Package org.veupathdb.lib.blast.psiblast.fields

Class Summary
Class	Description
CompBasedStatsPSI	-comp_based_stats `<String>`Use composition-based statistics: `D` or `d`: default (equivalent to 2) `0` or `F` or `f`: No composition-based statistics `1`: Composition-based statistics as in NAR 29:2994-3005, 2001 `2` or `T` or `t` : Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties `3`: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally Default = `2'
IgnoreMSAMaster	-ignore_msa_masterIgnore the master sequence when creating PSSMRequires: -in_msa
InMSAFile	-in_msa `<File_In>`File name of multiple sequence alignment to restart PSI-BLAST
MSAMasterIndex	-msa_master_idx `<Integer, >=1>`Ordinal number (1-based index) of the sequence to use as a master in the multiple sequence alignment.
MatrixPSI	-matrix `<String>`Scoring matrix name (normally BLOSUM62)
PHIPatternFile	-phi_pattern `<File_In>`File name containing pattern to search
SoftMaskingPSI	-soft_masking `<Boolean>`Apply filtering locations as soft masksDefault = `false`
WordSizePSI	-word_size `<Integer, >=2>`Word size for wordfinder algorithm

Enum Summary
Enum	Description
CompBasedStatsPSIValue
MatrixPSIType

Object Summary
Object	Description
Companion

Interface Summary
Interface	Description
SegPSI