NCBIQBlastAlignmentProperties (biojava 5.3.0 API)

java.lang.Object
- org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties

All Implemented Interfaces:

Serializable, RemotePairwiseAlignmentProperties
```
public class NCBIQBlastAlignmentProperties
extends Object
implements RemotePairwiseAlignmentProperties
```
This class wraps a QBlast search request parameter Map by adding several convenient parameter addition methods. Other QBlast URL API parameters should be added using setAlignmentOption(BlastAlignmentParameterEnum, String)
Required parameters are PROGRAM and DATABASE, other parameters are optional

Author:

Sylvain Foisy, Diploide BioIT, Gediminas Rimsa

See Also:

Serialized Form

Constructor Summary

Constructors
Constructor and Description

NCBIQBlastAlignmentProperties()

Constructors
Constructor and Description
`NCBIQBlastAlignmentProperties()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`String`	`getAlignmentOption(BlastAlignmentParameterEnum key)` Gets the value of specified parameter or `null` if it is not set.
`String`	`getAlignmentOption(String key)` This method forwards to `getAlignmentOption(BlastAlignmentParameterEnum)`.
`Set<String>`	`getAlignmentOptions()` Gets parameters, which are currently set
`String`	`getBlastAdvancedOptions()`
`String`	`getBlastDatabase()`
`double`	`getBlastExpect()`
`int`	`getBlastFromPosition()`
`String`	`getBlastGapCosts()` Returns the actual string for the GAPCOSTS parameter which is used to build the URL
`int`	`getBlastGapCreation()` Returns the value for the GAP_CREATION parameter (first half of GAPCOSTS parameter)
`int`	`getBlastGapExtension()` Returns the value for the gap extension parameter (second half of GAPCOSTS parameter)
`String`	`getBlastMatrix()` Returns the value of the specified substitution matrix
`BlastProgramEnum`	`getBlastProgram()`
`int`	`getBlastToPosition()`
`int`	`getBlastWordSize()` Returns the value of the WORD_SIZE parameter used for this blast run
`void`	`removeAlignmentOption(BlastAlignmentParameterEnum key)` Removes given parameter
`void`	`setAlignementOption(String key, String val)` This method forwards to `setAlignmentOption(BlastAlignmentParameterEnum, String)`.
`void`	`setAlignmentOption(BlastAlignmentParameterEnum key, String val)` Sets the value of specified parameter
`void`	`setBlastAdvancedOptions(String advancedOptions)` This method is to be used if a request is to use non-default values at submission.
`void`	`setBlastDatabase(String database)` Sets the database to be used with blastall A list of available databases can be acquired by calling `NCBIQBlastService#printRemoteBlastInfo()` Blastall equivalent: -d
`void`	`setBlastExpect(double expect)` Sets the EXPECT parameter to be use with blastall Example: if you want a EXPECT of 1e-10, pass `Double.parseDouble("1e-10")` as a parameter Blastall equivalent: -e
`void`	`setBlastFromToPosition(int start, int end)` Sets the QUERY_FROM and QUERY_TO parameters to be use by blast.
`void`	`setBlastGapCosts(int gapCreation, int gapExtension)` Sets the GAPCOSTS parameter
`void`	`setBlastMatrix(BlastMatrixEnum matrix)` Sets the value for the MATRIX parameter to use for blastall Blastall equivalent: -M
`void`	`setBlastProgram(BlastProgramEnum program)` Sets the program to be used with blastall
`void`	`setBlastWordSize(int word)` Sets the WORD_SIZE parameter to be use with blastall WARNING!!

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - NCBIQBlastAlignmentProperties
```
public NCBIQBlastAlignmentProperties()
```
- Method Detail
  - getAlignmentOption
```
public String getAlignmentOption(String key)
```
    This method forwards to getAlignmentOption(BlastAlignmentParameterEnum). Consider using it instead.
    
    Specified by:
    
    getAlignmentOption in interface RemotePairwiseAlignmentProperties
    
    Parameters:
    
    key - :a String with the required key for this map.
    
    Returns:
    
    a String with the value associated with this key
  - setAlignementOption
```
public void setAlignementOption(String key,
                                String val)
```
    This method forwards to setAlignmentOption(BlastAlignmentParameterEnum, String). Consider using it instead.
    
    Specified by:
    
    setAlignementOption in interface RemotePairwiseAlignmentProperties
    
    Parameters:
    
    key - :the key use to designate the value to be stored
    
    val - :the actual value matched to key
  - getAlignmentOptions
```
public Set<String> getAlignmentOptions()
```
    Gets parameters, which are currently set
    
    Specified by:
    
    getAlignmentOptions in interface RemotePairwiseAlignmentProperties
    
    Returns:
    
    a Set with all keys held in this instance of the object
  - getAlignmentOption
```
public String getAlignmentOption(BlastAlignmentParameterEnum key)
```
    Gets the value of specified parameter or null if it is not set.
  - setAlignmentOption
```
public void setAlignmentOption(BlastAlignmentParameterEnum key,
                               String val)
```
    Sets the value of specified parameter
  - removeAlignmentOption
```
public void removeAlignmentOption(BlastAlignmentParameterEnum key)
```
    Removes given parameter
  - getBlastProgram
```
public BlastProgramEnum getBlastProgram()
```
    Returns:
    
    BlastProgramEnum used for blast run
  - setBlastProgram
```
public void setBlastProgram(BlastProgramEnum program)
```
    Sets the program to be used with blastall
    
    Parameters:
    
    program - : one of blastall programs
  - getBlastDatabase
```
public String getBlastDatabase()
```
    Returns:
    
    name of database used with blastall
  - setBlastDatabase
```
public void setBlastDatabase(String database)
```
    Sets the database to be used with blastall
    A list of available databases can be acquired by calling NCBIQBlastService#printRemoteBlastInfo()
    Blastall equivalent: -d
    
    Parameters:
    
    db - : a valid name to a NCBI blastable database
  - getBlastExpect
```
public double getBlastExpect()
```
    Returns:
    
    double value of EXPECT parameter used for blast run
  - setBlastExpect
```
public void setBlastExpect(double expect)
```
    Sets the EXPECT parameter to be use with blastall
    Example: if you want a EXPECT of 1e-10, pass Double.parseDouble("1e-10") as a parameter
    Blastall equivalent: -e
    
    Parameters:
    
    expect: - a double value of EXPECT parameter
  - getBlastWordSize
```
public int getBlastWordSize()
```
    Returns the value of the WORD_SIZE parameter used for this blast run
    
    Returns:
    
    int value of WORD_SIZE used by this search
    
    Throws:
    
    IllegalArgumentException - when program type is not set and program type is not supported
  - setBlastWordSize
```
public void setBlastWordSize(int word)
```
    Sets the WORD_SIZE parameter to be use with blastall
    WARNING!! At this point, the method does not verify the validity of your choice; for example, word size of greater than 5 with blastp returns error messages from QBlast. Word size range depends on the algorithm chosen.
    More at https://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/new/node74.html
    Blastall equivalent: -W
    
    Parameters:
    
    word: - an int used to set WORD_SIZE
  - getBlastGapCreation
```
public int getBlastGapCreation()
```
    Returns the value for the GAP_CREATION parameter (first half of GAPCOSTS parameter)
    
    Returns:
    
    an integer value for gap creation used by this search, -1 if not set or not a number
  - getBlastGapExtension
```
public int getBlastGapExtension()
```
    Returns the value for the gap extension parameter (second half of GAPCOSTS parameter)
    
    Returns:
    
    an integer for the value for gap extension used by this search, -1 if not set or not a number
  - getBlastGapCosts
```
public String getBlastGapCosts()
```
    Returns the actual string for the GAPCOSTS parameter which is used to build the URL
    
    Returns:
    
    the string representation of the GAPCOSTS parameter formatted for the URL
  - setBlastGapCosts
```
public void setBlastGapCosts(int gapCreation,
                             int gapExtension)
```
    Sets the GAPCOSTS parameter
    
    Parameters:
    
    gapCreation - integer to use as gap creation value
    
    gapExtension - integer to use as gap extension value
  - getBlastMatrix
```
public String getBlastMatrix()
```
    Returns the value of the specified substitution matrix
    
    Returns:
    
    matrix: the name of the specified substitution matrix
  - setBlastMatrix
```
public void setBlastMatrix(BlastMatrixEnum matrix)
```
    Sets the value for the MATRIX parameter to use for blastall
    Blastall equivalent: -M
    
    Parameters:
    
    matrix - : a String to use as gap creation value
    
    See Also:
    
    BlastMatrixEnum
  - setBlastFromToPosition
```
public void setBlastFromToPosition(int start,
                                   int end)
```
    Sets the QUERY_FROM and QUERY_TO parameters to be use by blast. Do not use if you want to use the whole sequence.
    Blastall equivalent: -L
    
    Parameters:
    
    start - QUERY_FROM parameter
    
    end - QUERY_TO parameter
  - getBlastFromPosition
```
public int getBlastFromPosition()
```
    Returns:
    
    an integer value for the QUERY_FROM parameter
    
    See Also:
    
    setBlastFromToPosition(int, int)
  - getBlastToPosition
```
public int getBlastToPosition()
```
    Returns:
    
    QUERY_TO parameter
    
    See Also:
    
    setBlastFromToPosition(int, int)
  - setBlastAdvancedOptions
```
public void setBlastAdvancedOptions(String advancedOptions)
```
    This method is to be used if a request is to use non-default values at submission. Useful for the following blastall parameters:
    - -r: integer to reward for match. Default = 1
    - -q: negative integer for penalty to allow mismatch. Default = -3
    - -y: dropoff for blast extensions in bits, using default if not specified. Default = 20 for blastn, 7 for all others (except megablast for which it is not applicable).
    - -X: X dropoff value for gapped alignment, in bits. Default = 30 for blastn/megablast, 15 for all others.
    - -Z: final X dropoff value for gapped alignement, in bits. Default = 50 for blastn, 25 for all others (except megablast for which it is not applicable)
    - -P: equals 0 for multiple hits 1-pass, 1 for single hit 1-pass. Does not apply to blastn ou megablast.
    - -A: multiple hits window size. Default = 0 (for single hit algorithm)
    - -I: number of database sequences to save hits for. Default = 500
    - -Y: effective length of the search space. Default = 0 (0 represents using the whole space)
    - -z: a real specifying the effective length of the database to use. Default = 0 (0 represents the real size)
    - -c: an integer representing pseudocount constant for PSI-BLAST. Default = 7
    - -F: any filtering directive
    WARNING!! This method is still very much in flux and might not work as expected...
    
    You have to be aware that at no moment is there any error checking on the use of these parameters by this class.
    Parameters:
    
    advancedOptions - : a String with any number of optional parameters with an associated value.
  - getBlastAdvancedOptions
```
public String getBlastAdvancedOptions()
```
    Returns:
    
    the String with the advanced options

Class NCBIQBlastAlignmentProperties

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

NCBIQBlastAlignmentProperties

Method Detail

getAlignmentOption

setAlignementOption

getAlignmentOptions

getAlignmentOption

setAlignmentOption

removeAlignmentOption

getBlastProgram

setBlastProgram

getBlastDatabase

setBlastDatabase

getBlastExpect

setBlastExpect

getBlastWordSize

setBlastWordSize

getBlastGapCreation

getBlastGapExtension

getBlastGapCosts

setBlastGapCosts

getBlastMatrix

setBlastMatrix

setBlastFromToPosition

getBlastFromPosition

getBlastToPosition

setBlastAdvancedOptions

getBlastAdvancedOptions