java.lang.Object

java.lang.Enum<BlastAlignmentParameterEnum>

org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

All Implemented Interfaces:: Serializable, Comparable<BlastAlignmentParameterEnum>, Constable

public enum BlastAlignmentParameterEnum extends Enum<BlastAlignmentParameterEnum>

Alignment request parameters accepted by QBlast service.
Not all are mandatory. Certain parameters only work with a subset of other parameters in the list.

Taken from Blast URL API

Author:: Gediminas Rimsa

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Enum
Enum.EnumDesc<E extends Enum<E>>
Enum Constant Summary

Enum Constants

Enum Constant

Description

ALIGNMENTS

BLAST_PROGRAM

CDD_SEARCH

CMD

COMPOSITION_BASED_STATISTICS

DATABASE

DATABASE_PREFIX

DB_GENETIC_CODE

DESCRIPTIONS

EMAIL

ENTREZ_QUERY

EXPECT

FILTER

FIRST_QUERY_NUM

GAPCOSTS

GENETIC_CODE

HITLIST_SIZE

I_THRESH

LCASE_MASK

MATCH_SCORES

MATRIX_NAME

MAX_NUM_SEQ

MEGABLAST

NUM_OVERVIEW

OTHER_ADVANCED

PERC_IDENT

PHI_PATTERN

PROGRAM

PSSM

QUERY

QUERY_BELIEVE_DEFLINE

QUERY_FROM

QUERY_TO

REPEATS

SEARCHSP_EFF

SHORT_QUERY_ADJUST

TEMPLATE_LENTH

TEMPLATE_TYPE

THRESHOLD

TOOL

TWO_HITS

WORD_SIZE

WWW_BLAST_TYPE
Method Summary

Modifier and Type

Method

Description

static BlastAlignmentParameterEnum

valueOf(String name)

Returns the enum constant of this class with the specified name.

static BlastAlignmentParameterEnum[]

values()

Returns an array containing the constants of this enum class, in the order they are declared.

Methods inherited from class java.lang.Enum
clone, compareTo, describeConstable, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait

Enum Constant Details
- CMD
  
  public static final BlastAlignmentParameterEnum CMD
- TOOL
  
  public static final BlastAlignmentParameterEnum TOOL
- EMAIL
  
  public static final BlastAlignmentParameterEnum EMAIL
- ALIGNMENTS
  
  public static final BlastAlignmentParameterEnum ALIGNMENTS
- BLAST_PROGRAM
  
  public static final BlastAlignmentParameterEnum BLAST_PROGRAM
- CDD_SEARCH
  
  public static final BlastAlignmentParameterEnum CDD_SEARCH
- COMPOSITION_BASED_STATISTICS
  
  public static final BlastAlignmentParameterEnum COMPOSITION_BASED_STATISTICS
- DATABASE_PREFIX
  
  public static final BlastAlignmentParameterEnum DATABASE_PREFIX
- DATABASE
  
  public static final BlastAlignmentParameterEnum DATABASE
- DB_GENETIC_CODE
  
  public static final BlastAlignmentParameterEnum DB_GENETIC_CODE
- DESCRIPTIONS
  
  public static final BlastAlignmentParameterEnum DESCRIPTIONS
- ENTREZ_QUERY
  
  public static final BlastAlignmentParameterEnum ENTREZ_QUERY
- EXPECT
  
  public static final BlastAlignmentParameterEnum EXPECT
- FILTER
  
  public static final BlastAlignmentParameterEnum FILTER
- FIRST_QUERY_NUM
  
  public static final BlastAlignmentParameterEnum FIRST_QUERY_NUM
- GAPCOSTS
  
  public static final BlastAlignmentParameterEnum GAPCOSTS
- GENETIC_CODE
  
  public static final BlastAlignmentParameterEnum GENETIC_CODE
- HITLIST_SIZE
  
  public static final BlastAlignmentParameterEnum HITLIST_SIZE
- I_THRESH
  
  public static final BlastAlignmentParameterEnum I_THRESH
- LCASE_MASK
  
  public static final BlastAlignmentParameterEnum LCASE_MASK
- MATCH_SCORES
  
  public static final BlastAlignmentParameterEnum MATCH_SCORES
- MATRIX_NAME
  
  public static final BlastAlignmentParameterEnum MATRIX_NAME
- MAX_NUM_SEQ
  
  public static final BlastAlignmentParameterEnum MAX_NUM_SEQ
- MEGABLAST
  
  public static final BlastAlignmentParameterEnum MEGABLAST
- NUM_OVERVIEW
  
  public static final BlastAlignmentParameterEnum NUM_OVERVIEW
- OTHER_ADVANCED
  
  public static final BlastAlignmentParameterEnum OTHER_ADVANCED
- PERC_IDENT
  
  public static final BlastAlignmentParameterEnum PERC_IDENT
- PHI_PATTERN
  
  public static final BlastAlignmentParameterEnum PHI_PATTERN
- PROGRAM
  
  public static final BlastAlignmentParameterEnum PROGRAM
- PSSM
  
  public static final BlastAlignmentParameterEnum PSSM
- QUERY
  
  public static final BlastAlignmentParameterEnum QUERY
- QUERY_BELIEVE_DEFLINE
  
  public static final BlastAlignmentParameterEnum QUERY_BELIEVE_DEFLINE
- QUERY_FROM
  
  public static final BlastAlignmentParameterEnum QUERY_FROM
- QUERY_TO
  
  public static final BlastAlignmentParameterEnum QUERY_TO
- REPEATS
  
  public static final BlastAlignmentParameterEnum REPEATS
- SHORT_QUERY_ADJUST
  
  public static final BlastAlignmentParameterEnum SHORT_QUERY_ADJUST
- SEARCHSP_EFF
  
  public static final BlastAlignmentParameterEnum SEARCHSP_EFF
- TEMPLATE_LENTH
  
  public static final BlastAlignmentParameterEnum TEMPLATE_LENTH
- TEMPLATE_TYPE
  
  public static final BlastAlignmentParameterEnum TEMPLATE_TYPE
- THRESHOLD
  
  public static final BlastAlignmentParameterEnum THRESHOLD
- TWO_HITS
  
  public static final BlastAlignmentParameterEnum TWO_HITS
- WORD_SIZE
  
  public static final BlastAlignmentParameterEnum WORD_SIZE
- WWW_BLAST_TYPE
  
  public static final BlastAlignmentParameterEnum WWW_BLAST_TYPE
Method Details
- values
  
  public static BlastAlignmentParameterEnum[] values()
  
  Returns an array containing the constants of this enum class, in the order they are declared.
  
  Returns:
  
  an array containing the constants of this enum class, in the order they are declared
- valueOf
  
  public static BlastAlignmentParameterEnum valueOf(String name)
  
  Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (Extraneous whitespace characters are not permitted.)
  
  Parameters:
  
  name - the name of the enum constant to be returned.
  
  Returns:
  
  the enum constant with the specified name
  
  Throws:
  
  IllegalArgumentException - if this enum class has no constant with the specified name
  
  NullPointerException - if the argument is null

Enum Class BlastAlignmentParameterEnum

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Enum

Enum Constant Summary

Method Summary

Methods inherited from class java.lang.Enum

Methods inherited from class java.lang.Object

Enum Constant Details

CMD

TOOL

EMAIL

ALIGNMENTS

BLAST_PROGRAM

CDD_SEARCH

COMPOSITION_BASED_STATISTICS

DATABASE_PREFIX

DATABASE

DB_GENETIC_CODE

DESCRIPTIONS

ENTREZ_QUERY

EXPECT

FILTER

FIRST_QUERY_NUM

GAPCOSTS

GENETIC_CODE

HITLIST_SIZE

I_THRESH

LCASE_MASK

MATCH_SCORES

MATRIX_NAME

MAX_NUM_SEQ

MEGABLAST

NUM_OVERVIEW

OTHER_ADVANCED

PERC_IDENT

PHI_PATTERN

PROGRAM

PSSM

QUERY

QUERY_BELIEVE_DEFLINE

QUERY_FROM

QUERY_TO

REPEATS

SHORT_QUERY_ADJUST

SEARCHSP_EFF

TEMPLATE_LENTH

TEMPLATE_TYPE

THRESHOLD

TWO_HITS

WORD_SIZE

WWW_BLAST_TYPE

Method Details

values

valueOf