ajseqtype.c


Function ajSeqTypeCheckS

Tests the type of a sequence is compatible with a defined type. If the type can have gaps, also tests for gap characters. Used for input validation - writes error message if the type check fails

Prototype

AjBool ajSeqTypeCheckS (
      AjPStr* pthys,
      const AjPStr type_name
);

TypeNameRead/WriteDescription
AjPStr*pthysModifySequence string
const AjPStrtype_nameInputSequence type
AjBool RETURNajTrue if compatible.

From EMBOSS 2.7.0


Function ajSeqTypeCheckIn

Tests the type of a sequence is compatible with a defined type. If the type can have gaps, also tests for gap characters. Used for input validation - writes error message if the type check fails

Prototype

AjBool ajSeqTypeCheckIn (
      AjPSeq thys,
      const AjPSeqin seqin
);

TypeNameRead/WriteDescription
AjPSeqthysModifySequence object
const AjPSeqinseqinInputSequence input object
AjBool RETURNajTrue if compatible.

From EMBOSS 2.7.0


Function ajSeqTypeNucS

Checks sequence type for nucleotide without gaps.

Prototype

char ajSeqTypeNucS (
      const AjPStr thys
);

TypeNameRead/WriteDescription
const AjPStrthysInputSequence string (unchanged at present)
char RETURNinvalid character if any.

From EMBOSS 2.7.0


Function ajSeqTypeDnaS

Checks sequence type for DNA without gaps.

Prototype

char ajSeqTypeDnaS (
      const AjPStr thys
);

TypeNameRead/WriteDescription
const AjPStrthysInputSequence string (unchanged at present)
char RETURNinvalid character if any.

From EMBOSS 2.7.0


Function ajSeqTypeRnaS

Checks sequence type for RNA without gaps

Prototype

char ajSeqTypeRnaS (
      const AjPStr thys
);

TypeNameRead/WriteDescription
const AjPStrthysInputSequence string (unchanged at present)
char RETURNinvalid character if any.

From EMBOSS 2.7.0


Function ajSeqTypeGapdnaS

Checks sequence type for Dna with gaps

Prototype

char ajSeqTypeGapdnaS (
      const AjPStr thys
);

TypeNameRead/WriteDescription
const AjPStrthysInputSequence string (unchanged at present)
char RETURNinvalid character if any.

From EMBOSS 2.7.0


Function ajSeqTypeGaprnaS

Checks sequence type for RNA with gaps

Prototype

char ajSeqTypeGaprnaS (
      const AjPStr thys
);

TypeNameRead/WriteDescription
const AjPStrthysInputSequence string (unchanged at present)
char RETURNinvalid character if any.

From EMBOSS 2.7.0


Function ajSeqTypeGapnucS

Checks sequence type for nucleotide with gaps.

Prototype

char ajSeqTypeGapnucS (
      const AjPStr thys
);

TypeNameRead/WriteDescription
const AjPStrthysInputSequence string (unchanged at present)
char RETURNinvalid character if any.

From EMBOSS 2.7.0


Function ajSeqTypeAnyprotS

Checks sequence type for anything that can be in a protein sequence

Prototype

char ajSeqTypeAnyprotS (
      const AjPStr thys
);

TypeNameRead/WriteDescription
const AjPStrthysInputSequence string (unchanged at present)
char RETURNinvalid character if any.

From EMBOSS 2.7.0


Function ajSeqTypeProtS

Checks sequence type for anything that can be in a protein sequence

Prototype

char ajSeqTypeProtS (
      const AjPStr thys
);

TypeNameRead/WriteDescription
const AjPStrthysInputSequence string (unchanged at present)
char RETURNinvalid character if any.

From EMBOSS 2.7.0


Function ajSeqTypeGapanyS

Checks sequence type for any sequence with gaps.

Prototype

char ajSeqTypeGapanyS (
      const AjPStr thys
);

TypeNameRead/WriteDescription
const AjPStrthysInputSequence string (unchanged at present)
char RETURNinvalid character if any.

From EMBOSS 2.7.0


Function ajSeqGap

Sets non-sequence characters to valid gap characters, and pads with extra gaps if necessary to a specified length

Prototype

void ajSeqGap (
      AjPSeq thys,
      char gapc,
      char padc
);

TypeNameRead/WriteDescription
AjPSeqthysModifySequence
chargapcInputStandard gap character
charpadcInputGap character for ends of sequence
void RETURN

From EMBOSS 1.0.0


Function ajSeqGapLen

Sets non-sequence characters to valid gap characters, and pads with extra gaps if necessary to a specified length

Prototype

void ajSeqGapLen (
      AjPSeq thys,
      char gapc,
      char padc,
      ajint ilen
);

TypeNameRead/WriteDescription
AjPSeqthysModifySequence
chargapcInputStandard gap character
charpadcInputGap character for ends of sequence
ajintilenInputSequence length. Expanded if longer than current length
void RETURN

From EMBOSS 1.0.0


Function ajSeqGapS

Sets non-sequence characters to valid gap characters, and pads with extra gaps if necessary to a specified length

Prototype

void ajSeqGapS (
      AjPStr* seq,
      char gapc
);

TypeNameRead/WriteDescription
AjPStr*seqModifySequence
chargapcInputStandard gap character
void RETURN

From EMBOSS 1.0.0


Function ajSeqSetNuc

Sets a sequence type to "nucleotide"

Prototype

void ajSeqSetNuc (
      AjPSeq thys
);

TypeNameRead/WriteDescription
AjPSeqthysModifySequence object
void RETURN

From EMBOSS 1.0.0


Function ajSeqSetProt

Sets a sequence type to "protein"

Prototype

void ajSeqSetProt (
      AjPSeq thys
);

TypeNameRead/WriteDescription
AjPSeqthysModifySequence object
void RETURN

From EMBOSS 1.0.0


Function ajSeqsetSetNuc

Sets a sequence set type to "nucleotide"

Prototype

void ajSeqsetSetNuc (
      AjPSeqset thys
);

TypeNameRead/WriteDescription
AjPSeqsetthysModifySequence set object
void RETURN

From EMBOSS 2.8.0


Function ajSeqsetSetProt

Sets a sequence set type to "protein"

Prototype

void ajSeqsetSetProt (
      AjPSeqset thys
);

TypeNameRead/WriteDescription
AjPSeqsetthysModifySequence set object
void RETURN

From EMBOSS 2.8.0


Function ajSeqType

Sets the type of a sequence if it has not yet been defined.

Prototype

void ajSeqType (
      AjPSeq thys
);

TypeNameRead/WriteDescription
AjPSeqthysModifySequence object
void RETURN

From EMBOSS 1.0.0


Function ajSeqPrintType

Prints the seqType definitions. For EMBOSS entrails output

Prototype

void ajSeqPrintType (
      AjPFile outf,
      AjBool full
);

TypeNameRead/WriteDescription
AjPFileoutfModifyOutput file
AjBoolfullInputFull output
void RETURN

From EMBOSS 2.5.0


Function ajSeqTypeIsProt

Returns ajTrue is sequence type can be a protein (or 'any')

Prototype

AjBool ajSeqTypeIsProt (
      const AjPStr type_name
);

TypeNameRead/WriteDescription
const AjPStrtype_nameInputSequence type
AjBool RETURNajTrue if sequence can be protein

From EMBOSS 2.7.0


Function ajSeqTypeIsNuc

Returns ajTrue is sequence type can be a nucleotide (or 'any')

Prototype

AjBool ajSeqTypeIsNuc (
      const AjPStr type_name
);

TypeNameRead/WriteDescription
const AjPStrtype_nameInputSequence type
AjBool RETURNajTrue if sequence can be nucleotide

From EMBOSS 2.7.0


Function ajSeqTypeIsAny

Returns ajTrue is sequence type can be a protein or nucleotide

Prototype

AjBool ajSeqTypeIsAny (
      const AjPStr type_name
);

TypeNameRead/WriteDescription
const AjPStrtype_nameInputSequence type
AjBool RETURNajTrue if sequence can be protein or nucleotide

From EMBOSS 2.7.0


Function ajSeqTypeSummary

Returns ajTrue is sequence type can be a protein or nucleotide

Prototype

AjBool ajSeqTypeSummary (
      const AjPStr type_name,
      AjPStr* Ptype,
      AjBool* gaps
);

TypeNameRead/WriteDescription
const AjPStrtype_nameInputSequence type
AjPStr*PtypeOutputSequence type 'protein' 'nucleotide' or 'any'
AjBool*gapsOutputTrue if gap characters are preserved
AjBool RETURNajTrue if sequence can be protein or nucleotide

From EMBOSS 4.0.0


Function ajSeqTypeExit

Cleans up sequence type processing internal memory

Prototype

void ajSeqTypeExit (
      void
);

TypeNameRead/WriteDescription
void RETURN

From EMBOSS 4.0.0


Function ajSeqTypeUnused

Dummy function to catch all unused functions defined in the ajseqtype source file.

Prototype

void ajSeqTypeUnused (
      void
);

TypeNameRead/WriteDescription
void RETURN

From EMBOSS 4.1.0