BLAST_Settings (com.hfg API Documentation)

java.lang.Object
- com.hfg.setting.Settings
- - com.hfg.bio.seq.alignment.blast.BLAST_Settings

All Implemented Interfaces:

Cloneable
```
public class BLAST_Settings
extends Settings
implements Cloneable
```
Settings used for BLAST search execution.

Field Summary

Fields
Modifier and Type	Field and Description
`static String`	`BLAST_DATABASE`
`static String`	`BLAST_PROGRAM`
`static String`	`COMMAND_LINE_PARAMS`
`static String`	`EVALUE`
`static String`	`EXECUTABLE_DIR`
`static String`	`HTML`
`static String`	`NUM_ALIGNMENTS`
`static String`	`NUM_DESCRIPTIONS`
`static String`	`NUM_THREADS`
`static String`	`OUTPUT_FILENAME`
`static String`	`SOFT_MASKING`
`static String`	`WORD_SIZE`

Constructor Summary

Constructors
Constructor and Description

BLAST_Settings()

BLAST_Settings(XMLTag inXMLTag)

Constructors
Constructor and Description
`BLAST_Settings()`
`BLAST_Settings(XMLTag inXMLTag)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`BLAST_Settings`	`addBLAST_Database(BLAST_Database inValue)`
`List<BLAST_Database>`	`getBLAST_Databases()`
`BLAST_Program`	`getBLAST_Program()`
`String`	`getCommandLineParams()`
`Float`	`getEValue()`
`File`	`getExecutableDir()`
`Integer`	`getNumAlignments()`
`Integer`	`getNumDescriptions()`
`Integer`	`getNumThreads()`
`File`	`getOutputFile()`
`Boolean`	`getSoftMasking()`
`Integer`	`getWordSize()`
`Boolean`	`htmlOutput()`
`protected void`	`init()` For subclasses to override.
`BLAST_Settings`	`setBLAST_Databases(Collection<BLAST_Database> inValues)`
`BLAST_Settings`	`setBLAST_Program(BLAST_Program inValue)`
`BLAST_Settings`	`setCommandLineParams(String inValue)` Additional (optional) command line parameters for the end of the BLAST command
`BLAST_Settings`	`setEValue(Float inValue)` Expect value (E) for saving hits.
`BLAST_Settings`	`setExecutableDir(File inValue)`
`BLAST_Settings`	`setHTMLOutput(Boolean inValue)` Produce HTML output.
`BLAST_Settings`	`setNumAlignments(Integer inValue)` Show alignments for this number of database sequences.
`BLAST_Settings`	`setNumDescriptions(Integer inValue)` Show one-line descriptions for this number of database sequences.
`BLAST_Settings`	`setNumThreads(Integer inValue)` Number of threads (CPUs) to use in the BLAST search.
`BLAST_Settings`	`setOutputFile(File inValue)`
`BLAST_Settings`	`setSoftMasking(Boolean inValue)` Apply filtering locations as soft masks.
`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 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 String EXECUTABLE_DIR
```
    See Also:
    
    Constant Field Values
  - BLAST_PROGRAM
```
public static final String BLAST_PROGRAM
```
    See Also:
    
    Constant Field Values
  - BLAST_DATABASE
```
public static final String BLAST_DATABASE
```
    See Also:
    
    Constant Field Values
  - OUTPUT_FILENAME
```
public static final String OUTPUT_FILENAME
```
    See Also:
    
    Constant Field Values
  - NUM_DESCRIPTIONS
```
public static final String NUM_DESCRIPTIONS
```
    See Also:
    
    Constant Field Values
  - NUM_ALIGNMENTS
```
public static final String NUM_ALIGNMENTS
```
    See Also:
    
    Constant Field Values
  - NUM_THREADS
```
public static final String NUM_THREADS
```
    See Also:
    
    Constant Field Values
  - EVALUE
```
public static final String EVALUE
```
    See Also:
    
    Constant Field Values
  - HTML
```
public static final String HTML
```
    See Also:
    
    Constant Field Values
  - WORD_SIZE
```
public static final String WORD_SIZE
```
    See Also:
    
    Constant Field Values
  - SOFT_MASKING
```
public static final String SOFT_MASKING
```
    See Also:
    
    Constant Field Values
  - COMMAND_LINE_PARAMS
```
public static final 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 File getExecutableDir()
```
  - setExecutableDir
```
public BLAST_Settings setExecutableDir(File inValue)
```
  - getBLAST_Program
```
public BLAST_Program getBLAST_Program()
```
  - setBLAST_Program
```
public BLAST_Settings setBLAST_Program(BLAST_Program inValue)
```
  - getBLAST_Databases
```
public List<BLAST_Database> getBLAST_Databases()
```
  - addBLAST_Database
```
public BLAST_Settings addBLAST_Database(BLAST_Database inValue)
```
  - setBLAST_Databases
```
public BLAST_Settings setBLAST_Databases(Collection<BLAST_Database> inValues)
```
  - getOutputFile
```
public File getOutputFile()
```
  - setOutputFile
```
public BLAST_Settings setOutputFile(File inValue)
```
  - getNumDescriptions
```
public Integer getNumDescriptions()
```
  - setNumDescriptions
```
public BLAST_Settings setNumDescriptions(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 Integer getNumAlignments()
```
  - setNumAlignments
```
public BLAST_Settings setNumAlignments(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 Integer getWordSize()
```
  - setWordSize
```
public 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. 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 Integer getNumThreads()
```
  - setNumThreads
```
public BLAST_Settings setNumThreads(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 Float getEValue()
```
  - setEValue
```
public BLAST_Settings setEValue(Float inValue)
```
    Expect value (E) for saving hits.
    
    Parameters:
    
    inValue - the e-value threshold
    
    Returns:
    
    this Settings object to enable chaining
  - htmlOutput
```
public Boolean htmlOutput()
```
  - setHTMLOutput
```
public BLAST_Settings setHTMLOutput(Boolean inValue)
```
    Produce HTML output.
    
    Parameters:
    
    inValue - whether to produce HTML output or not
    
    Returns:
    
    this Settings object to enable chaining
  - getSoftMasking
```
public Boolean getSoftMasking()
```
  - setSoftMasking
```
public BLAST_Settings setSoftMasking(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 String getCommandLineParams()
```
  - setCommandLineParams
```
public BLAST_Settings setCommandLineParams(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

Class BLAST_Settings

Field Summary

Constructor Summary

Method Summary

Methods inherited from class com.hfg.setting.Settings

Methods inherited from class java.lang.Object

Field Detail

EXECUTABLE_DIR

BLAST_PROGRAM

BLAST_DATABASE

OUTPUT_FILENAME

NUM_DESCRIPTIONS

NUM_ALIGNMENTS

NUM_THREADS

EVALUE

HTML

WORD_SIZE

SOFT_MASKING

COMMAND_LINE_PARAMS

Constructor Detail

BLAST_Settings

BLAST_Settings

Method Detail

init

getExecutableDir

setExecutableDir

getBLAST_Program

setBLAST_Program

getBLAST_Databases

addBLAST_Database

setBLAST_Databases

getOutputFile

setOutputFile

getNumDescriptions

setNumDescriptions

getNumAlignments

setNumAlignments

getWordSize

setWordSize

getNumThreads

setNumThreads

getEValue

setEValue

htmlOutput

setHTMLOutput

getSoftMasking

setSoftMasking

getCommandLineParams

setCommandLineParams