Uses of Class
com.hfg.bio.seq.alignment.blast.BLAST_Settings

Packages that use BLAST_Settings

Package	Description
com.hfg.bio.seq.alignment.blast

Uses of BLAST_Settings in com.hfg.bio.seq.alignment.blast

Methods in com.hfg.bio.seq.alignment.blast that return BLAST_Settings

Modifier and Type	Method and Description
BLAST_Settings	BLAST_Settings.addBLAST_Database(BLAST_Database inValue)
static BLAST_Settings	BLAST.getDefaultSettings()
BLAST_Settings	BLAST.getSettings()
BLAST_Settings	BLAST_Settings.setBLAST_Databases(Collection<BLAST_Database> inValues)
BLAST_Settings	BLAST_Settings.setBLAST_Program(BLAST_Program inValue)
BLAST_Settings	BLAST_Settings.setCommandLineParams(String inValue) Additional (optional) command line parameters for the end of the BLAST command
BLAST_Settings	BLAST_Settings.setEValue(Float inValue) Expect value (E) for saving hits.
BLAST_Settings	BLAST_Settings.setExecutableDir(File inValue)
BLAST_Settings	BLAST_Settings.setHTMLOutput(Boolean inValue) Produce HTML output.
BLAST_Settings	BLAST_Settings.setNumAlignments(Integer inValue) Show alignments for this number of database sequences.
BLAST_Settings	BLAST_Settings.setNumDescriptions(Integer inValue) Show one-line descriptions for this number of database sequences.
BLAST_Settings	BLAST_Settings.setNumThreads(Integer inValue) Number of threads (CPUs) to use in the BLAST search.
BLAST_Settings	BLAST_Settings.setOutputFile(File inValue)
BLAST_Settings	BLAST_Settings.setSoftMasking(Boolean inValue) Apply filtering locations as soft masks.
BLAST_Settings	BLAST_Settings.setWordSize(Integer inValue) From the BLAST documentation: "BLAST is a heuristic that works by finding word-matches between the query and database sequences.

Methods in com.hfg.bio.seq.alignment.blast with parameters of type BLAST_Settings

Modifier and Type	Method and Description
static void	BLAST.setDefaultSettings(BLAST_Settings inValue)

Constructors in com.hfg.bio.seq.alignment.blast with parameters of type BLAST_Settings

Constructor and Description
BLAST(BLAST_Settings inSettings)