com.hfg.bio.seq.alignment.blast

Class BLAST_Settings

java.lang.Object

com.hfg.setting.Settings

com.hfg.bio.seq.alignment.blast.BLAST_Settings

All Implemented Interfaces:

java.lang.Cloneable

public class BLAST_Settings
extends Settings
implements java.lang.Cloneable

Settings used for BLAST search execution.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	BLAST_DATABASE
static java.lang.String	BLAST_PROGRAM
static java.lang.String	COMMAND_LINE_PARAMS
static java.lang.String	EVALUE
static java.lang.String	EXECUTABLE_DIR
static java.lang.String	HTML
static java.lang.String	NUM_ALIGNMENTS
static java.lang.String	NUM_DESCRIPTIONS
static java.lang.String	NUM_THREADS
static java.lang.String	OUTPUT_FILENAME
static java.lang.String	SOFT_MASKING
static java.lang.String	WORD_SIZE

Constructor Summary

Constructors

Constructor and Description
BLAST_Settings()
BLAST_Settings(XMLTag inXMLTag)

Method Summary

Modifier and Type	Method and Description
BLAST_Settings	addBLAST_Database(BLAST_Database inValue)
java.util.List<BLAST_Database>	getBLAST_Databases()
BLAST_Program	getBLAST_Program()
java.lang.String	getCommandLineParams()
java.lang.Float	getEValue()
java.io.File	getExecutableDir()
java.lang.Integer	getNumAlignments()
java.lang.Integer	getNumDescriptions()
java.lang.Integer	getNumThreads()
java.io.File	getOutputFile()
java.lang.Boolean	getSoftMasking()
java.lang.Integer	getWordSize()
java.lang.Boolean	htmlOutput()
protected void	init() For subclasses to override.
BLAST_Settings	setBLAST_Databases(java.util.Collection<BLAST_Database> inValues)
BLAST_Settings	setBLAST_Program(BLAST_Program inValue)
BLAST_Settings	setCommandLineParams(java.lang.String inValue) Additional (optional) command line parameters for the end of the BLAST command
BLAST_Settings	setEValue(java.lang.Float inValue) Expect value (E) for saving hits.
BLAST_Settings	setExecutableDir(java.io.File inValue)
BLAST_Settings	setHTMLOutput(java.lang.Boolean inValue) Produce HTML output.
BLAST_Settings	setNumAlignments(java.lang.Integer inValue) Show alignments for this number of database sequences.
BLAST_Settings	setNumDescriptions(java.lang.Integer inValue) Show one-line descriptions for this number of database sequences.
BLAST_Settings	setNumThreads(java.lang.Integer inValue) Number of threads (CPUs) to use in the BLAST search.
BLAST_Settings	setOutputFile(java.io.File inValue)
BLAST_Settings	setSoftMasking(java.lang.Boolean inValue) Apply filtering locations as soft masks.
BLAST_Settings	setWordSize(java.lang.Integer inValue) From the BLAST documentation: "BLAST is a heuristic that works by finding word-matches between the query and database sequences.

Methods inherited from class com.hfg.setting.Settings

add, clone, get, name, setName, setTagName, size, toXMLTag

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

EXECUTABLE_DIR

public static final java.lang.String EXECUTABLE_DIR

See Also:

Constant Field Values

BLAST_PROGRAM

public static final java.lang.String BLAST_PROGRAM

See Also:

Constant Field Values

BLAST_DATABASE

public static final java.lang.String BLAST_DATABASE

See Also:

Constant Field Values

OUTPUT_FILENAME

public static final java.lang.String OUTPUT_FILENAME

See Also:

Constant Field Values

NUM_DESCRIPTIONS

public static final java.lang.String NUM_DESCRIPTIONS

See Also:

Constant Field Values

NUM_ALIGNMENTS

public static final java.lang.String NUM_ALIGNMENTS

See Also:

Constant Field Values

NUM_THREADS

public static final java.lang.String NUM_THREADS

See Also:

Constant Field Values

EVALUE

public static final java.lang.String EVALUE

See Also:

Constant Field Values

HTML

public static final java.lang.String HTML

See Also:

Constant Field Values

WORD_SIZE

public static final java.lang.String WORD_SIZE

See Also:

Constant Field Values

SOFT_MASKING

public static final java.lang.String SOFT_MASKING

See Also:

Constant Field Values

COMMAND_LINE_PARAMS

public static final java.lang.String COMMAND_LINE_PARAMS

See Also:

Constant Field Values

Constructor Detail

BLAST_Settings

public BLAST_Settings()

BLAST_Settings

public BLAST_Settings(XMLTag inXMLTag)

Method Detail

init

protected void init()

Description copied from class: Settings

For subclasses to override.

Overrides:

init in class Settings

getExecutableDir

public java.io.File getExecutableDir()

setExecutableDir

public BLAST_Settings setExecutableDir(java.io.File inValue)

getBLAST_Program

public BLAST_Program getBLAST_Program()

setBLAST_Program

public BLAST_Settings setBLAST_Program(BLAST_Program inValue)

getBLAST_Databases

public java.util.List<BLAST_Database> getBLAST_Databases()

addBLAST_Database

public BLAST_Settings addBLAST_Database(BLAST_Database inValue)

setBLAST_Databases

public BLAST_Settings setBLAST_Databases(java.util.Collection<BLAST_Database> inValues)

getOutputFile

public java.io.File getOutputFile()

setOutputFile

public BLAST_Settings setOutputFile(java.io.File inValue)

getNumDescriptions

public java.lang.Integer getNumDescriptions()

setNumDescriptions

public BLAST_Settings setNumDescriptions(java.lang.Integer inValue)

Show one-line descriptions for this number of database sequences.

Parameters:

inValue - the number of description lines

Returns:

this Settings object to enable chaining

getNumAlignments

public java.lang.Integer getNumAlignments()

setNumAlignments

public BLAST_Settings setNumAlignments(java.lang.Integer inValue)

Show alignments for this number of database sequences.

Parameters:

inValue - the number of alignments to show

Returns:

this Settings object to enable chaining

getWordSize

public java.lang.Integer getWordSize()

setWordSize

public BLAST_Settings setWordSize(java.lang.Integer inValue)

From the BLAST documentation:
"BLAST is a heuristic that works by finding word-matches between the query and database sequences. One may think of this process as finding "hot-spots" that BLAST can then use to initiate extensions that might eventually lead to full-blown alignments. For nucleotide-nucleotide searches (i.e., "blastn") an exact match of the entire word is required before an extension is initiated, so that one normally regulates the sensitivity and speed of the search by increasing or decreasing the word-size. For other BLAST searches non-exact word matches are taken into account based upon the similarity between words."

Parameters:

inValue - the word size to use

Returns:

this Settings object to enable chaining

getNumThreads

public java.lang.Integer getNumThreads()

setNumThreads

public BLAST_Settings setNumThreads(java.lang.Integer inValue)

Number of threads (CPUs) to use in the BLAST search.

Parameters:

inValue - the number of threads

Returns:

this Settings object to enable chaining

getEValue

public java.lang.Float getEValue()

setEValue

public BLAST_Settings setEValue(java.lang.Float inValue)

Expect value (E) for saving hits.

Parameters:

inValue - the e-value threshold

Returns:

this Settings object to enable chaining

htmlOutput

public java.lang.Boolean htmlOutput()

setHTMLOutput

public BLAST_Settings setHTMLOutput(java.lang.Boolean inValue)

Produce HTML output.

Parameters:

inValue - whether to produce HTML output or not

Returns:

this Settings object to enable chaining

getSoftMasking

public java.lang.Boolean getSoftMasking()

setSoftMasking

public BLAST_Settings setSoftMasking(java.lang.Boolean inValue)

Apply filtering locations as soft masks.

Parameters:

inValue - whether to apply filtering locations as soft masks or not

Returns:

this Settings object to enable chaining

getCommandLineParams

public java.lang.String getCommandLineParams()

setCommandLineParams

public BLAST_Settings setCommandLineParams(java.lang.String inValue)

Additional (optional) command line parameters for the end of the BLAST command

Parameters:

inValue - the additional command line parameters to be appended to the end of the command

Returns:

this Settings object to enable chaining