org.biojava3.ws.alignment.qblast
Enum BlastAlignmentParameterEnum

java.lang.Object
  extended by java.lang.Enum<BlastAlignmentParameterEnum>
      extended by org.biojava3.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
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
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