org.biojava.nbio.ws.alignment.qblast

Enum BlastAlignmentParameterEnum

java.lang.Object

java.lang.Enum<BlastAlignmentParameterEnum>

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

All Implemented Interfaces:

Serializable, Comparable<BlastAlignmentParameterEnum>

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

Enum Constant Summary

Enum Constants

Enum Constant and 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 and Description
static BlastAlignmentParameterEnum	valueOf(String name) Returns the enum constant of this type with the specified name.
static BlastAlignmentParameterEnum[]	values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

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 Detail

values

public static BlastAlignmentParameterEnum[] values()

Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:

for (BlastAlignmentParameterEnum c : BlastAlignmentParameterEnum.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static BlastAlignmentParameterEnum valueOf(String name)

Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (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 type has no constant with the specified name

NullPointerException - if the argument is null