A  B  C  D  E  F  G  H  I  L  M  N  O  P  Q  R  S  T  U  V  W  Y 

B

BestHitOverhang - class in org.veupathdb.lib.blast.common.fields

-best_hit_overhang <Real, (>0 and <0.5)>Best Hit algorithm overhang value (recommended value: 0.

BestHitScoreEdge - class in org.veupathdb.lib.blast.common.fields

-best_hit_score_edge <Real, (>0 and <0.5)>Best Hit algorithm score edge value (recommended value: 0.

BitScore - enum entry in org.veupathdb.lib.blast.common.fields.FormatField

 

Blast - class in org.veupathdb.lib.blast

Entrypoint to the Blast library.

BlastArchiveASN1 - enum entry in org.veupathdb.lib.blast.common.fields.FormatType

 

BlastCLI - class in org.veupathdb.lib.blast.common

Fields common to all BLAST+ tools.

BlastCommand - class in org.veupathdb.lib.blast.serial

Blast Command Type Base

BlastField - class in org.veupathdb.lib.blast.serial

Represents a single, defaultable field/argument for a blast tool.

blastFormatter(ObjectNode) - function in org.veupathdb.lib.blast.Blast

Creates a new BlastFormatter instance by parsing the given JSON input.

blastFormatter() - function in org.veupathdb.lib.blast.Blast

Creates a new, defaulted BlastFormatter instance.

BlastFormatter - enum entry in org.veupathdb.lib.blast.BlastTool

 

BlastFormatter - class in org.veupathdb.lib.blast.formatter

Stand-alone BLAST formatter client, version 2.11.

blastn(ObjectNode) - function in org.veupathdb.lib.blast.Blast

Creates a new BlastN instance by parsing the given JSON input.

blastn() - function in org.veupathdb.lib.blast.Blast

Creates a new, defaulted BlastN instance.

BlastN - enum entry in org.veupathdb.lib.blast.BlastTool

 

BlastN - class in org.veupathdb.lib.blast.blastn

Nucleotide-Nucleotide BLAST 2.11.

BlastN - enum entry in org.veupathdb.lib.blast.blastn.fields.BlastNTaskType

 

BlastNShort - enum entry in org.veupathdb.lib.blast.blastn.fields.BlastNTaskType

 

BlastNTask - class in org.veupathdb.lib.blast.blastn.fields

-task <String>Permissible values:

• 'blastn'

• 'blastn-short'

• 'dc-megablast'

• 'megablast'

• 'rmblastn'

Task to executeDefault = megablast

BlastNTaskType - class in org.veupathdb.lib.blast.blastn.fields

 

blastp(ObjectNode) - function in org.veupathdb.lib.blast.Blast

Creates a new BlastP instance by parsing the given JSON input.

blastp() - function in org.veupathdb.lib.blast.Blast

Creates a new, defaulted BlastP instance.

BlastP - enum entry in org.veupathdb.lib.blast.BlastTool

 

BlastP - class in org.veupathdb.lib.blast.blastp

Protein-Protein BLAST 2.11.

BlastP - enum entry in org.veupathdb.lib.blast.blastp.field.BlastPTaskType

 

BlastPFast - enum entry in org.veupathdb.lib.blast.blastp.field.BlastPTaskType

 

BlastPShort - enum entry in org.veupathdb.lib.blast.blastp.field.BlastPTaskType

 

BlastPTask - class in org.veupathdb.lib.blast.blastp.field

-task <String>Permissible values:

• blastp

• blastp-fast

• blastp-short

Task to executeDefault = blastp

BlastPTaskType - class in org.veupathdb.lib.blast.blastp.field

 

BlastQueryBase - class in org.veupathdb.lib.blast.common

Basic fields common to all BLAST+ query tools.

BlastQueryWithIPG - class in org.veupathdb.lib.blast.common

 

BlastQueryWithLists - class in org.veupathdb.lib.blast.common

List fields common to most BLAST+ query tools.

BlastTool - class in org.veupathdb.lib.blast

Enum of the valid BLAST+ tools.

BlastTracebackOperations - enum entry in org.veupathdb.lib.blast.common.fields.FormatField

 

blastx(ObjectNode) - function in org.veupathdb.lib.blast.Blast

Creates a new BlastX instance by parsing the given JSON input.

blastx() - function in org.veupathdb.lib.blast.Blast

Creates a new, defaulted BlastX instance.

BlastX - enum entry in org.veupathdb.lib.blast.BlastTool

 

BlastX - class in org.veupathdb.lib.blast.blastx

Translated Query-Protein Subject BLAST 2.11.

BlastX - enum entry in org.veupathdb.lib.blast.blastx.field.BlastXTaskType

 

BlastXFast - enum entry in org.veupathdb.lib.blast.blastx.field.BlastXTaskType

 

BlastXML - enum entry in org.veupathdb.lib.blast.common.fields.FormatType

 

BlastXTask - class in org.veupathdb.lib.blast.blastx.field

-task <String>Permissible values:

• blastx

• blastx-fast

Task to executeDefault = blastx

BlastXTaskType - class in org.veupathdb.lib.blast.blastx.field

 

Blosum45 - enum entry in org.veupathdb.lib.blast.blastp.field.ScoringMatrixPType

 

Blosum45 - enum entry in org.veupathdb.lib.blast.blastx.field.ScoringMatrixXType

 

Blosum45 - enum entry in org.veupathdb.lib.blast.deltablast.fields.MatrixDeltaType

 

Blosum45 - enum entry in org.veupathdb.lib.blast.psiblast.fields.MatrixPSIType

 

Blosum45 - enum entry in org.veupathdb.lib.blast.tblastn.fields.ScoringMatrixTNType

 

Blosum45 - enum entry in org.veupathdb.lib.blast.tblastx.fields.ScoringMatrixTXType

 

Blosum50 - enum entry in org.veupathdb.lib.blast.blastp.field.ScoringMatrixPType

 

Blosum50 - enum entry in org.veupathdb.lib.blast.blastx.field.ScoringMatrixXType

 

Blosum50 - enum entry in org.veupathdb.lib.blast.deltablast.fields.MatrixDeltaType

 

Blosum50 - enum entry in org.veupathdb.lib.blast.psiblast.fields.MatrixPSIType

 

Blosum50 - enum entry in org.veupathdb.lib.blast.tblastn.fields.ScoringMatrixTNType

 

Blosum50 - enum entry in org.veupathdb.lib.blast.tblastx.fields.ScoringMatrixTXType

 

Blosum62 - enum entry in org.veupathdb.lib.blast.blastp.field.ScoringMatrixPType

 

Blosum62 - enum entry in org.veupathdb.lib.blast.blastx.field.ScoringMatrixXType

 

Blosum62 - enum entry in org.veupathdb.lib.blast.deltablast.fields.MatrixDeltaType

 

Blosum62 - enum entry in org.veupathdb.lib.blast.psiblast.fields.MatrixPSIType

 

Blosum62 - enum entry in org.veupathdb.lib.blast.tblastn.fields.ScoringMatrixTNType

 

Blosum62 - enum entry in org.veupathdb.lib.blast.tblastx.fields.ScoringMatrixTXType

 

Blosum80 - enum entry in org.veupathdb.lib.blast.blastp.field.ScoringMatrixPType

 

Blosum80 - enum entry in org.veupathdb.lib.blast.blastx.field.ScoringMatrixXType

 

Blosum80 - enum entry in org.veupathdb.lib.blast.deltablast.fields.MatrixDeltaType

 

Blosum80 - enum entry in org.veupathdb.lib.blast.psiblast.fields.MatrixPSIType

 

Blosum80 - enum entry in org.veupathdb.lib.blast.tblastn.fields.ScoringMatrixTNType

 

Blosum80 - enum entry in org.veupathdb.lib.blast.tblastx.fields.ScoringMatrixTXType

 

Blosum90 - enum entry in org.veupathdb.lib.blast.blastp.field.ScoringMatrixPType

 

Blosum90 - enum entry in org.veupathdb.lib.blast.blastx.field.ScoringMatrixXType

 

Blosum90 - enum entry in org.veupathdb.lib.blast.deltablast.fields.MatrixDeltaType

 

Blosum90 - enum entry in org.veupathdb.lib.blast.psiblast.fields.MatrixPSIType

 

Blosum90 - enum entry in org.veupathdb.lib.blast.tblastn.fields.ScoringMatrixTNType

 

Blosum90 - enum entry in org.veupathdb.lib.blast.tblastx.fields.ScoringMatrixTXType

 

Both - enum entry in org.veupathdb.lib.blast.common.fields.StrandType

 

ByBitScore - enum entry in org.veupathdb.lib.blast.common.fields.HitSorting

 

ByExpectValue - enum entry in org.veupathdb.lib.blast.common.fields.HitSorting

 

ByHSPExpectValue - enum entry in org.veupathdb.lib.blast.common.fields.HSPSorting

 

ByHSPPercentIdentity - enum entry in org.veupathdb.lib.blast.common.fields.HSPSorting

 

ByHSPQueryStart - enum entry in org.veupathdb.lib.blast.common.fields.HSPSorting

 

ByHSPScore - enum entry in org.veupathdb.lib.blast.common.fields.HSPSorting

 

ByHSPSubjectStart - enum entry in org.veupathdb.lib.blast.common.fields.HSPSorting

 

ByPercentIdentity - enum entry in org.veupathdb.lib.blast.common.fields.HitSorting

 

ByQueryCoverage - enum entry in org.veupathdb.lib.blast.common.fields.HitSorting

 

ByTotalScore - enum entry in org.veupathdb.lib.blast.common.fields.HitSorting

 

A  B  C  D  E  F  G  H  I  L  M  N  O  P  Q  R  S  T  U  V  W  Y