Function ajSeqNewRes

Creates and initialises a sequence object with a specified sequence length.

Prototype

AjPSeq ajSeqNewRes (
      size_t size
);

TypeNameRead/WriteDescription
size_tsizeInputReserved space for the sequence, including a trailing null character.
AjPSeq RETURNNew sequence object.

From EMBOSS 4.0.0


Function ajSeqNewSeq

Creates and initialises a sequence object with a specified existing sequence.

Prototype

AjPSeq ajSeqNewSeq (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputOld sequence object
AjPSeq RETURNNew sequence object.

From EMBOSS 4.0.0


AjPSeq: destructors

Destruction destroys all internal data structures and frees the memory allocated for the sequence.

Functions:
ajSeqDelDeletes a sequence object.
ajSeqDelarrayDestructor for array of sequence objects


Function ajSeqDel

Deletes a sequence object.

Prototype

void ajSeqDel (
      AjPSeq* Pseq
);

TypeNameRead/WriteDescription
AjPSeq*PseqDeleteSequence object
void RETURN

From EMBOSS 1.0.0


Function ajSeqDelarray

Destructor for array of sequence objects

Prototype

void ajSeqDelarray (
      AjPSeq** PPseq
);

TypeNameRead/WriteDescription
AjPSeq**PPseqDeleteSequence object array
void RETURN

From EMBOSS 6.0.0


AjPSeq: modifiers

These functions update contents of a sequence object.

Functions:
ajSeqAddCmtAdds a comment to a sequence object
ajSeqAddGeneAdds a gene to a sequence object
ajSeqAddKeyAdds a keyword to a sequence object
ajSeqAddRefAdds a literature reference to a sequence object
ajSeqAddXrefAdds a cross-reference to a sequence object
ajSeqAssignAccCAssigns the sequence accession number.
ajSeqAssignAccSAssigns the sequence accession number.
ajSeqAssignDescCAssigns a modified description to an existing AjPSeq sequence.
ajSeqAssignDescSAssigns a modified description to an existing AjPSeq sequence.
ajSeqAssignEntryCAssigns the sequence entryname.
ajSeqAssignEntrySAssigns the sequence entryname.
ajSeqAssignFileCAssigns the sequence filename.
ajSeqAssignFileSAssigns the sequence file name.
ajSeqAssignFullCAssigns the sequence name.
ajSeqAssignFullSAssigns the sequence full name.
ajSeqAssignGiCAssigns the GI version number.
ajSeqAssignGiSAssigns the GI version number.
ajSeqAssignNameCAssigns the sequence name.
ajSeqAssignNameSAssigns the sequence name.
ajSeqAssignQualLenAssigns base quality scores to an existing sequence.
ajSeqAssignSeqCAssigns a modified sequence to an existing AjPSeq sequence.
ajSeqAssignSeqLenCAssigns a modified sequence to an existing AjPSeq sequence.
ajSeqAssignSeqSAssigns a modified sequence to an existing AjPSeq sequence.
ajSeqAssignSvCAssigns the sequence version number.
ajSeqAssignSvSAssigns the sequence version number.
ajSeqAssignUfoCAssigns the sequence feature file name.
ajSeqAssignUfoSAssigns the sequence feature file name.
ajSeqAssignUsaCAssigns the sequence full name.
ajSeqAssignUsaSAssigns the sequence full name.
ajSeqClearResets all data for a sequence object so that it can be reused.
ajSeqSetNameProvides a unique (for this program run) name for a sequence.
ajSeqSetNameMultiProvides a unique (for this program run) name for a sequence. If a name is generated, append a count
ajSeqSetOffsetsSets the offsets for each end of a subsequence.
ajSeqSetRangeSets the start and end positions for a sequence (not for a sequence set). Trim the sequence to convert to the subsequence.
ajSeqSetRangeRevSets the start and end positions for a sequence (not for a sequence set), and set the sequence to be reversed.
ajSeqSetUniqueMakes a sequence modifiable by making sure there is no duplicate copy of the sequence.
ajSeqTagRevAdds a tag to the sequence description to note it has been reversed


Function ajSeqAddCmt

Adds a comment to a sequence object

Prototype

void ajSeqAddCmt (
      AjPSeq seq,
      AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
AjPStrstrModifyComment.
void RETURN

From EMBOSS 6.2.0


Function ajSeqAddGene

Adds a gene to a sequence object

Prototype

void ajSeqAddGene (
      AjPSeq seq,
      AjPSeqGene gene
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
AjPSeqGenegeneModifyGene object
void RETURN

From EMBOSS 6.2.0


Function ajSeqAddKey

Adds a keyword to a sequence object

Prototype

void ajSeqAddKey (
      AjPSeq seq,
      AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
AjPStrstrModifyComment.
void RETURN

From EMBOSS 6.2.0


Function ajSeqAddRef

Adds a literature reference to a sequence object

Prototype

void ajSeqAddRef (
      AjPSeq seq,
      AjPSeqRef ref
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
AjPSeqRefrefModifyLiterature reference.
void RETURN

From EMBOSS 6.2.0


Function ajSeqAddXref

Adds a cross-reference to a sequence object

Prototype

void ajSeqAddXref (
      AjPSeq seq,
      AjPSeqXref xref
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
AjPSeqXrefxrefModifyComment.
void RETURN

From EMBOSS 6.2.0


Function ajSeqAssignAccC

Assigns the sequence accession number.

Prototype

void ajSeqAssignAccC (
      AjPSeq seq,
      const char* txt
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
const char*txtInputAccession number as a C character string.
void RETURN

From EMBOSS 4.0.0


Function ajSeqAssignAccS

Assigns the sequence accession number.

Prototype

void ajSeqAssignAccS (
      AjPSeq seq,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
const AjPStrstrInputAccession number as a string.
void RETURN

From EMBOSS 4.0.0


Function ajSeqAssignDescC

Assigns a modified description to an existing AjPSeq sequence.

Prototype

void ajSeqAssignDescC (
      AjPSeq seq,
      const char* txt
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
const char*txtInputNew description as a C character string.
void RETURN

From EMBOSS 4.0.0


Function ajSeqAssignDescS

Assigns a modified description to an existing AjPSeq sequence.

Prototype

void ajSeqAssignDescS (
      AjPSeq seq,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
const AjPStrstrInputNew description as a string.
void RETURN

From EMBOSS 4.0.0


Function ajSeqAssignEntryC

Assigns the sequence entryname.

Prototype

void ajSeqAssignEntryC (
      AjPSeq seq,
      const char* txt
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
const char*txtInputEntry name as a C character string.
void RETURN

From EMBOSS 4.0.0


Function ajSeqAssignEntryS

Assigns the sequence entryname.

Prototype

void ajSeqAssignEntryS (
      AjPSeq seq,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
const AjPStrstrInputEntry name as a string.
void RETURN

From EMBOSS 4.0.0


Function ajSeqAssignFileC

Assigns the sequence filename.

Prototype

void ajSeqAssignFileC (
      AjPSeq seq,
      const char* txt
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
const char*txtInputFile name as a C character string.
void RETURN

From EMBOSS 4.0.0


Function ajSeqAssignFileS

Assigns the sequence file name.

Prototype

void ajSeqAssignFileS (
      AjPSeq seq,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
const AjPStrstrInputFile name as a string.
void RETURN

From EMBOSS 4.0.0


Function ajSeqAssignFullC

Assigns the sequence name.

Prototype

void ajSeqAssignFullC (
      AjPSeq seq,
      const char* txt
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
const char*txtInputFull name as a C character string.
void RETURN

From EMBOSS 4.0.0


Function ajSeqAssignFullS

Assigns the sequence full name.

Prototype

void ajSeqAssignFullS (
      AjPSeq seq,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
const AjPStrstrInputFull name as a string.
void RETURN

From EMBOSS 4.0.0


Function ajSeqAssignGiC

Assigns the GI version number.

Prototype

void ajSeqAssignGiC (
      AjPSeq seq,
      const char* txt
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
const char*txtInputGI number as a C character string.
void RETURN

From EMBOSS 4.0.0


Function ajSeqAssignGiS

Assigns the GI version number.

Prototype

void ajSeqAssignGiS (
      AjPSeq seq,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
const AjPStrstrInputGI number as a string.
void RETURN

From EMBOSS 4.0.0


Function ajSeqAssignNameC

Assigns the sequence name.

Prototype

void ajSeqAssignNameC (
      AjPSeq seq,
      const char* txt
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
const char*txtInputName as a string.
void RETURN

From EMBOSS 4.0.0


Function ajSeqAssignNameS

Assigns the sequence name.

Prototype

void ajSeqAssignNameS (
      AjPSeq seq,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
const AjPStrstrInputName as a string.
void RETURN

From EMBOSS 4.0.0


Function ajSeqAssignQualLen

Assigns base quality scores to an existing sequence.

Prototype

void ajSeqAssignQualLen (
      AjPSeq seq,
      const float* qual,
      ajuint len
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
const float*qualInputBase quality scores.
ajuintlenInputNumber of quality scores to use
void RETURN

From EMBOSS 6.3.0


Function ajSeqAssignSeqC

Assigns a modified sequence to an existing AjPSeq sequence.

Prototype

void ajSeqAssignSeqC (
      AjPSeq seq,
      const char* txt
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
const char*txtInputNew sequence as a C character string.
void RETURN

From EMBOSS 4.0.0


Function ajSeqAssignSeqLenC

Assigns a modified sequence to an existing AjPSeq sequence.

Prototype

void ajSeqAssignSeqLenC (
      AjPSeq seq,
      const char* txt,
      ajuint len
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
const char*txtInputNew sequence as a C character string.
ajuintlenInputNumber of characters to use
void RETURN

From EMBOSS 4.0.0


Function ajSeqAssignSeqS

Assigns a modified sequence to an existing AjPSeq sequence.

Prototype

void ajSeqAssignSeqS (
      AjPSeq seq,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
const AjPStrstrInputNew sequence as a string.
void RETURN

From EMBOSS 4.0.0


Function ajSeqAssignSvC

Assigns the sequence version number.

Prototype

void ajSeqAssignSvC (
      AjPSeq seq,
      const char* txt
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
const char*txtInputSeqVersion number as a C character string.
void RETURN

From EMBOSS 4.0.0


Function ajSeqAssignSvS

Assigns the sequence version number.

Prototype

void ajSeqAssignSvS (
      AjPSeq seq,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
const AjPStrstrInputSeqVersion number as a string.
void RETURN

From EMBOSS 4.0.0


Function ajSeqAssignUfoC

Assigns the sequence feature file name.

Prototype

void ajSeqAssignUfoC (
      AjPSeq seq,
      const char* txt
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
const char*txtInputUFO as a C character string.
void RETURN

From EMBOSS 4.0.0


Function ajSeqAssignUfoS

Assigns the sequence feature file name.

Prototype

void ajSeqAssignUfoS (
      AjPSeq seq,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
const AjPStrstrInputUFO as a string.
void RETURN

From EMBOSS 4.0.0


Function ajSeqAssignUsaC

Assigns the sequence full name.

Prototype

void ajSeqAssignUsaC (
      AjPSeq seq,
      const char* txt
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
const char*txtInputUSA as a C character string.
void RETURN

From EMBOSS 4.0.0


Function ajSeqAssignUsaS

Assigns the sequence full name.

Prototype

void ajSeqAssignUsaS (
      AjPSeq seq,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object.
const AjPStrstrInputUSA as a string.
void RETURN

From EMBOSS 4.0.0


Function ajSeqClear

Resets all data for a sequence object so that it can be reused.

Prototype

void ajSeqClear (
      AjPSeq seq
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence
void RETURN

From EMBOSS 1.0.0


Function ajSeqSetName

Provides a unique (for this program run) name for a sequence.

Prototype

void ajSeqSetName (
      AjPSeq seq,
      const AjPStr setname
);

TypeNameRead/WriteDescription
AjPSeqseqOutputSequence object
const AjPStrsetnameInputName set by caller
void RETURN

From EMBOSS 4.1.0


Function ajSeqSetNameMulti

Provides a unique (for this program run) name for a sequence. If a name is generated, append a count

Prototype

void ajSeqSetNameMulti (
      AjPSeq seq,
      const AjPStr setname
);

TypeNameRead/WriteDescription
AjPSeqseqOutputSequence object
const AjPStrsetnameInputName set by caller
void RETURN

From EMBOSS 4.1.0


Function ajSeqSetOffsets

Sets the offsets for each end of a subsequence.

Prototype

void ajSeqSetOffsets (
      AjPSeq seq,
      ajint offset,
      ajint origlen
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object to be set.
ajintoffsetInputOffset from start of original sequence
ajintoriglenInputOriginal length, used to calculate the offset from the end.
void RETURN

From EMBOSS 3.0.0


Function ajSeqSetRange

Sets the start and end positions for a sequence (not for a sequence set). Trim the sequence to convert to the subsequence.

Prototype

void ajSeqSetRange (
      AjPSeq seq,
      ajint pos1,
      ajint pos2
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object to be set.
ajintpos1InputStart position. Negative values are from the end.
ajintpos2InputEnd position. Negative values are from the end.
void RETURN

From EMBOSS 1.0.0


Function ajSeqSetRangeRev

Sets the start and end positions for a sequence (not for a sequence set), and set the sequence to be reversed.

Prototype

void ajSeqSetRangeRev (
      AjPSeq seq,
      ajint pos1,
      ajint pos2
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object to be set.
ajintpos1InputStart position. Negative values are from the end.
ajintpos2InputEnd position. Negative values are from the end.
void RETURN

From EMBOSS 4.0.0


Function ajSeqSetUnique

Makes a sequence modifiable by making sure there is no duplicate copy of the sequence.

Prototype

void ajSeqSetUnique (
      AjPSeq seq
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence
void RETURN

From EMBOSS 4.1.0


Function ajSeqTagRev

Adds a tag to the sequence description to note it has been reversed

Prototype

void ajSeqTagRev (
      AjPSeq seq
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object to be set.
void RETURN

From EMBOSS 6.1.0


AjPSeq: process

These functions use the contents of a sequence object to produce a subsequence from the range, or to reverse a sequence whose direction has been set to be reversed.

Functions:
ajSeqComplementComplements but does not reverse a nucleotide sequence.
ajSeqFmtLowerConverts a sequence to lower case.
ajSeqFmtUpperConverts a sequence to upper case.
ajSeqGapFillFills a single sequence with gaps up to a specified length.
ajSeqGapStandardMakes all gaps in a string use a standard gap character
ajSeqReverseDoReverses and complements a nucleotide sequence, unless it is already done.
ajSeqReverseForceReverses and complements a nucleotide sequence. Forces reversal to be done even if the sequence is flagged as already reversed.
ajSeqReverseOnlyReverses but does not complement a nucleotide sequence.
ajSeqTrimTrim a sequence using the Begin and Ends. Also reverse complements a nucleotide sequence if required.


Function ajSeqComplement

Complements but does not reverse a nucleotide sequence.

Prototype

void ajSeqComplement (
      AjPSeq seq
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence
void RETURN

From EMBOSS 4.1.0


Function ajSeqFmtLower

Converts a sequence to lower case.

Prototype

void ajSeqFmtLower (
      AjPSeq seq
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence
void RETURN

From EMBOSS 4.0.0


Function ajSeqFmtUpper

Converts a sequence to upper case.

Prototype

void ajSeqFmtUpper (
      AjPSeq seq
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence
void RETURN

From EMBOSS 4.0.0


Function ajSeqGapFill

Fills a single sequence with gaps up to a specified length.

Prototype

void ajSeqGapFill (
      AjPSeq seq,
      ajuint len
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence object to be set.
ajuintlenInputLength to pad fill to.
void RETURN

From EMBOSS 4.1.0


Function ajSeqGapStandard

Makes all gaps in a string use a standard gap character

Prototype

void ajSeqGapStandard (
      AjPSeq seq,
      char gapchar
);

TypeNameRead/WriteDescription
AjPSeqseqOutputSequence object
chargapcharInputGap character (or '-' if zero)
void RETURN

From EMBOSS 2.1.0


Function ajSeqReverseDo

Reverses and complements a nucleotide sequence, unless it is already done.

Prototype

void ajSeqReverseDo (
      AjPSeq seq
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence
void RETURN

From EMBOSS 4.0.0


Function ajSeqReverseForce

Reverses and complements a nucleotide sequence. Forces reversal to be done even if the sequence is flagged as already reversed.

Prototype

void ajSeqReverseForce (
      AjPSeq seq
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence
void RETURN

From EMBOSS 2.7.0


Function ajSeqReverseOnly

Reverses but does not complement a nucleotide sequence.

Prototype

void ajSeqReverseOnly (
      AjPSeq seq
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence
void RETURN

From EMBOSS 4.0.0


Function ajSeqTrim

Trim a sequence using the Begin and Ends. Also reverse complements a nucleotide sequence if required.

Prototype

void ajSeqTrim (
      AjPSeq seq
);

TypeNameRead/WriteDescription
AjPSeqseqModifySequence to be trimmed.
void RETURN

From EMBOSS 1.0.0


AjPSeq: element retrieval

These functions return the contents of a sequence object.

Functions:
ajSeqGetAccCReturns the sequence accession number. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqGetAccSReturns the sequence accession number. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqGetBeginReturns the sequence start position within the current stored sequence, or 1 if no start has been set.
ajSeqGetBeginTrueReturns the sequence start position in the original sequence, which may have been trimmed.
ajSeqGetDbCReturns the sequence database name. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqGetDbSReturns the sequence database name. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqGetDescCReturns the sequence description. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqGetDescSReturns the sequence description. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqGetEndReturns the sequence end position, or the sequence length if no end has been set.
ajSeqGetEndTrueReturns the sequence end position, or the sequence length if no end has been set.
ajSeqGetEntryCReturns the sequence full text entry. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqGetEntrySReturns the sequence full text entry. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqGetFeatReturns the sequence feature table. Because this is a pointer to the real internal table the caller must take care not to change it in any way, or to delete it.
ajSeqGetFeatCopyReturns a copy of the sequence feature table. Because this is a copy of all the data, the caller is responsible for deleting it after use.
ajSeqGetGiCReturns the GI version number. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqGetGiSReturns the GI version number. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqGetLenReturns the sequence length.
ajSeqGetLenTrimmedReturns the sequence length after trimming begin and end positions
ajSeqGetLenTrueReturns the length of the original sequence, including any gap characters.
ajSeqGetLenUngappedReturns the sequence length excluding all gap characters.
ajSeqGetNameCReturns the sequence name. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqGetNameSReturns the sequence name. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqGetOffendReturns the sequence offend value. This is the number of positions removed from the original end.
ajSeqGetOffsetReturns the sequence offset from -sbegin originally.
ajSeqGetQualReturns the base quality scores as an array. Because this is a pointer to the real internal array the caller must take care not to change the array in any way.
ajSeqGetRangeReturns the sequence range for a sequence.
ajSeqGetRevReturns the sequence direction.
ajSeqGetSeqCReturns the sequence in a sequence object as a character string. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqGetSeqSReturns the sequence in a sequence object as a string. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqGetSeqCopyCReturns a sequence as a C character string. This is a copy of the string so the caller can do anything with it. It must be copied back to a sequence (e.g. with ajSeqReplace) before output.
ajSeqGetSeqCopySReturns the sequence in a sequence object as a string. Because this is a copy of the internal string the caller may change the string. It must be copied back to a sequence (e.g. with ajSeqReplace) before output.
ajSeqGetSvCReturns the sequence version number. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqGetSvSReturns the sequence version number. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqGetTaxCReturns the sequence primary taxon (species). Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqGetTaxSReturns the sequence primary taxon (species). Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqGetTaxidReturns the numeric identifier of the sequence primary taxon (species). This is an identifier from the NCBI taxonomy
ajSeqGetUsaCReturns the original USA of a sequence. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqGetUsaSReturns the original USA of a sequence. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqGetXrefsReturns the list of cross-references derived from the sequence


Function ajSeqGetAccC

Returns the sequence accession number. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const char* ajSeqGetAccC (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object.
const char* RETURNAccession number as a character string.

From EMBOSS 4.0.0


Function ajSeqGetAccS

Returns the sequence accession number. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const AjPStr ajSeqGetAccS (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object.
const AjPStr RETURNAccession number as a string.

From EMBOSS 4.0.0


Function ajSeqGetBegin

Returns the sequence start position within the current stored sequence, or 1 if no start has been set.

Prototype

ajuint ajSeqGetBegin (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object
ajuint RETURNStart position.

From EMBOSS 4.0.0


Function ajSeqGetBeginTrue

Returns the sequence start position in the original sequence, which may have been trimmed.

Prototype

ajuint ajSeqGetBeginTrue (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object
ajuint RETURNStart position.

From EMBOSS 4.0.0


Function ajSeqGetDbC

Returns the sequence database name. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const char* ajSeqGetDbC (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object.
const char* RETURNDatabase name as a character string.

From EMBOSS 5.0.0


Function ajSeqGetDbS

Returns the sequence database name. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const AjPStr ajSeqGetDbS (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object.
const AjPStr RETURNDatabase name as a string.

From EMBOSS 5.0.0


Function ajSeqGetDescC

Returns the sequence description. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const char* ajSeqGetDescC (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object.
const char* RETURNDescription as a character string.

From EMBOSS 4.0.0


Function ajSeqGetDescS

Returns the sequence description. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const AjPStr ajSeqGetDescS (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object.
const AjPStr RETURNDescription as a string.

From EMBOSS 4.0.0


Function ajSeqGetEnd

Returns the sequence end position, or the sequence length if no end has been set.

Prototype

ajuint ajSeqGetEnd (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object
ajuint RETURNEnd position.

From EMBOSS 4.0.0


Function ajSeqGetEndTrue

Returns the sequence end position, or the sequence length if no end has been set.

Prototype

ajuint ajSeqGetEndTrue (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object
ajuint RETURNEnd position.

From EMBOSS 4.0.0


Function ajSeqGetEntryC

Returns the sequence full text entry. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const char* ajSeqGetEntryC (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object.
const char* RETURNEntry as a character string.

From EMBOSS 4.0.0


Function ajSeqGetEntryS

Returns the sequence full text entry. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const AjPStr ajSeqGetEntryS (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object.
const AjPStr RETURNEntry as a string.

From EMBOSS 4.0.0


Function ajSeqGetFeat

Returns the sequence feature table. Because this is a pointer to the real internal table the caller must take care not to change it in any way, or to delete it.

Prototype

const AjPFeattable ajSeqGetFeat (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object.
const AjPFeattable RETURNfeature table (if any)

From EMBOSS 1.0.0


Function ajSeqGetFeatCopy

Returns a copy of the sequence feature table. Because this is a copy of all the data, the caller is responsible for deleting it after use.

Prototype

AjPFeattable ajSeqGetFeatCopy (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object.
AjPFeattable RETURNfeature table (if any)

From EMBOSS 4.0.0


Function ajSeqGetGiC

Returns the GI version number. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const char* ajSeqGetGiC (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object.
const char* RETURNSeqVersion number as a character string.

From EMBOSS 4.0.0


Function ajSeqGetGiS

Returns the GI version number. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const AjPStr ajSeqGetGiS (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object.
const AjPStr RETURNSeqVersion number as a string.

From EMBOSS 4.0.0


Function ajSeqGetLen

Returns the sequence length.

Prototype

ajuint ajSeqGetLen (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object
ajuint RETURNSequence length.

From EMBOSS 4.0.0


Function ajSeqGetLenTrimmed

Returns the sequence length after trimming begin and end positions

Prototype

ajuint ajSeqGetLenTrimmed (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object
ajuint RETURNSequence length.

From EMBOSS 6.1.0


Function ajSeqGetLenTrue

Returns the length of the original sequence, including any gap characters.

Prototype

ajuint ajSeqGetLenTrue (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputTarget sequence.
ajuint RETURNstring position between 1 and length.

From EMBOSS 4.0.0


Function ajSeqGetLenUngapped

Returns the sequence length excluding all gap characters.

Prototype

ajuint ajSeqGetLenUngapped (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object
ajuint RETURNSequence length.

From EMBOSS 6.1.0


Function ajSeqGetNameC

Returns the sequence name. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const char* ajSeqGetNameC (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object.
const char* RETURNName as a character string.

From EMBOSS 4.0.0


Function ajSeqGetNameS

Returns the sequence name. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const AjPStr ajSeqGetNameS (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object.
const AjPStr RETURNName as a string.

From EMBOSS 4.0.0


Function ajSeqGetOffend

Returns the sequence offend value. This is the number of positions removed from the original end.

Prototype

ajuint ajSeqGetOffend (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object
ajuint RETURNSequence offend.

From EMBOSS 4.0.0


Function ajSeqGetOffset

Returns the sequence offset from -sbegin originally.

Prototype

ajuint ajSeqGetOffset (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object
ajuint RETURNSequence offset.

From EMBOSS 4.0.0


Function ajSeqGetQual

Returns the base quality scores as an array. Because this is a pointer to the real internal array the caller must take care not to change the array in any way.

Prototype

const float* ajSeqGetQual (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence.
const float* RETURNBase quality scores.

From EMBOSS 6.3.0


Function ajSeqGetRange

Returns the sequence range for a sequence.

Prototype

ajuint ajSeqGetRange (
      const AjPSeq seq,
      ajint* begin,
      ajint* end
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object.
ajint*beginOutputSequence range begin
ajint*endOutputSequence range end
ajuint RETURNSequence range length

From EMBOSS 1.0.0


Function ajSeqGetRev

Returns the sequence direction.

Prototype

AjBool ajSeqGetRev (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object
AjBool RETURNSequence Direction.

From EMBOSS 4.0.0


Function ajSeqGetSeqC

Returns the sequence in a sequence object as a character string. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const char* ajSeqGetSeqC (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence.
const char* RETURNSequence as a character string.

From EMBOSS 4.0.0


Function ajSeqGetSeqS

Returns the sequence in a sequence object as a string. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const AjPStr ajSeqGetSeqS (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence.
const AjPStr RETURNSequence as a string.

From EMBOSS 4.0.0


Function ajSeqGetSeqCopyC

Returns a sequence as a C character string. This is a copy of the string so the caller can do anything with it. It must be copied back to a sequence (e.g. with ajSeqReplace) before output.

Prototype

char* ajSeqGetSeqCopyC (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object
char* RETURNSequence as a null terminated character string.

From EMBOSS 4.0.0


Function ajSeqGetSeqCopyS

Returns the sequence in a sequence object as a string. Because this is a copy of the internal string the caller may change the string. It must be copied back to a sequence (e.g. with ajSeqReplace) before output.

Prototype

AjPStr ajSeqGetSeqCopyS (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence.
AjPStr RETURNSequence as a string.

From EMBOSS 4.0.0


Function ajSeqGetSvC

Returns the sequence version number. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const char* ajSeqGetSvC (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object.
const char* RETURNSeqVersion number as a character string.

From EMBOSS 4.0.0


Function ajSeqGetSvS

Returns the sequence version number. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const AjPStr ajSeqGetSvS (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object.
const AjPStr RETURNSeqVersion number as a string.

From EMBOSS 4.0.0


Function ajSeqGetTaxC

Returns the sequence primary taxon (species). Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const char* ajSeqGetTaxC (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object.
const char* RETURNDescription as a character string.

From EMBOSS 4.0.0


Function ajSeqGetTaxS

Returns the sequence primary taxon (species). Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const AjPStr ajSeqGetTaxS (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object.
const AjPStr RETURNDescription as a string.

From EMBOSS 4.0.0


Function ajSeqGetTaxid

Returns the numeric identifier of the sequence primary taxon (species). This is an identifier from the NCBI taxonomy

Prototype

ajuint ajSeqGetTaxid (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object.
ajuint RETURNTaxon ID.

From EMBOSS 6.1.0


Function ajSeqGetUsaC

Returns the original USA of a sequence. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const char* ajSeqGetUsaC (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object.
const char* RETURNUSA as a character string.

From EMBOSS 4.0.0


Function ajSeqGetUsaS

Returns the original USA of a sequence. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const AjPStr ajSeqGetUsaS (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object.
const AjPStr RETURNUSA as a string.

From EMBOSS 4.0.0


Function ajSeqGetXrefs

Returns the list of cross-references derived from the sequence

Prototype

ajuint ajSeqGetXrefs (
      const AjPSeq seq,
      AjPList list
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object.
AjPListlistModifyList of cross-reference objects
ajuint RETURNNUmber of cross-references returned

From EMBOSS 6.4.0


AjPSeq: testing properties

Functions:
ajSeqIsNucTests whether a sequence is nucleotide.
ajSeqIsProtTests whether a sequence is protein.
ajSeqIsReversedReturns whether the sequence has been reversed
ajSeqIsReversedTrueReturns ajTrue if the sequence is reversed relative to the original sequence
ajSeqIsSpeciesBsubtilisTests whether a sequence is annotated as B. subtilis
ajSeqIsSpeciesHumanTests whether a sequence is annotated as human
ajSeqIsSpeciesMouseTests whether a sequence is annotated as mouse
ajSeqIsSpeciesYeastTests whether a sequence is annotated as yeast (S. cerevisiae)
ajSeqIsTaxonTests whether a sequence is annotated as from a specific taxon ID.
ajSeqIsTrimmedReturns ajTrue if the sequence is already trimmed


Function ajSeqIsNuc

Tests whether a sequence is nucleotide.

Prototype

AjBool ajSeqIsNuc (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence
AjBool RETURNajTrue for a nucleotide sequence.

From EMBOSS 1.0.0


Function ajSeqIsProt

Tests whether a sequence is protein.

Prototype

AjBool ajSeqIsProt (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence
AjBool RETURNajTrue for a protein sequence.

From EMBOSS 1.0.0


Function ajSeqIsReversed

Returns whether the sequence has been reversed

Prototype

AjBool ajSeqIsReversed (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object
AjBool RETURNSequence Direction.

From EMBOSS 3.0.0


Function ajSeqIsReversedTrue

Returns ajTrue if the sequence is reversed relative to the original sequence

Prototype

AjBool ajSeqIsReversedTrue (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object
AjBool RETURNajTrue if sequence is set to be reversed

From EMBOSS 4.0.0


Function ajSeqIsSpeciesBsubtilis

Tests whether a sequence is annotated as B. subtilis

Prototype

AjBool ajSeqIsSpeciesBsubtilis (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence
AjBool RETURNajTrue for a nucleotide sequence.

From EMBOSS 6.1.0


Function ajSeqIsSpeciesHuman

Tests whether a sequence is annotated as human

Prototype

AjBool ajSeqIsSpeciesHuman (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence
AjBool RETURNajTrue for a nucleotide sequence.

From EMBOSS 6.1.0


Function ajSeqIsSpeciesMouse

Tests whether a sequence is annotated as mouse

Prototype

AjBool ajSeqIsSpeciesMouse (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence
AjBool RETURNajTrue for a nucleotide sequence.

From EMBOSS 6.1.0


Function ajSeqIsSpeciesYeast

Tests whether a sequence is annotated as yeast (S. cerevisiae)

Prototype

AjBool ajSeqIsSpeciesYeast (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence
AjBool RETURNajTrue for a nucleotide sequence.

From EMBOSS 6.1.0


Function ajSeqIsTaxon

Tests whether a sequence is annotated as from a specific taxon ID.

Prototype

AjBool ajSeqIsTaxon (
      const AjPSeq seq,
      ajuint taxid
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence
ajuinttaxidInputNCBI Taxonomy ID
AjBool RETURNajTrue for a nucleotide sequence.

From EMBOSS 6.1.0


Function ajSeqIsTrimmed

Returns ajTrue if the sequence is already trimmed

Prototype

AjBool ajSeqIsTrimmed (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object
AjBool RETURNajTrue if sequence is set to be reversed

From EMBOSS 3.0.0


AjPSeq: conversion

Convert sequence to numbers for efficient processing

Functions:
ajSeqConvertNumConverts a string of sequence characters to numbers using a conversion table.


Function ajSeqConvertNum

Converts a string of sequence characters to numbers using a conversion table.

Prototype

AjBool ajSeqConvertNum (
      const AjPSeq seq,
      const AjPSeqCvt cvt,
      AjPStr* Pnumseq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence as a string
const AjPSeqCvtcvtInputConversion table.
AjPStr*PnumseqOutputOutput numeric version of the sequence.
AjBool RETURNajTrue on success.

From EMBOSS 4.1.0


AjPSeq: calculated properties

Functions:
ajSeqCalcCheckgcgCalculates a GCG checksum for a sequence.
ajSeqCalcCountCounts the numbers of A, C, G and T in a nucleotide sequence.
ajSeqCalcMolwtCalculates the molecular weight of a protein sequence.
ajSeqCalcTrueposConverts a string position into a true position. If ipos is negative, it is counted from the end of the string rather than the beginning.
ajSeqCalcTrueposMinConverts a string position into a true position. If ipos is negative, it is counted from the end of the string rather than the beginning.
ajSeqCountGapsReturns the number of gaps in a sequence (counting any possible gap character


Function ajSeqCalcCheckgcg

Calculates a GCG checksum for a sequence.

Prototype

ajint ajSeqCalcCheckgcg (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence.
ajint RETURNGCG checksum.

From EMBOSS 4.0.0


Function ajSeqCalcCount

Counts the numbers of A, C, G and T in a nucleotide sequence.

Prototype

void ajSeqCalcCount (
      const AjPSeq seq,
      ajint* b
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object
ajint*bOutputinteger array, minimum size 5, to hold the results.
void RETURN

From EMBOSS 4.0.0


Function ajSeqCalcMolwt

Calculates the molecular weight of a protein sequence.

Prototype

float ajSeqCalcMolwt (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence
float RETURNMolecular weight.

From EMBOSS 4.0.0


Function ajSeqCalcTruepos

Converts a string position into a true position. If ipos is negative, it is counted from the end of the string rather than the beginning.

Prototype

ajint ajSeqCalcTruepos (
      const AjPSeq seq,
      ajint ipos
);

TypeNameRead/WriteDescription
const AjPSeqseqInputTarget sequence.
ajintiposInputPosition.
ajint RETURNstring position between 1 and length.

From EMBOSS 4.0.0


Function ajSeqCalcTrueposMin

Converts a string position into a true position. If ipos is negative, it is counted from the end of the string rather than the beginning.

Prototype

ajint ajSeqCalcTrueposMin (
      const AjPSeq seq,
      ajint imin,
      ajint ipos
);

TypeNameRead/WriteDescription
const AjPSeqseqInputTarget sequence.
ajintiminInputStart position.
ajintiposInputPosition.
ajint RETURNstring position between 1 and length.

From EMBOSS 4.0.0


Function ajSeqCountGaps

Returns the number of gaps in a sequence (counting any possible gap character

Prototype

ajuint ajSeqCountGaps (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence object
ajuint RETURNNumber of gaps

From EMBOSS 4.1.0


AjPSeq: exit

Functions called on exit from the program by ajExit to do any necessary cleanup and to report internal statistics to the debug file

Functions:
ajSeqExitCleans up sequence processing internal memory


Function ajSeqExit

Cleans up sequence processing internal memory

Prototype

void ajSeqExit (
      void
);

TypeNameRead/WriteDescription
void RETURN

From EMBOSS 4.0.0


AjPSeq: debug

Reports sequence contents for debugging purposes

Functions:
ajSeqTraceDebug calls to trace the data in a sequence object.
ajSeqTraceTitleReports an AjPSeq object to debug output


Function ajSeqTrace

Debug calls to trace the data in a sequence object.

Prototype

void ajSeqTrace (
      const AjPSeq seq
);

TypeNameRead/WriteDescription
const AjPSeqseqInputSequence.
void RETURN

From EMBOSS 1.0.0


Function ajSeqTraceTitle

Reports an AjPSeq object to debug output

Prototype

void ajSeqTraceTitle (
      const AjPSeq seq,
      const char* title
);

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

From EMBOSS 4.1.0


Datatype: AjPSeqall

Function is for manipulating sequence stream objects

Sections:
Sequence Stream ConstructorsConstructors
destructorsDestructors
modifiersModifiers
castsCasts


AjPSeqall: Sequence Stream Constructors

Functions:
ajSeqallNewCreates a new sequence stream object to hold one sequence at a time.


Function ajSeqallNew

Creates a new sequence stream object to hold one sequence at a time.

Prototype

AjPSeqall ajSeqallNew (
      void
);

TypeNameRead/WriteDescription
AjPSeqall RETURNNew sequence stream object.

From EMBOSS 1.0.0


AjPSeqall: destructors

Destruction destroys all internal data structures and frees the memory allocated for the sequence.

Functions:
ajSeqallDelDestructor for sequence stream objects


Function ajSeqallDel

Destructor for sequence stream objects

Prototype

void ajSeqallDel (
      AjPSeqall* Pseq
);

TypeNameRead/WriteDescription
AjPSeqall*PseqDeleteSequence stream object reference
void RETURN

From EMBOSS 2.0.0


AjPSeqall: modifiers

These functions use the contents of a sequence stream object and update them.

Functions:
ajSeqallClearResets all data internals for a sequence stream object when input has been read, but leaves statistics for reporting.
ajSeqallClearStatsResets all data for a sequence stream object so that it can be reused, including statistics.
ajSeqallSetRangeSets the start and end positions for a sequence stream.
ajSeqallSetRangeRevSets the start and end positions for a sequence stream, and set the sequences to be reversed.


Function ajSeqallClear

Resets all data internals for a sequence stream object when input has been read, but leaves statistics for reporting.

Prototype

void ajSeqallClear (
      AjPSeqall seq
);

TypeNameRead/WriteDescription
AjPSeqallseqModifySequence stream
void RETURN

From EMBOSS 2.7.0


Function ajSeqallClearStats

Resets all data for a sequence stream object so that it can be reused, including statistics.

Prototype

void ajSeqallClearStats (
      AjPSeqall seq
);

TypeNameRead/WriteDescription
AjPSeqallseqModifySequence stream
void RETURN

From EMBOSS 6.1.0


Function ajSeqallSetRange

Sets the start and end positions for a sequence stream.

Prototype

void ajSeqallSetRange (
      AjPSeqall seq,
      ajint pos1,
      ajint pos2
);

TypeNameRead/WriteDescription
AjPSeqallseqModifySequence stream object to be set.
ajintpos1InputStart position. Negative values are from the end.
ajintpos2InputEnd position. Negative values are from the end.
void RETURN

From EMBOSS 1.0.0


Function ajSeqallSetRangeRev

Sets the start and end positions for a sequence stream, and set the sequences to be reversed.

Prototype

void ajSeqallSetRangeRev (
      AjPSeqall seq,
      ajint pos1,
      ajint pos2
);

TypeNameRead/WriteDescription
AjPSeqallseqModifySequence stream object to be set.
ajintpos1InputStart position. Negative values are from the end.
ajintpos2InputEnd position. Negative values are from the end.
void RETURN

From EMBOSS 4.0.0


AjPSeqall: casts

These functions examine the contents of a sequence stream object and return some derived information. Some of them provide access to the internal components of a sequence stream object. They are provided for programming convenience but should be used with caution.

Functions:
ajSeqallGetCountReturns the number of sequences read by a seqall object
ajSeqallGetFilenameReturns the filename of a seqall object. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqallGetNameReturns the sequence name of a sequence stream. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqallGetTotlengthReturns the total length of sequences read by a seqall object
ajSeqallGetUsaReturns the sequence name of a sequence stream. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqallGetseqBeginReturns the sequence stream start position, or 1 if no start has been set.
ajSeqallGetseqEndReturns the sequence stream end position, or the sequence length if no end has been set.
ajSeqallGetseqLenReturns the length of a sequence stream, which is the length of the latest sequence read.
ajSeqallGetseqNameReturns the sequence name of a sequence stream. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqallGetseqRangeReturns the sequence range for a sequence stream


Function ajSeqallGetCount

Returns the number of sequences read by a seqall object

Prototype

ajlong ajSeqallGetCount (
      const AjPSeqall seq
);

TypeNameRead/WriteDescription
const AjPSeqallseqInputSeqall object pointer.
ajlong RETURNNumber of sequences read.

From EMBOSS 6.1.0


Function ajSeqallGetFilename

Returns the filename of a seqall object. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const AjPStr ajSeqallGetFilename (
      const AjPSeqall seq
);

TypeNameRead/WriteDescription
const AjPSeqallseqInputSeqall object pointer.
const AjPStr RETURNName as a string.

From EMBOSS 4.0.0


Function ajSeqallGetName

Returns the sequence name of a sequence stream. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const AjPStr ajSeqallGetName (
      const AjPSeqall seq
);

TypeNameRead/WriteDescription
const AjPSeqallseqInputSequence stream object.
const AjPStr RETURNName as a string.

From EMBOSS 1.0.0


Function ajSeqallGetTotlength

Returns the total length of sequences read by a seqall object

Prototype

ajlong ajSeqallGetTotlength (
      const AjPSeqall seq
);

TypeNameRead/WriteDescription
const AjPSeqallseqInputSeqall object pointer.
ajlong RETURNTotal length of sequences read.

From EMBOSS 6.1.0


Function ajSeqallGetUsa

Returns the sequence name of a sequence stream. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const AjPStr ajSeqallGetUsa (
      const AjPSeqall seq
);

TypeNameRead/WriteDescription
const AjPSeqallseqInputSequence object.
const AjPStr RETURNName as a string.

From EMBOSS 1.8.0


Function ajSeqallGetseqBegin

Returns the sequence stream start position, or 1 if no start has been set.

Prototype

ajint ajSeqallGetseqBegin (
      const AjPSeqall seq
);

TypeNameRead/WriteDescription
const AjPSeqallseqInputSequence stream object
ajint RETURNStart position.

From EMBOSS 4.1.0


Function ajSeqallGetseqEnd

Returns the sequence stream end position, or the sequence length if no end has been set.

Prototype

ajint ajSeqallGetseqEnd (
      const AjPSeqall seq
);

TypeNameRead/WriteDescription
const AjPSeqallseqInputSequence stream object
ajint RETURNStart position.

From EMBOSS 4.1.0


Function ajSeqallGetseqLen

Returns the length of a sequence stream, which is the length of the latest sequence read.

Prototype

ajint ajSeqallGetseqLen (
      const AjPSeqall seq
);

TypeNameRead/WriteDescription
const AjPSeqallseqInputSequence stream object
ajint RETURNsequence length.

From EMBOSS 4.1.0


Function ajSeqallGetseqName

Returns the sequence name of a sequence stream. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const AjPStr ajSeqallGetseqName (
      const AjPSeqall seq
);

TypeNameRead/WriteDescription
const AjPSeqallseqInputSequence stream object.
const AjPStr RETURNName as a string.

From EMBOSS 4.1.0


Function ajSeqallGetseqRange

Returns the sequence range for a sequence stream

Prototype

ajint ajSeqallGetseqRange (
      const AjPSeqall seq,
      ajint* begin,
      ajint* end
);

TypeNameRead/WriteDescription
const AjPSeqallseqInputSequence stream object.
ajint*beginOutputSequence range begin
ajint*endOutputSequence range end
ajint RETURNSequence range length

From EMBOSS 4.1.0


Datatype: AjPSeqset

Function is for manipulating sequence set objects

Sections:
constructorsConstructors
destructorsDestructors
castsCasts
modifiersModifiers
element assignmentModifiers
castsCasts
testing propertiesCasts


AjPSeqset: constructors

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

Functions:
ajSeqsetNewCreates a new sequence set object to hold all sequences in memory.


Function ajSeqsetNew

Creates a new sequence set object to hold all sequences in memory.

Prototype

AjPSeqset ajSeqsetNew (
      void
);

TypeNameRead/WriteDescription
AjPSeqset RETURNNew sequence set object.

From EMBOSS 1.0.0


AjPSeqset: destructors

Destruction destroys all internal data structures and frees the memory allocated for the sequence.

Functions:
ajSeqsetDelDestructor for sequence set objects
ajSeqsetDelarrayDestructor for array of sequence set objects


Function ajSeqsetDel

Destructor for sequence set objects

Prototype

void ajSeqsetDel (
      AjPSeqset* Pseq
);

TypeNameRead/WriteDescription
AjPSeqset*PseqDeleteSequence set object reference
void RETURN

From EMBOSS 2.1.0


Function ajSeqsetDelarray

Destructor for array of sequence set objects

Prototype

void ajSeqsetDelarray (
      AjPSeqset** PPseq
);

TypeNameRead/WriteDescription
AjPSeqset**PPseqDeleteSequence set object array
void RETURN

From EMBOSS 4.0.0


AjPSeqset: casts

These functions examine the contents of a sequence set object and return some derived information. Some of them provide access to the internal components of a sequence stream object. They are provided for programming convenience but should be used with caution.

Functions:
ajSeqsetGetFilenameReturns the filename of a sequence set. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqsetGetFormatReturns the sequence format for a sequence set
ajSeqsetGetOffendReturns the sequence set offend value. This is the number of positions removed from the original end.
ajSeqsetGetOffsetReturns the sequence set offset value. This is the number of positions removed from the original end.
ajSeqsetGetRangeReturns the sequence range for a sequence set
ajSeqsetGetTotlengthReturns the total number of bases or residues in a sequence set, ignoring any gap characters in aligned sequences.
ajSeqsetGetUsaReturns the sequence name of a sequence set. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.


Function ajSeqsetGetFilename

Returns the filename of a sequence set. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const AjPStr ajSeqsetGetFilename (
      const AjPSeqset seq
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set object.
const AjPStr RETURNName as a string.

From EMBOSS 4.0.0


Function ajSeqsetGetFormat

Returns the sequence format for a sequence set

Prototype

const AjPStr ajSeqsetGetFormat (
      const AjPSeqset seq
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set object.
const AjPStr RETURNSequence format

From EMBOSS 2.0.1


Function ajSeqsetGetOffend

Returns the sequence set offend value. This is the number of positions removed from the original end.

Prototype

ajint ajSeqsetGetOffend (
      const AjPSeqset seq
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set object
ajint RETURNSequence offend.

From EMBOSS 4.1.0


Function ajSeqsetGetOffset

Returns the sequence set offset value. This is the number of positions removed from the original end.

Prototype

ajint ajSeqsetGetOffset (
      const AjPSeqset seq
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set object
ajint RETURNSequence offset.

From EMBOSS 4.1.0


Function ajSeqsetGetRange

Returns the sequence range for a sequence set

Prototype

ajint ajSeqsetGetRange (
      const AjPSeqset seq,
      ajint* begin,
      ajint* end
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set object.
ajint*beginOutputSequence range begin
ajint*endOutputSequence range end
ajint RETURNSequence range length

From EMBOSS 1.0.0


Function ajSeqsetGetTotlength

Returns the total number of bases or residues in a sequence set, ignoring any gap characters in aligned sequences.

Prototype

ajint ajSeqsetGetTotlength (
      const AjPSeqset seq
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set object.
ajint RETURNTotal ungapped length

From EMBOSS 6.1.0


Function ajSeqsetGetUsa

Returns the sequence name of a sequence set. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const AjPStr ajSeqsetGetUsa (
      const AjPSeqset seq
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set object.
const AjPStr RETURNName as a string.

From EMBOSS 2.1.0


AjPSeqset: modifiers

These functions use the contents of a sequence set object and update them.

Functions:
ajSeqsetFillFills a sequence set with gaps at the ends of any shorter sequences.
ajSeqsetFmtLowerConverts all sequences in a set to lower case.
ajSeqsetFmtUpperConverts all sequences in a set to upper case.
ajSeqsetReverseReverse complements all sequences in a sequence set.
ajSeqsetSortLenSorts a sequence set by sequence length
ajSeqsetTrimTrims a sequence set to start and end positions


Function ajSeqsetFill

Fills a sequence set with gaps at the ends of any shorter sequences.

Prototype

ajint ajSeqsetFill (
      AjPSeqset seq
);

TypeNameRead/WriteDescription
AjPSeqsetseqModifySequence set object to be set.
ajint RETURNNumber of gaps inserted

From EMBOSS 1.0.0


Function ajSeqsetFmtLower

Converts all sequences in a set to lower case.

Prototype

void ajSeqsetFmtLower (
      AjPSeqset seq
);

TypeNameRead/WriteDescription
AjPSeqsetseqModifySequence set object
void RETURN

From EMBOSS 4.1.0


Function ajSeqsetFmtUpper

Converts all sequences in a set to upper case.

Prototype

void ajSeqsetFmtUpper (
      AjPSeqset seq
);

TypeNameRead/WriteDescription
AjPSeqsetseqModifySequence set object
void RETURN

From EMBOSS 4.1.0


Function ajSeqsetReverse

Reverse complements all sequences in a sequence set.

Prototype

void ajSeqsetReverse (
      AjPSeqset seq
);

TypeNameRead/WriteDescription
AjPSeqsetseqModifySequence set object
void RETURN

From EMBOSS 1.0.0


Function ajSeqsetSortLen

Sorts a sequence set by sequence length

Prototype

void ajSeqsetSortLen (
      AjPSeqset seq
);

TypeNameRead/WriteDescription
AjPSeqsetseqModifySequence set object
void RETURN

From EMBOSS 6.1.0


Function ajSeqsetTrim

Trims a sequence set to start and end positions

Prototype

void ajSeqsetTrim (
      AjPSeqset seq
);

TypeNameRead/WriteDescription
AjPSeqsetseqModifySequence set object
void RETURN

From EMBOSS 2.9.0


AjPSeqset: element assignment

Functions for assigning elements of a sequence set object.

Functions:
ajSeqsetSetRangeSets the start and end positions for a sequence set.


Function ajSeqsetSetRange

Sets the start and end positions for a sequence set.

Prototype

void ajSeqsetSetRange (
      AjPSeqset seq,
      ajint pos1,
      ajint pos2
);

TypeNameRead/WriteDescription
AjPSeqsetseqModifySequence set object to be set.
ajintpos1InputStart position. Negative values are from the end.
ajintpos2InputEnd position. Negative values are from the end.
void RETURN

From EMBOSS 1.0.0


AjPSeqset: casts

These functions examine the contents of a sequence set object and return some derived information. Some of them provide access to the internal components of a sequence set object. They are provided for programming convenience but should be used with caution.

Functions:
ajSeqsetGetBeginReturns the sequence set start position, or 1 if no start has been set.
ajSeqsetGetEndReturns the sequence set end position, or the sequence length if no end has been set.
ajSeqsetGetLenReturns the length of a sequence set, which is the maximum sequence length in the set.
ajSeqsetGetNameCReturns the sequence name of a sequence set. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqsetGetNameSReturns the sequence name of a sequence set. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.
ajSeqsetGetSeqarrayReturns an array of sequences. Because this is a pointer to the real internal sequence the caller must take care not to change the data in any way. If the sequence is to be changed (case for example) then it must first be copied.
ajSeqsetGetSizeReturns the number of sequences in a sequence set
ajSeqsetGetTotweightReturns the weight of all sequences in a sequence set
ajSeqsetGetseqAccCReturns the accession number of a sequence in a sequence set
ajSeqsetGetseqAccSReturns the accession number of a sequence in a sequence set
ajSeqsetGetseqNameCReturns the name of a sequence in a sequence set
ajSeqsetGetseqNameSReturns the name of a sequence in a sequence set
ajSeqsetGetseqSeqReturns one sequence from a sequence set. Because this is a pointer to the real internal sequence the caller must take care not to change the data in any way. If the sequence is to be changed (case for example) then it must first be copied.
ajSeqsetGetseqSeqCReturns one sequence from a sequence set. Because this is a pointer to the real internal sequence the caller must take care not to change the data in any way. If the sequence is to be changed (case for example) then it must first be copied.
ajSeqsetGetseqSeqSReturns one sequence from a sequence set. Because this is a pointer to the real internal sequence the caller must take care not to change the data in any way. If the sequence is to be changed (case for example) then it must first be copied.
ajSeqsetGetseqWeightReturns the weight of a sequence in a sequence set


Function ajSeqsetGetBegin

Returns the sequence set start position, or 1 if no start has been set.

Prototype

ajuint ajSeqsetGetBegin (
      const AjPSeqset seq
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set object
ajuint RETURNStart position.

From EMBOSS 4.1.0


Function ajSeqsetGetEnd

Returns the sequence set end position, or the sequence length if no end has been set.

Prototype

ajuint ajSeqsetGetEnd (
      const AjPSeqset seq
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set object
ajuint RETURNStart position.

From EMBOSS 4.1.0


Function ajSeqsetGetLen

Returns the length of a sequence set, which is the maximum sequence length in the set.

Prototype

ajuint ajSeqsetGetLen (
      const AjPSeqset seq
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set object
ajuint RETURNsequence set length.

From EMBOSS 4.1.0


Function ajSeqsetGetNameC

Returns the sequence name of a sequence set. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const char* ajSeqsetGetNameC (
      const AjPSeqset seq
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set object.
const char* RETURNName as a C character string.

From EMBOSS 4.1.0


Function ajSeqsetGetNameS

Returns the sequence name of a sequence set. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

const AjPStr ajSeqsetGetNameS (
      const AjPSeqset seq
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set object.
const AjPStr RETURNName as a string.

From EMBOSS 4.1.0


Function ajSeqsetGetSeqarray

Returns an array of sequences. Because this is a pointer to the real internal sequence the caller must take care not to change the data in any way. If the sequence is to be changed (case for example) then it must first be copied.

Prototype

AjPSeq* ajSeqsetGetSeqarray (
      const AjPSeqset seq
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set object.
AjPSeq* RETURNSequence object.

From EMBOSS 4.1.0


Function ajSeqsetGetSize

Returns the number of sequences in a sequence set

Prototype

ajuint ajSeqsetGetSize (
      const AjPSeqset seq
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set object
ajuint RETURNsequence set size.

From EMBOSS 4.1.0


Function ajSeqsetGetTotweight

Returns the weight of all sequences in a sequence set

Prototype

float ajSeqsetGetTotweight (
      const AjPSeqset seq
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set object
float RETURNsequence weight as a float.

From EMBOSS 4.1.0


Function ajSeqsetGetseqAccC

Returns the accession number of a sequence in a sequence set

Prototype

const char* ajSeqsetGetseqAccC (
      const AjPSeqset seq,
      ajuint i
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set object
ajuintiInputSequence index
const char* RETURNaccession number as a string.

From EMBOSS 4.1.0


Function ajSeqsetGetseqAccS

Returns the accession number of a sequence in a sequence set

Prototype

const AjPStr ajSeqsetGetseqAccS (
      const AjPSeqset seq,
      ajuint i
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set object
ajuintiInputSequence index
const AjPStr RETURNaccession number as a string.

From EMBOSS 4.1.0


Function ajSeqsetGetseqNameC

Returns the name of a sequence in a sequence set

Prototype

const char* ajSeqsetGetseqNameC (
      const AjPSeqset seq,
      ajuint i
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set object
ajuintiInputSequence index
const char* RETURNsequence name as a string.

From EMBOSS 4.1.0


Function ajSeqsetGetseqNameS

Returns the name of a sequence in a sequence set

Prototype

const AjPStr ajSeqsetGetseqNameS (
      const AjPSeqset seq,
      ajuint i
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set object
ajuintiInputSequence index
const AjPStr RETURNsequence name as a string.

From EMBOSS 4.1.0


Function ajSeqsetGetseqSeq

Returns one sequence from a sequence set. Because this is a pointer to the real internal sequence the caller must take care not to change the data in any way. If the sequence is to be changed (case for example) then it must first be copied.

Prototype

const AjPSeq ajSeqsetGetseqSeq (
      const AjPSeqset seq,
      ajuint i
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set object.
ajuintiInputSequence index number in set
const AjPSeq RETURNSequence object.

From EMBOSS 4.1.0


Function ajSeqsetGetseqSeqC

Returns one sequence from a sequence set. Because this is a pointer to the real internal sequence the caller must take care not to change the data in any way. If the sequence is to be changed (case for example) then it must first be copied.

Prototype

const char* ajSeqsetGetseqSeqC (
      const AjPSeqset seq,
      ajuint i
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set object.
ajuintiInputSequence index number in set
const char* RETURNSequence as a C string.

From EMBOSS 4.1.0


Function ajSeqsetGetseqSeqS

Returns one sequence from a sequence set. Because this is a pointer to the real internal sequence the caller must take care not to change the data in any way. If the sequence is to be changed (case for example) then it must first be copied.

Prototype

const AjPStr ajSeqsetGetseqSeqS (
      const AjPSeqset seq,
      ajuint i
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set object.
ajuintiInputSequence index number in set
const AjPStr RETURNSequence object.

From EMBOSS 4.1.0


Function ajSeqsetGetseqWeight

Returns the weight of a sequence in a sequence set

Prototype

float ajSeqsetGetseqWeight (
      const AjPSeqset seq,
      ajuint i
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set object
ajuintiInputSequence index
float RETURNsequence weight as a float.

From EMBOSS 4.1.0


AjPSeqset: testing properties

Tests properties of a sequence set

Functions:
ajSeqsetIsDnaTests whether a sequence set is DNA.
ajSeqsetIsNucTests whether a sequence set is nucleotide.
ajSeqsetIsProtTests whether a sequence set is protein.
ajSeqsetIsRnaTests whether a sequence set is RNA.


Function ajSeqsetIsDna

Tests whether a sequence set is DNA.

Prototype

AjBool ajSeqsetIsDna (
      const AjPSeqset seq
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set
AjBool RETURNajTrue for a nucleotide sequence set.

From EMBOSS 2.3.0


Function ajSeqsetIsNuc

Tests whether a sequence set is nucleotide.

Prototype

AjBool ajSeqsetIsNuc (
      const AjPSeqset seq
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set
AjBool RETURNajTrue for a nucleotide sequence set.

From EMBOSS 1.0.0


Function ajSeqsetIsProt

Tests whether a sequence set is protein.

Prototype

AjBool ajSeqsetIsProt (
      const AjPSeqset seq
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set
AjBool RETURNajTrue for a protein sequence set.

From EMBOSS 1.0.0


Function ajSeqsetIsRna

Tests whether a sequence set is RNA.

Prototype

AjBool ajSeqsetIsRna (
      const AjPSeqset seq
);

TypeNameRead/WriteDescription
const AjPSeqsetseqInputSequence set
AjBool RETURNajTrue for a nucleotide sequence set.

From EMBOSS 2.0.1


Datatype: AjPStr

Sequences represented as string objects

Sections:
conversionDerievd values


AjPStr: conversion

Convert sequence to numbers for efficient processing

Functions:
ajSeqstrConvertNumConverts a string of sequence characters to numbers using a conversion table.


Function ajSeqstrConvertNum

Converts a string of sequence characters to numbers using a conversion table.

Prototype

AjBool ajSeqstrConvertNum (
      const AjPStr seq,
      const AjPSeqCvt cvt,
      AjPStr* Pnumseq
);

TypeNameRead/WriteDescription
const AjPStrseqInputSequence as a string
const AjPSeqCvtcvtInputConversion table.
AjPStr*PnumseqOutputOutput numeric version of the sequence.
AjBool RETURNajTrue on success.

From EMBOSS 4.1.0


Datatype: AjPSeqCvt

Sequences represented as string objects

Sections:
Sequence Conversion FunctionsMiscellaneous
constructorsConstructors
Sequence DestructorsDestructors
element retrievalGeneral use


AjPSeqCvt: Sequence Conversion Functions

Functions:
ajSeqcvtTraceTraces a conversion table with debug calls.


Function ajSeqcvtTrace

Traces a conversion table with debug calls.

Prototype

void ajSeqcvtTrace (
      const AjPSeqCvt cvt
);

TypeNameRead/WriteDescription
const AjPSeqCvtcvtInputConversion table.
void RETURN

From EMBOSS 4.1.0


AjPSeqCvt: constructors

Functions:
ajSeqcvtNewCGenerates a new conversion table in which the first character in the string provided is converted to 1, the second to 2, and so on. Upper and lower case characters are converted to the same numbers. All other characters are set to zero.
ajSeqcvtNewEndCGenerates a new conversion table in which the first character in the string provided is converted to 0, the second to 1, and so on. Upper and lower case characters are converted to the same numbers. All other characters are converted to one more than the highest char.
ajSeqcvtNewNumberCGenerates a new conversion table in which the characters are retained as upper case, numbers are set to -1 and all other characters are set to -2.
ajSeqcvtNewStrGenerates a new conversion table in which the first character of the first string in the array provided is converted to 1, the first character of the second string is converted to 2, the first character of the third string is converted to 3 and so on. Upper and lower case characters are converted to the same numbers. All other characters are set to zero.
ajSeqcvtNewStrAsymGenerates a new conversion table in which the first character of the first string in the array provided is converted to 1, the first character of the second string is converted to 2, the first character of the third string is converted to 3 and so on. Upper and lower case characters are converted to the same numbers. All other characters are set to zero. For use with asymmetrical matrices.


Function ajSeqcvtNewC

Generates a new conversion table in which the first character in the string provided is converted to 1, the second to 2, and so on. Upper and lower case characters are converted to the same numbers. All other characters are set to zero.

Prototype

AjPSeqCvt ajSeqcvtNewC (
      const char* bases
);

TypeNameRead/WriteDescription
const char*basesInputAllowed sequence characters.
AjPSeqCvt RETURNConversion table.

From EMBOSS 4.1.0


Function ajSeqcvtNewEndC

Generates a new conversion table in which the first character in the string provided is converted to 0, the second to 1, and so on. Upper and lower case characters are converted to the same numbers. All other characters are converted to one more than the highest char.

Prototype

AjPSeqCvt ajSeqcvtNewEndC (
      const char* bases
);

TypeNameRead/WriteDescription
const char*basesInputAllowed sequence characters.
AjPSeqCvt RETURNConversion table.

From EMBOSS 4.1.0


Function ajSeqcvtNewNumberC

Generates a new conversion table in which the characters are retained as upper case, numbers are set to -1 and all other characters are set to -2.

Prototype

AjPSeqCvt ajSeqcvtNewNumberC (
      const char* bases
);

TypeNameRead/WriteDescription
const char*basesInputAllowed sequence characters.
AjPSeqCvt RETURNConversion table.

From EMBOSS 4.1.0


Function ajSeqcvtNewStr

Generates a new conversion table in which the first character of the first string in the array provided is converted to 1, the first character of the second string is converted to 2, the first character of the third string is converted to 3 and so on. Upper and lower case characters are converted to the same numbers. All other characters are set to zero.

Prototype

AjPSeqCvt ajSeqcvtNewStr (
      const AjPPStr basearray,
      ajint numbases
);

TypeNameRead/WriteDescription
const AjPPStrbasearrayInputAllowed sequence character strings (size specified by parameter n)
ajintnumbasesInputNumber of strings
AjPSeqCvt RETURNConversion table.

From EMBOSS 4.1.0


Function ajSeqcvtNewStrAsym

Generates a new conversion table in which the first character of the first string in the array provided is converted to 1, the first character of the second string is converted to 2, the first character of the third string is converted to 3 and so on. Upper and lower case characters are converted to the same numbers. All other characters are set to zero. For use with asymmetrical matrices.

Prototype

AjPSeqCvt ajSeqcvtNewStrAsym (
      const AjPPStr basearray,
      ajint numbases,
      const AjPPStr matchbases,
      ajint nummatch
);

TypeNameRead/WriteDescription
const AjPPStrbasearrayInputAllowed sequence character strings (size specified by parameter n)
ajintnumbasesInputNumber of strings
const AjPPStrmatchbasesInputAllowed sequence character strings for rows (size specified by parameter rn)
ajintnummatchInputNumber of strings (rows)
AjPSeqCvt RETURNConversion table.

From EMBOSS 4.1.0


AjPSeqCvt: Sequence Destructors

Destruction destroys all internal data structures and frees the memory allocated for the sequence.

Functions:
ajSeqcvtDelDelete a conversion table


Function ajSeqcvtDel

Delete a conversion table

Prototype

void ajSeqcvtDel (
      AjPSeqCvt* Pcvt
);

TypeNameRead/WriteDescription
AjPSeqCvt*PcvtOutputConversion table reference
void RETURN

From EMBOSS 4.1.0


AjPSeqCvt: element retrieval

These functions use the contents of a sequence conversion object

Functions:
ajSeqcvtGetCodeKReturns the integer code corresponding to a sequence character in a conversion table
ajSeqcvtGetCodeSReturns the integer code corresponding to a sequence character string in a conversion table (for rows in asymmetrical matrices).
ajSeqcvtGetCodeAsymSReturns the integer code corresponding to a sequence character string in a conversion table (for columns in asymmetrical matrices).
ajSeqcvtGetCodeAsymrowSReturns the integer code corresponding to a sequence character string in a conversion table (for rows in asymmetrical matrices).
ajSeqcvtGetLenReturns the length of a conversion table string (number of sequence characters explicitly included)


Function ajSeqcvtGetCodeK

Returns the integer code corresponding to a sequence character in a conversion table

Prototype

ajint ajSeqcvtGetCodeK (
      const AjPSeqCvt cvt,
      char ch
);

TypeNameRead/WriteDescription
const AjPSeqCvtcvtInputConversion table
charchInputSequence character
ajint RETURNConversion code

From EMBOSS 4.1.0


Function ajSeqcvtGetCodeS

Returns the integer code corresponding to a sequence character string in a conversion table (for rows in asymmetrical matrices).

Prototype

ajint ajSeqcvtGetCodeS (
      const AjPSeqCvt cvt,
      const AjPStr str
);

TypeNameRead/WriteDescription
const AjPSeqCvtcvtInputConversion table
const AjPStrstrInputSequence character string
ajint RETURNConversion code

From EMBOSS 4.1.0


Function ajSeqcvtGetCodeAsymS

Returns the integer code corresponding to a sequence character string in a conversion table (for columns in asymmetrical matrices).

Prototype

ajint ajSeqcvtGetCodeAsymS (
      const AjPSeqCvt cvt,
      const AjPStr str
);

TypeNameRead/WriteDescription
const AjPSeqCvtcvtInputConversion table
const AjPStrstrInputSequence character string
ajint RETURNConversion code

From EMBOSS 4.1.0


Function ajSeqcvtGetCodeAsymrowS

Returns the integer code corresponding to a sequence character string in a conversion table (for rows in asymmetrical matrices).

Prototype

ajint ajSeqcvtGetCodeAsymrowS (
      const AjPSeqCvt cvt,
      const AjPStr str
);

TypeNameRead/WriteDescription
const AjPSeqCvtcvtInputConversion table
const AjPStrstrInputSequence character string
ajint RETURNConversion code

From EMBOSS 6.3.0


Function ajSeqcvtGetLen

Returns the length of a conversion table string (number of sequence characters explicitly included)

Prototype

ajuint ajSeqcvtGetLen (
      const AjPSeqCvt cvt
);

TypeNameRead/WriteDescription
const AjPSeqCvtcvtInputConversion table
ajuint RETURNLength

From EMBOSS 4.1.0


Datatype: AjPSeqDate

Functions handling sequence dates

Sections:
sequence date constructorsConstructors
destructorsDestructors
modifiersModifiers


AjPSeqDate: sequence date constructors

Functions:
ajSeqdateNewConstructor for empty sequence date object
ajSeqdateNewDateConstructor for copy of a sequence date object


Function ajSeqdateNew

Constructor for empty sequence date object

Prototype

AjPSeqDate ajSeqdateNew (
      void
);

TypeNameRead/WriteDescription
AjPSeqDate RETURNEmpty sequence date object

From EMBOSS 5.0.0


Function ajSeqdateNewDate

Constructor for copy of a sequence date object

Prototype

AjPSeqDate ajSeqdateNewDate (
      const AjPSeqDate date
);

TypeNameRead/WriteDescription
const AjPSeqDatedateInputSequence date object
AjPSeqDate RETURNEmpty sequence date object

From EMBOSS 5.0.0


AjPSeqDate: destructors

Destruction destroys all internal data structures and frees the memory allocated for the sequence.

Functions:
ajSeqdateDelDeletes a sequence date object.


Function ajSeqdateDel

Deletes a sequence date object.

Prototype

void ajSeqdateDel (
      AjPSeqDate* Pdate
);

TypeNameRead/WriteDescription
AjPSeqDate*PdateDeleteSequence date object
void RETURN

From EMBOSS 5.0.0


AjPSeqDate: modifiers

These functions update contents of a sequence date object.

Functions:
ajSeqdateClearResets all data for a sequence date object.
ajSeqdateSetCreateSSet the sequence creation date
ajSeqdateSetModifySSet the entry modification date
ajSeqdateSetModseqSSet the sequence modification date


Function ajSeqdateClear

Resets all data for a sequence date object.

Prototype

void ajSeqdateClear (
      AjPSeqDate date
);

TypeNameRead/WriteDescription
AjPSeqDatedateModifySequence date object
void RETURN

From EMBOSS 6.1.0


Function ajSeqdateSetCreateS

Set the sequence creation date

Prototype

AjBool ajSeqdateSetCreateS (
      AjPSeqDate date,
      const AjPStr datestr
);

TypeNameRead/WriteDescription
AjPSeqDatedateOutputSequence date
const AjPStrdatestrInputDate string
AjBool RETURNajTrue on success

From EMBOSS 5.0.0


Function ajSeqdateSetModifyS

Set the entry modification date

Prototype

AjBool ajSeqdateSetModifyS (
      AjPSeqDate date,
      const AjPStr datestr
);

TypeNameRead/WriteDescription
AjPSeqDatedateOutputSequence date
const AjPStrdatestrInputDate string
AjBool RETURNajTrue on success

From EMBOSS 5.0.0


Function ajSeqdateSetModseqS

Set the sequence modification date

Prototype

AjBool ajSeqdateSetModseqS (
      AjPSeqDate date,
      const AjPStr datestr
);

TypeNameRead/WriteDescription
AjPSeqDatedateOutputSequence date
const AjPStrdatestrInputDate string
AjBool RETURNajTrue on success

From EMBOSS 5.0.0


Datatype: AjPSeqDesc

Functions handling complex descriptions (e.g. in UniProt)

Sections:
descriptions constructorsConstructors
destructorsDestructors
modifiersModifiers


AjPSeqDesc: descriptions constructors

Functions:
ajSeqdescNewConstructor for empty description object
ajSeqdescNewDescConstructor for copy of a description object


Function ajSeqdescNew

Constructor for empty description object

Prototype

AjPSeqDesc ajSeqdescNew (
      void
);

TypeNameRead/WriteDescription
AjPSeqDesc RETURNEmpty sequence description object

From EMBOSS 6.1.0


Function ajSeqdescNewDesc

Constructor for copy of a description object

Prototype

AjPSeqDesc ajSeqdescNewDesc (
      const AjPSeqDesc desc
);

TypeNameRead/WriteDescription
const AjPSeqDescdescInputDescription object
AjPSeqDesc RETURNCopied description object

From EMBOSS 6.1.0


AjPSeqDesc: destructors

Destruction destroys all internal data structures and frees the memory allocated for a description object

Functions:
ajSeqdescDelDeletes a description object.


Function ajSeqdescDel

Deletes a description object.

Prototype

void ajSeqdescDel (
      AjPSeqDesc* Pdesc
);

TypeNameRead/WriteDescription
AjPSeqDesc*PdescDeleteDescription object
void RETURN

From EMBOSS 6.1.0


AjPSeqDesc: modifiers

These functions update contents of a description object.

Functions:
ajSeqdescAppendNameAppend to the name of a description
ajSeqdescClearResets data for a description object.
ajSeqdescSetNameSet the name of a description object


Function ajSeqdescAppendName

Append to the name of a description

Prototype

AjBool ajSeqdescAppendName (
      AjPSeqDesc desc,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqDescdescModifyDescription object
const AjPStrstrInputName string
AjBool RETURNTrue on success

From EMBOSS 6.1.0


Function ajSeqdescClear

Resets data for a description object.

Prototype

void ajSeqdescClear (
      AjPSeqDesc desc
);

TypeNameRead/WriteDescription
AjPSeqDescdescModifyDescription object
void RETURN

From EMBOSS 6.1.0


Function ajSeqdescSetName

Set the name of a description object

Prototype

AjBool ajSeqdescSetName (
      AjPSeqDesc desc,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqDescdescModifyDescription object
const AjPStrstrInputSynonyms string
AjBool RETURNTrue on success

From EMBOSS 6.1.0


Datatype: AjPList

Manipulating lists of descriptions

Sections:
Description list operationsGeneral use


AjPList: Description list operations

Manipulating lists of descriptions

Functions:
ajSeqdesclistCloneCopy a list of genes to another list


Function ajSeqdesclistClone

Copy a list of genes to another list

Prototype

AjBool ajSeqdesclistClone (
      const AjPList src,
      AjPList dest
);

TypeNameRead/WriteDescription
const AjPListsrcInputSource list of descriptions
AjPListdestOutputDestination list of descriptions
AjBool RETURNTrue on success

From EMBOSS 6.1.0


Datatype: AjPSeqSubdesc

Functions handling complex sub-descriptions (e.g. in UniProt)

Sections:
sub-descriptions constructorsConstructors
destructorsDestructors
modifiersModifiers


AjPSeqSubdesc: sub-descriptions constructors

Functions:
ajSeqsubdescNewConstructor for empty sub-description object
ajSeqsubdescNewSubdescConstructor for copy of a sub-description object


Function ajSeqsubdescNew

Constructor for empty sub-description object

Prototype

AjPSeqSubdesc ajSeqsubdescNew (
      void
);

TypeNameRead/WriteDescription
AjPSeqSubdesc RETURNEmpty sequence sub-description object

From EMBOSS 6.1.0


Function ajSeqsubdescNewSubdesc

Constructor for copy of a sub-description object

Prototype

AjPSeqSubdesc ajSeqsubdescNewSubdesc (
      const AjPSeqSubdesc desc
);

TypeNameRead/WriteDescription
const AjPSeqSubdescdescInputSub-description object
AjPSeqSubdesc RETURNCopied sub-description object

From EMBOSS 6.1.0


AjPSeqSubdesc: destructors

Destruction destroys all internal data structures and frees the memory allocated for a sub-description object

Functions:
ajSeqsubdescDelDeletes a sub-description object.


Function ajSeqsubdescDel

Deletes a sub-description object.

Prototype

void ajSeqsubdescDel (
      AjPSeqSubdesc* Pdesc
);

TypeNameRead/WriteDescription
AjPSeqSubdesc*PdescDeleteSub-description object
void RETURN

From EMBOSS 6.1.0


AjPSeqSubdesc: modifiers

These functions update contents of a sub-description object.

Functions:
ajSeqsubdescAppendNameAppend to the name of a description
ajSeqsubdescClearResets data for a sub-description object.
ajSeqsubdescSetNameSet the name of a sub-description object


Function ajSeqsubdescAppendName

Append to the name of a description

Prototype

AjBool ajSeqsubdescAppendName (
      AjPSeqSubdesc desc,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqSubdescdescModifyDescription object
const AjPStrstrInputName string
AjBool RETURNTrue on success

From EMBOSS 6.1.0


Function ajSeqsubdescClear

Resets data for a sub-description object.

Prototype

void ajSeqsubdescClear (
      AjPSeqSubdesc desc
);

TypeNameRead/WriteDescription
AjPSeqSubdescdescModifySub-description object
void RETURN

From EMBOSS 6.1.0


Function ajSeqsubdescSetName

Set the name of a sub-description object

Prototype

AjBool ajSeqsubdescSetName (
      AjPSeqSubdesc desc,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqSubdescdescModifySub-description object
const AjPStrstrInputSynonyms string
AjBool RETURNTrue on success

From EMBOSS 6.1.0


Datatype: AjPList

Manipulating lists of sub-descriptions

Sections:
Description list operationsGeneral use


AjPList: Description list operations

Manipulating lists of sub-descriptions

Functions:
ajSeqsubdesclistCloneCopy a list of sub-descriptions to another list


Function ajSeqsubdesclistClone

Copy a list of sub-descriptions to another list

Prototype

AjBool ajSeqsubdesclistClone (
      const AjPList src,
      AjPList dest
);

TypeNameRead/WriteDescription
const AjPListsrcInputSource list of sub-descriptions
AjPListdestOutputDestination list of sub-descriptions
AjBool RETURNTrue on success

From EMBOSS 6.1.0


Datatype: AjPSeqGene

Functions handling gene names, synonyms and other terms

Sections:
gene names constructorsConstructors
destructorsDestructors
modifiersModifiers


AjPSeqGene: gene names constructors

Functions:
ajSeqgeneNewConstructor for empty gene object
ajSeqgeneNewGeneConstructor for copy of a gene object
ajSeqgeneNewNameConstructor for gene with given name


Function ajSeqgeneNew

Constructor for empty gene object

Prototype

AjPSeqGene ajSeqgeneNew (
      void
);

TypeNameRead/WriteDescription
AjPSeqGene RETURNEmpty sequence gene object

From EMBOSS 6.1.0


Function ajSeqgeneNewGene

Constructor for copy of a gene object

Prototype

AjPSeqGene ajSeqgeneNewGene (
      const AjPSeqGene gene
);

TypeNameRead/WriteDescription
const AjPSeqGenegeneInputGene object
AjPSeqGene RETURNCopied gene object

From EMBOSS 6.1.0


Function ajSeqgeneNewName

Constructor for gene with given name

Prototype

AjPSeqGene ajSeqgeneNewName (
      const AjPStr str
);

TypeNameRead/WriteDescription
const AjPStrstrInputGene name
AjPSeqGene RETURNNew gene object

From EMBOSS 6.1.0


AjPSeqGene: destructors

Destruction destroys all internal data structures and frees the memory allocated for a gene object

Functions:
ajSeqgeneDelDeletes a gene object.


Function ajSeqgeneDel

Deletes a gene object.

Prototype

void ajSeqgeneDel (
      AjPSeqGene* Pgene
);

TypeNameRead/WriteDescription
AjPSeqGene*PgeneDeleteGene object
void RETURN

From EMBOSS 6.1.0


AjPSeqGene: modifiers

These functions update contents of a gene object.

Functions:
ajSeqgeneAppendNameAppend to the name of a gene
ajSeqgeneAppendOlnAppend to ordered locus names of a gene
ajSeqgeneAppendOrfAppend to the ORF name of a gene
ajSeqgeneAppendSynonymsAppend to the name of a gene
ajSeqgeneSetNameSet the name of a gene
ajSeqgeneSetOlnSet the ordered locus names of a gene
ajSeqgeneSetOrfSet the ORF name of a gene
ajSeqgeneSetSynonymsSet the name of a gene


Function ajSeqgeneAppendName

Append to the name of a gene

Prototype

AjBool ajSeqgeneAppendName (
      AjPSeqGene gene,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqGenegeneModifyGene object
const AjPStrstrInputName string
AjBool RETURNTrue on success

From EMBOSS 6.1.0


Function ajSeqgeneAppendOln

Append to ordered locus names of a gene

Prototype

AjBool ajSeqgeneAppendOln (
      AjPSeqGene gene,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqGenegeneModifyGene object
const AjPStrstrInputOrdered locus names string
AjBool RETURNTrue on success

From EMBOSS 6.1.0


Function ajSeqgeneAppendOrf

Append to the ORF name of a gene

Prototype

AjBool ajSeqgeneAppendOrf (
      AjPSeqGene gene,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqGenegeneModifyGene object
const AjPStrstrInputORF name string
AjBool RETURNTrue on success

From EMBOSS 6.1.0


Function ajSeqgeneAppendSynonyms

Append to the name of a gene

Prototype

AjBool ajSeqgeneAppendSynonyms (
      AjPSeqGene gene,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqGenegeneModifyGene object
const AjPStrstrInputSynonyms string
AjBool RETURNTrue on success

From EMBOSS 6.1.0


Function ajSeqgeneSetName

Set the name of a gene

Prototype

AjBool ajSeqgeneSetName (
      AjPSeqGene gene,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqGenegeneModifyGene object
const AjPStrstrInputName string
AjBool RETURNTrue on success

From EMBOSS 6.1.0


Function ajSeqgeneSetOln

Set the ordered locus names of a gene

Prototype

AjBool ajSeqgeneSetOln (
      AjPSeqGene gene,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqGenegeneModifyGene object
const AjPStrstrInputOrdered locus names string
AjBool RETURNTrue on success

From EMBOSS 6.1.0


Function ajSeqgeneSetOrf

Set the ORF name of a gene

Prototype

AjBool ajSeqgeneSetOrf (
      AjPSeqGene gene,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqGenegeneModifyGene object
const AjPStrstrInputORF name string
AjBool RETURNTrue on success

From EMBOSS 6.1.0


Function ajSeqgeneSetSynonyms

Set the name of a gene

Prototype

AjBool ajSeqgeneSetSynonyms (
      AjPSeqGene gene,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqGenegeneModifyGene object
const AjPStrstrInputSynonyms string
AjBool RETURNTrue on success

From EMBOSS 6.1.0


Datatype: AjPList

Manipulating lists of genes

Sections:
Reference list operationsGeneral use


AjPList: Reference list operations

Manipulating lists of genes

Functions:
ajSeqgenelistCloneCopy a list of genes to another list


Function ajSeqgenelistClone

Copy a list of genes to another list

Prototype

AjBool ajSeqgenelistClone (
      const AjPList src,
      AjPList dest
);

TypeNameRead/WriteDescription
const AjPListsrcInputSource list of genes
AjPListdestOutputDestination list of genes
AjBool RETURNTrue on success

From EMBOSS 6.1.0


Datatype: AjPSeqXref

Functions handling sequence cross-references

Sections:
sequence cross-reference constructorsConstructors
destructorsDestructors


AjPSeqXref: sequence cross-reference constructors

Functions:
ajSeqxrefNewConstructor for empty sequence citation object
ajSeqxrefNewDbCConstructor for copy of a sequence citation object
ajSeqxrefNewDbSConstructor for copy of a sequence citation object
ajSeqxrefNewRefConstructor for copy of a sequence citation object


Function ajSeqxrefNew

Constructor for empty sequence citation object

Prototype

AjPSeqXref ajSeqxrefNew (
      void
);

TypeNameRead/WriteDescription
AjPSeqXref RETURNEmpty sequence cross-reference object

From EMBOSS 6.1.0


Function ajSeqxrefNewDbC

Constructor for copy of a sequence citation object

Prototype

AjPSeqXref ajSeqxrefNewDbC (
      const AjPStr id,
      const char* db,
      ajuint reftype
);

TypeNameRead/WriteDescription
const AjPStridInputPrimary identifier
const char*dbInputDatabase name
ajuintreftypeInputReference type
AjPSeqXref RETURNNew sequence cross-reference object

From EMBOSS 6.1.0


Function ajSeqxrefNewDbS

Constructor for copy of a sequence citation object

Prototype

AjPSeqXref ajSeqxrefNewDbS (
      const AjPStr id,
      const AjPStr db,
      ajuint reftype
);

TypeNameRead/WriteDescription
const AjPStridInputPrimary identifier
const AjPStrdbInputDatabase name
ajuintreftypeInputReference type
AjPSeqXref RETURNNew sequence cross-reference object

From EMBOSS 6.1.0


Function ajSeqxrefNewRef

Constructor for copy of a sequence citation object

Prototype

AjPSeqXref ajSeqxrefNewRef (
      const AjPSeqXref xref
);

TypeNameRead/WriteDescription
const AjPSeqXrefxrefInputSequence cross-reference object
AjPSeqXref RETURNCopied sequence cross-reference object

From EMBOSS 6.1.0


AjPSeqXref: destructors

Destruction destroys all internal data structures and frees the memory allocated for the sequence cross-reference

Functions:
ajSeqxrefDelDeletes a sequence cross-reference object.


Function ajSeqxrefDel

Deletes a sequence cross-reference object.

Prototype

void ajSeqxrefDel (
      AjPSeqXref* Pxref
);

TypeNameRead/WriteDescription
AjPSeqXref*PxrefDeleteSequence cross-reference object
void RETURN

From EMBOSS 6.1.0


Datatype: AjPList

Manipulating lists of sequence cross-references

Sections:
Reference list operationsGeneral use


AjPList: Reference list operations

Manipulating lists of sequence cross-references

Functions:
ajSeqxreflistCloneCopy a list of cross-references to another list


Function ajSeqxreflistClone

Copy a list of cross-references to another list

Prototype

AjBool ajSeqxreflistClone (
      const AjPList src,
      AjPList dest
);

TypeNameRead/WriteDescription
const AjPListsrcInputSource list of cross-references
AjPListdestOutputDestination list of cross-references
AjBool RETURNTrue on success

From EMBOSS 6.1.0


Function ajSeqxreflistSort

Sort a list of cross-references

Prototype

AjBool ajSeqxreflistSort (
      AjPList list
);

TypeNameRead/WriteDescription
AjPListlistModifySource list of cross-references
AjBool RETURNTrue on success

From EMBOSS 6.4.0


Datatype: AjPSeqRef

Functions handling sequence citations

Sections:
sequence citation constructorsConstructors
destructorsDestructors
modifiersModifiers


AjPSeqRef: sequence citation constructors

Functions:
ajSeqrefNewConstructor for empty sequence citation object
ajSeqrefNewRefConstructor for copy of a sequence citation object


Function ajSeqrefNew

Constructor for empty sequence citation object

Prototype

AjPSeqRef ajSeqrefNew (
      void
);

TypeNameRead/WriteDescription
AjPSeqRef RETURNEmpty sequence citation object

From EMBOSS 5.0.0


Function ajSeqrefNewRef

Constructor for copy of a sequence citation object

Prototype

AjPSeqRef ajSeqrefNewRef (
      const AjPSeqRef ref
);

TypeNameRead/WriteDescription
const AjPSeqRefrefInputSequence citation object
AjPSeqRef RETURNCopied sequence citation object

From EMBOSS 5.0.0


AjPSeqRef: destructors

Destruction destroys all internal data structures and frees the memory allocated for the sequence citation

Functions:
ajSeqrefDelDeletes a sequence citation object.


Function ajSeqrefDel

Deletes a sequence citation object.

Prototype

void ajSeqrefDel (
      AjPSeqRef* Pref
);

TypeNameRead/WriteDescription
AjPSeqRef*PrefDeleteSequence citation object
void RETURN

From EMBOSS 5.0.0


AjPSeqRef: modifiers

These functions update contents of a sequence citation object.

Functions:
ajSeqrefAppendAuthorsAppend to the Authors string of a citation
ajSeqrefAppendCommentAppend to the Comment string of a citation
ajSeqrefAppendGroupnameAppend to the group name string of a citation
ajSeqrefAppendLocationAppend to the location string of a citation
ajSeqrefAppendPositionAppend to the position string of a citation
ajSeqrefAppendTitleAppend to the title string of a citation
ajSeqrefAppendXrefAppend to the Cross reference string of a citation
ajSeqrefFmtAuthorsEmblReturn the Authors string of a citation in EMBL format
ajSeqrefFmtAuthorsGbReturn the Authors string of a citation in Genbank format
ajSeqrefFmtLocationEmblReturn the location string of a citation in EMBL format
ajSeqrefFmtLocationGbReturn the location string of a citation in Genbank format
ajSeqrefFmtTitleGbReturn the title string of a citation in Genbank format
ajSeqrefSetAuthorsSet the Authors string of a citation
ajSeqrefSetCommentSet the Comment string of a citation
ajSeqrefSetGroupnameSet the group name string of a citation
ajSeqrefSetLocationSet the location string of a citation
ajSeqrefSetLoctypeSet the location type of a citation
ajSeqrefSetPositionSet the position string of a citation
ajSeqrefSetTitleSet the title string of a citation
ajSeqrefSetXrefSet the cross reference string of a citation
ajSeqrefSetnumNumberSets the citation number
ajSeqrefStandardStandardise internal representation of a sequence reference


Function ajSeqrefAppendAuthors

Append to the Authors string of a citation

Prototype

AjBool ajSeqrefAppendAuthors (
      AjPSeqRef ref,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqRefrefModifySequence citation object
const AjPStrstrInputAuthors string
AjBool RETURNTrue on success

From EMBOSS 5.0.0


Function ajSeqrefAppendComment

Append to the Comment string of a citation

Prototype

AjBool ajSeqrefAppendComment (
      AjPSeqRef ref,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqRefrefModifySequence citation object
const AjPStrstrInputComment string
AjBool RETURNTrue on success

From EMBOSS 5.0.0


Function ajSeqrefAppendGroupname

Append to the group name string of a citation

Prototype

AjBool ajSeqrefAppendGroupname (
      AjPSeqRef ref,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqRefrefModifySequence citation object
const AjPStrstrInputGroup name string
AjBool RETURNTrue on success

From EMBOSS 5.0.0


Function ajSeqrefAppendLocation

Append to the location string of a citation

Prototype

AjBool ajSeqrefAppendLocation (
      AjPSeqRef ref,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqRefrefModifySequence citation object
const AjPStrstrInputLocation string
AjBool RETURNTrue on success

From EMBOSS 5.0.0


Function ajSeqrefAppendPosition

Append to the position string of a citation

Prototype

AjBool ajSeqrefAppendPosition (
      AjPSeqRef ref,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqRefrefModifySequence citation object
const AjPStrstrInputPosition string
AjBool RETURNTrue on success

From EMBOSS 5.0.0


Function ajSeqrefAppendTitle

Append to the title string of a citation

Prototype

AjBool ajSeqrefAppendTitle (
      AjPSeqRef ref,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqRefrefModifySequence citation object
const AjPStrstrInputTitle string
AjBool RETURNTrue on success

From EMBOSS 5.0.0


Function ajSeqrefAppendXref

Append to the Cross reference string of a citation

Prototype

AjBool ajSeqrefAppendXref (
      AjPSeqRef ref,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqRefrefModifySequence citation object
const AjPStrstrInputXref string
AjBool RETURNTrue on success

From EMBOSS 5.0.0


Function ajSeqrefFmtAuthorsEmbl

Return the Authors string of a citation in EMBL format

Prototype

AjBool ajSeqrefFmtAuthorsEmbl (
      const AjPSeqRef ref,
      AjPStr* Pdest
);

TypeNameRead/WriteDescription
const AjPSeqRefrefInputSequence citation object
AjPStr*PdestOutputAuthors string in EMBL format
AjBool RETURNTrue if author list exists

From EMBOSS 5.0.0


Function ajSeqrefFmtAuthorsGb

Return the Authors string of a citation in Genbank format

Prototype

AjBool ajSeqrefFmtAuthorsGb (
      const AjPSeqRef ref,
      AjPStr* Pdest
);

TypeNameRead/WriteDescription
const AjPSeqRefrefInputSequence citation object
AjPStr*PdestOutputAuthors string in Genbank format
AjBool RETURNTrue if author list exists

From EMBOSS 5.0.0


Function ajSeqrefFmtLocationEmbl

Return the location string of a citation in EMBL format

Prototype

AjBool ajSeqrefFmtLocationEmbl (
      const AjPSeqRef ref,
      AjPStr* Pdest
);

TypeNameRead/WriteDescription
const AjPSeqRefrefInputSequence citation object
AjPStr*PdestOutputAuthors string in EMBL format
AjBool RETURNTrue if author list exists

From EMBOSS 5.0.0


Function ajSeqrefFmtLocationGb

Return the location string of a citation in Genbank format

Prototype

AjBool ajSeqrefFmtLocationGb (
      const AjPSeqRef ref,
      AjPStr* Pdest
);

TypeNameRead/WriteDescription
const AjPSeqRefrefInputSequence citation object
AjPStr*PdestOutputAuthors string in Genbank format
AjBool RETURNTrue if author list exists

From EMBOSS 5.0.0


Function ajSeqrefFmtTitleGb

Return the title string of a citation in Genbank format

Prototype

AjBool ajSeqrefFmtTitleGb (
      const AjPSeqRef ref,
      AjPStr* Pdest
);

TypeNameRead/WriteDescription
const AjPSeqRefrefInputSequence citation object
AjPStr*PdestOutputAuthors string in Genbank format
AjBool RETURNTrue if author list exists

From EMBOSS 5.0.0


Function ajSeqrefSetAuthors

Set the Authors string of a citation

Prototype

AjBool ajSeqrefSetAuthors (
      AjPSeqRef ref,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqRefrefModifySequence citation object
const AjPStrstrInputAuthors string
AjBool RETURNTrue on success

From EMBOSS 5.0.0


Function ajSeqrefSetComment

Set the Comment string of a citation

Prototype

AjBool ajSeqrefSetComment (
      AjPSeqRef ref,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqRefrefModifySequence citation object
const AjPStrstrInputComment string
AjBool RETURNTrue on success

From EMBOSS 5.0.0


Function ajSeqrefSetGroupname

Set the group name string of a citation

Prototype

AjBool ajSeqrefSetGroupname (
      AjPSeqRef ref,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqRefrefModifySequence citation object
const AjPStrstrInputGroupname string
AjBool RETURNTrue on success

From EMBOSS 5.0.0


Function ajSeqrefSetLocation

Set the location string of a citation

Prototype

AjBool ajSeqrefSetLocation (
      AjPSeqRef ref,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqRefrefModifySequence citation object
const AjPStrstrInputLocation string
AjBool RETURNTrue on success

From EMBOSS 5.0.0


Function ajSeqrefSetLoctype

Set the location type of a citation

Prototype

AjBool ajSeqrefSetLoctype (
      AjPSeqRef ref,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqRefrefModifySequence citation object
const AjPStrstrInputLocation string
AjBool RETURNTrue on success

From EMBOSS 5.0.0


Function ajSeqrefSetPosition

Set the position string of a citation

Prototype

AjBool ajSeqrefSetPosition (
      AjPSeqRef ref,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqRefrefModifySequence citation object
const AjPStrstrInputpPosition string
AjBool RETURNTrue on success

From EMBOSS 5.0.0


Function ajSeqrefSetTitle

Set the title string of a citation

Prototype

AjBool ajSeqrefSetTitle (
      AjPSeqRef ref,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqRefrefModifySequence citation object
const AjPStrstrInputTitle string
AjBool RETURNTrue on success

From EMBOSS 5.0.0


Function ajSeqrefSetXref

Set the cross reference string of a citation

Prototype

AjBool ajSeqrefSetXref (
      AjPSeqRef ref,
      const AjPStr str
);

TypeNameRead/WriteDescription
AjPSeqRefrefModifySequence citation object
const AjPStrstrInputXref string
AjBool RETURNTrue on success

From EMBOSS 5.0.0


Function ajSeqrefSetnumNumber

Sets the citation number

Prototype

AjBool ajSeqrefSetnumNumber (
      AjPSeqRef ref,
      ajuint num
);

TypeNameRead/WriteDescription
AjPSeqRefrefModifySequence citation object
ajuintnumInputCitation number
AjBool RETURNTrue on success

From EMBOSS 5.0.0


Function ajSeqrefStandard

Standardise internal representation of a sequence reference

Prototype

AjBool ajSeqrefStandard (
      AjPSeqRef ref
);

TypeNameRead/WriteDescription
AjPSeqRefrefModifySequence citation object
AjBool RETURNTrue on success

From EMBOSS 5.0.0


Datatype: AjPList

8 Manipulating lists of sequence citations

Sections:
Reference list operationsGeneral use
element retrievalGeneral use


AjPList: Reference list operations

Manipulating lists of sequence citations

Functions:
ajSeqreflistCloneCopy a list of citations to another list


Function ajSeqreflistClone

Copy a list of citations to another list

Prototype

AjBool ajSeqreflistClone (
      const AjPList src,
      AjPList dest
);

TypeNameRead/WriteDescription
const AjPListsrcInputSource list of citations
AjPListdestOutputDestination list of citations
AjBool RETURNTrue on success

From EMBOSS 5.0.0


AjPList: element retrieval

These functions return contents of a list of sequence cross-reference objects.

Functions:
ajSeqreflistGetXrefsCopy a cross-reference list


Function ajSeqreflistGetXrefs

Copy a cross-reference list

Prototype

ajuint ajSeqreflistGetXrefs (
      const AjPList src,
      AjPList* Plist
);

TypeNameRead/WriteDescription
const AjPListsrcInputSource cross-reference list
AjPList*PlistOutputTarget list, created if it does not already exist
ajuint RETURNnumber of cross-references copied

From EMBOSS 6.2.0


Datatype: AjPStr

Functions handling strings for specialist sequence-related tests

Sections:
string testsGeneral use


AjPStr: string tests

Functions:
ajSeqtestIsAccessionTests whether a string is a potential sequence accession number. The current definition is one or two alpha characters, then a possible underscore (for REFSEQ accessions), followed by a string of digits and a minimum length of 6.
ajSeqtestIsSeqversionTests whether a string is a potential sequence version number. The current definition is an accession number, followed by a dot and a number.


Function ajSeqtestIsAccession

Tests whether a string is a potential sequence accession number. The current definition is one or two alpha characters, then a possible underscore (for REFSEQ accessions), followed by a string of digits and a minimum length of 6.

Prototype

AjBool ajSeqtestIsAccession (
      const AjPStr str
);

TypeNameRead/WriteDescription
const AjPStrstrInputString to be tested
AjBool RETURNajTrue if the string is a possible accession number.

From EMBOSS 4.1.0


Function ajSeqtestIsSeqversion

Tests whether a string is a potential sequence version number. The current definition is an accession number, followed by a dot and a number.

Prototype

const AjPStr ajSeqtestIsSeqversion (
      const AjPStr str
);

TypeNameRead/WriteDescription
const AjPStrstrInputString to be tested
const AjPStr RETURNaccession number part of the string if successful

From EMBOSS 4.1.0


AjPStr: string properties

Functions:
ajSeqstrCalcMolwtCalculates the molecular weight of a protein sequence using average molecular weights
ajSeqstrCountGapsComplements but does not reverse a nucleotide sequence provided as a string.


Function ajSeqstrCalcMolwt

Calculates the molecular weight of a protein sequence using average molecular weights

Prototype

float ajSeqstrCalcMolwt (
      const AjPStr seq
);

TypeNameRead/WriteDescription
const AjPStrseqInputSequence
float RETURNMolecular weight.

From EMBOSS 4.0.0


Function ajSeqstrCountGaps

Complements but does not reverse a nucleotide sequence provided as a string.

Prototype

ajuint ajSeqstrCountGaps (
      const AjPStr seq
);

TypeNameRead/WriteDescription
const AjPStrseqInputSequence as a string.
ajuint RETURNNumber of gap characters

From EMBOSS 4.1.0


AjPStr: string processing

Functions:
ajSeqstrComplementComplements but does not reverse a nucleotide sequence provided as a string.
ajSeqstrReverseReverses and complements a nucleotide sequence provided as a string.


Function ajSeqstrComplement

Complements but does not reverse a nucleotide sequence provided as a string.

Prototype

void ajSeqstrComplement (
      AjPStr* Pseq
);

TypeNameRead/WriteDescription
AjPStr*PseqModifySequence as a string.
void RETURN

From EMBOSS 4.1.0


Function ajSeqstrReverse

Reverses and complements a nucleotide sequence provided as a string.

Prototype

void ajSeqstrReverse (
      AjPStr* Pseq
);

TypeNameRead/WriteDescription
AjPStr*PseqModifySequence as a string.
void RETURN

From EMBOSS 4.0.0


AjPStr: assignment

Assign values for sequence entry classes

Functions:
ajSeqclsSetEmblSets the internal entry class for a sequence
ajSeqclsSetGbSets the internal entry class for a sequence


Function ajSeqclsSetEmbl

Sets the internal entry class for a sequence

Prototype

AjBool ajSeqclsSetEmbl (
      AjPStr* Pcls,
      const AjPStr clsembl
);

TypeNameRead/WriteDescription
AjPStr*PclsModifyInternal entry class name
const AjPStrclsemblInputEMBL database entry class
AjBool RETURNTrue if a known type

From EMBOSS 5.0.0


Function ajSeqclsSetGb

Sets the internal entry class for a sequence

Prototype

AjBool ajSeqclsSetGb (
      AjPStr* Pcls,
      const AjPStr clsgb
);

TypeNameRead/WriteDescription
AjPStr*PclsModifyInternal entry class name
const AjPStrclsgbInputGenbank database entry class
AjBool RETURNTrue if a known type

From EMBOSS 5.0.0


AjPStr: retrieval

Return values for sequence entry class

Functions:
ajSeqclsGetEmblReturns the EMBL entry class for a sequence


Function ajSeqclsGetEmbl

Returns the EMBL entry class for a sequence

Prototype

const char* ajSeqclsGetEmbl (
      const AjPStr cls
);

TypeNameRead/WriteDescription
const AjPStrclsInputInternal entry class name
const char* RETURNEMBL entry class name

From EMBOSS 5.0.0


AjPStr: assignment

Assign values for sequence entry division

Functions:
ajSeqdivSetEmblSets the internal database division for a sequence
ajSeqdivSetGbSets the internal database division for a sequence


Function ajSeqdivSetEmbl

Sets the internal database division for a sequence

Prototype

AjBool ajSeqdivSetEmbl (
      AjPStr* Pdivi,
      const AjPStr divembl
);

TypeNameRead/WriteDescription
AjPStr*PdiviModifyInternal database division
const AjPStrdivemblInputEMBL database division
AjBool RETURNTrue if a known type

From EMBOSS 5.0.0


Function ajSeqdivSetGb

Sets the internal database division for a sequence

Prototype

AjBool ajSeqdivSetGb (
      AjPStr* Pdivi,
      const AjPStr divgb
);

TypeNameRead/WriteDescription
AjPStr*PdiviModifyInternal database division
const AjPStrdivgbInputGenbank database division
AjBool RETURNTrue if a known type

From EMBOSS 5.0.0


AjPStr: retrieval

Return values for sequence entry division

Functions:
ajSeqdivGetEmblReturns the EMBL database division for a sequence
ajSeqdivGetGbReturns the Genbank database division for a sequence


Function ajSeqdivGetEmbl

Returns the EMBL database division for a sequence

Prototype

const char* ajSeqdivGetEmbl (
      const AjPStr divi
);

TypeNameRead/WriteDescription
const AjPStrdiviInputInternal database division
const char* RETURNEMBL database division

From EMBOSS 5.0.0


Function ajSeqdivGetGb

Returns the Genbank database division for a sequence

Prototype

const char* ajSeqdivGetGb (
      const AjPStr divi
);

TypeNameRead/WriteDescription
const AjPStrdiviInputInternal database division
const char* RETURNGenbank database division

From EMBOSS 5.0.0


AjPStr: assignment

Assign values for sequence entry molecule types

Functions:
ajSeqmolSetEmblSets the internal molecule type for a sequence
ajSeqmolSetGbSets the internal molecule type for a sequence


Function ajSeqmolSetEmbl

Sets the internal molecule type for a sequence

Prototype

AjBool ajSeqmolSetEmbl (
      AjPStr* Pmol,
      const AjPStr molembl
);

TypeNameRead/WriteDescription
AjPStr*PmolModifySequence object
const AjPStrmolemblInputMolecule type
AjBool RETURNTrue if a known type

From EMBOSS 5.0.0


Function ajSeqmolSetGb

Sets the internal molecule type for a sequence

Prototype

AjBool ajSeqmolSetGb (
      AjPStr* Pmol,
      const AjPStr molgb
);

TypeNameRead/WriteDescription
AjPStr*PmolModifySequence object
const AjPStrmolgbInputMolecule type
AjBool RETURNTrue if a known type

From EMBOSS 5.0.0


AjPStr: retrieval

Return values for sequence molecule type division

Functions:
ajSeqmolGetEmblReturns the EMBL molecule type for a sequence
ajSeqmolGetGbReturns the Genbank molecule type for a sequence


Function ajSeqmolGetEmbl

Returns the EMBL molecule type for a sequence

Prototype

const char* ajSeqmolGetEmbl (
      const AjPStr mol
);

TypeNameRead/WriteDescription
const AjPStrmolInputInternal molecule type
const char* RETURNEMBL molecule type

From EMBOSS 5.0.0


Function ajSeqmolGetGb

Returns the Genbank molecule type for a sequence

Prototype

const char* ajSeqmolGetGb (
      const AjPStr mol
);

TypeNameRead/WriteDescription
const AjPStrmolInputInternal molecule type
const char* RETURNGenbank molecule type

From EMBOSS 5.0.0