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C

Coding - enum entry in org.veupathdb.lib.blast.blastn.fields.TemplateTypeType
 
CodingAndOptimal - enum entry in org.veupathdb.lib.blast.blastn.fields.TemplateTypeType
 
CommaSeparatedValues - enum entry in org.veupathdb.lib.blast.common.fields.FormatType
 
CompBasedStats - enum entry in org.veupathdb.lib.blast.deltablast.fields.CompBasedStatsDeltaValue
 
CompBasedStats - enum entry in org.veupathdb.lib.blast.rpsblast.fields.CompBasedStatsRPSValue
 
CompBasedStats - enum entry in org.veupathdb.lib.blast.rpstblastn.fields.CompBasedStatsRPSTNValue
 
CompBasedStatsDelta - class in org.veupathdb.lib.blast.deltablast.fields
-comp_based_stats <String>Use composition-based statistics:

  • D or d: default (equivalent to 1)

  • 0 or F or f: No composition-based statistics

  • 1 or T or t: Composition-based statistics as in NAR 29:2994-3005, 2001

Default = 1
CompBasedStatsDeltaValue - class in org.veupathdb.lib.blast.deltablast.fields
 
CompBasedStatsP - class in org.veupathdb.lib.blast.blastp.field
-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
CompBasedStatsPSI - class in org.veupathdb.lib.blast.psiblast.fields
-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'
CompBasedStatsPSIValue - class in org.veupathdb.lib.blast.psiblast.fields
 
CompBasedStatsPValue - class in org.veupathdb.lib.blast.blastp.field
 
CompBasedStatsRPS - class in org.veupathdb.lib.blast.rpsblast.fields
-comp_based_stats <String>Use composition-based statistics:

  • D or d: default (equivalent to 1)

  • 0 or F or f: Simplified Composition-based statistics as in Bioinformatics 15:1000-1011, 1999

  • 1 or T or t: Composition-based statistics as in NAR 29:2994-3005, 2001

Default = 1
CompBasedStatsRPSTN - class in org.veupathdb.lib.blast.rpstblastn.fields
-comp_based_stats <String>Use composition-based statistics:

  • D or d: default (equivalent to 1)

  • 0 or F or f: No composition-based statistics

  • 1 or T or t: Composition-based statistics as in NAR 29:2994-3005, 2001

Default = 1
CompBasedStatsRPSTNValue - class in org.veupathdb.lib.blast.rpstblastn.fields
 
CompBasedStatsRPSValue - class in org.veupathdb.lib.blast.rpsblast.fields
 
CompBasedStatsTN - class in org.veupathdb.lib.blast.tblastn.fields
-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
CompBasedStatsTNValue - class in org.veupathdb.lib.blast.tblastn.fields
 
CompBasedStatsX - class in org.veupathdb.lib.blast.blastx.field
-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
CompBasedStatsXValue - class in org.veupathdb.lib.blast.blastx.field
 
ConditionalScoreAdjustment - enum entry in org.veupathdb.lib.blast.blastp.field.CompBasedStatsPValue
 
ConditionalScoreAdjustment - enum entry in org.veupathdb.lib.blast.blastx.field.CompBasedStatsXValue
 
ConditionalScoreAdjustment - enum entry in org.veupathdb.lib.blast.psiblast.fields.CompBasedStatsPSIValue
 
ConditionalScoreAdjustment - enum entry in org.veupathdb.lib.blast.tblastn.fields.CompBasedStatsTNValue
 
CullingLimit - class in org.veupathdb.lib.blast.common.fields
-culling_limit <Integer, >=0>If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit
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