O-index

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O

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

Creates a new BlastCLI instance of one of the following types from the given input JSON:

This method is intended to be used to construct a BLAST+ configuration instance from a JSON value where the type of the config is not known beforehand.

of(Integer,Integer,Integer) - function in org.veupathdb.lib.blast.blastn.fields.Dust.Companion

Returns a value based Dust value wrapping the given inputs.

of(Integer,Double,Double) - function in org.veupathdb.lib.blast.blastp.field.SegP.Companion

of(Integer,Double,Double) - function in org.veupathdb.lib.blast.blastx.field.SegX.Companion

of(Integer,Double,Double) - function in org.veupathdb.lib.blast.deltablast.fields.SegDelta.Companion

of(Integer,Double,Double) - function in org.veupathdb.lib.blast.psiblast.fields.SegPSI.Companion

of(Integer,Double,Double) - function in org.veupathdb.lib.blast.rpsblast.fields.SegRPS.Companion

of(Integer,Double,Double) - function in org.veupathdb.lib.blast.rpstblastn.fields.SegRPSTN.Companion

of(Integer,Double,Double) - function in org.veupathdb.lib.blast.tblastn.fields.SegTN.Companion

of(Integer,Double,Double) - function in org.veupathdb.lib.blast.tblastx.fields.SegTX.Companion

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

-off_diagonal_range <Integer, >=0>Number of off-diagonals to search for the 2nd hit, use 0 to turn offDefault = 0

Optimal - enum entry in org.veupathdb.lib.blast.blastn.fields.TemplateTypeType

org.veupathdb.lib.blast - package org.veupathdb.lib.blast

org.veupathdb.lib.blast.blastn - package org.veupathdb.lib.blast.blastn

org.veupathdb.lib.blast.blastn.fields - package org.veupathdb.lib.blast.blastn.fields

org.veupathdb.lib.blast.blastp - package org.veupathdb.lib.blast.blastp

org.veupathdb.lib.blast.blastp.field - package org.veupathdb.lib.blast.blastp.field

org.veupathdb.lib.blast.blastx - package org.veupathdb.lib.blast.blastx

org.veupathdb.lib.blast.blastx.field - package org.veupathdb.lib.blast.blastx.field

org.veupathdb.lib.blast.common - package org.veupathdb.lib.blast.common

org.veupathdb.lib.blast.common.fields - package org.veupathdb.lib.blast.common.fields

org.veupathdb.lib.blast.deltablast - package org.veupathdb.lib.blast.deltablast

org.veupathdb.lib.blast.deltablast.fields - package org.veupathdb.lib.blast.deltablast.fields

org.veupathdb.lib.blast.err - package org.veupathdb.lib.blast.err

org.veupathdb.lib.blast.formatter - package org.veupathdb.lib.blast.formatter

org.veupathdb.lib.blast.formatter.fields - package org.veupathdb.lib.blast.formatter.fields

org.veupathdb.lib.blast.psiblast - package org.veupathdb.lib.blast.psiblast

org.veupathdb.lib.blast.psiblast.fields - package org.veupathdb.lib.blast.psiblast.fields

org.veupathdb.lib.blast.rpsblast - package org.veupathdb.lib.blast.rpsblast

org.veupathdb.lib.blast.rpsblast.fields - package org.veupathdb.lib.blast.rpsblast.fields

org.veupathdb.lib.blast.rpstblastn - package org.veupathdb.lib.blast.rpstblastn

org.veupathdb.lib.blast.rpstblastn.fields - package org.veupathdb.lib.blast.rpstblastn.fields

org.veupathdb.lib.blast.serial - package org.veupathdb.lib.blast.serial

org.veupathdb.lib.blast.tblastn - package org.veupathdb.lib.blast.tblastn

org.veupathdb.lib.blast.tblastn.fields - package org.veupathdb.lib.blast.tblastn.fields

org.veupathdb.lib.blast.tblastx - package org.veupathdb.lib.blast.tblastx

org.veupathdb.lib.blast.tblastx.fields - package org.veupathdb.lib.blast.tblastx.fields

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

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

-out_ascii_pssm <File_Out>File name to store ASCII version of PSSM

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

-out <File_Out>Output file nameDefault = -

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

-outfmt <String>Alignment view options:

0  = Pairwise
1  = Query-anchored showing identities
2  = Query-anchored no identities
3  = Flat query-anchored showing identities
4  = Flat query-anchored no identities
5  = BLAST XML
6  = Tabular
7  = Tabular with comment lines
8  = Seqalign (Text ASN.1)
9  = Seqalign (Binary ASN.1)
10 = Comma-separated values
11 = BLAST archive (ASN.1)
12 = Seqalign (JSON)
13 = Multiple-file BLAST JSON
14 = Multiple-file BLAST XML2
15 = Single-file BLAST JSON
16 = Single-file BLAST XML2
17 = Sequence Alignment/Map (SAM)
18 = Organism Report

Options 6, 7, 10 and 17 can be additionally configured to produce a custom format specified by space delimited format specifiers, or in the case of options 6, 7, and 10, by a token specified by the delim keyword.

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

-out_pssm <File_Out>File name to store checkpoint file

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