Index (biojava-ws 7.2.0 API)

A B C D E F G H I L M N O P Q R S T V W X
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

ALIGNMENT_VIEW - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
ALIGNMENTS - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
ALIGNMENTS - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

B

BLAST_PROGRAM - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
BlastAlignmentParameterEnum - Enum Class in org.biojava.nbio.ws.alignment.qblast: Alignment request parameters accepted by QBlast service.
Not all are mandatory.
BlastJob - Class in org.biojava.nbio.ws.alignment.qblast: Information about QBlast search job
BlastJob() - Constructor for class org.biojava.nbio.ws.alignment.qblast.BlastJob
BlastMatrixEnum - Enum Class in org.biojava.nbio.ws.alignment.qblast: Enum representing matrices supported by QBlast
blastn - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
BlastOutputAlignmentFormatEnum - Enum Class in org.biojava.nbio.ws.alignment.qblast: Enum representing available output alignment types.
BlastOutputFormatEnum - Enum Class in org.biojava.nbio.ws.alignment.qblast: Enum representing available output formats.
BlastOutputParameterEnum - Enum Class in org.biojava.nbio.ws.alignment.qblast: Output parameters accepted by QBlast service.
blastp - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
BlastProgramEnum - Enum Class in org.biojava.nbio.ws.alignment.qblast: Enum representing available blast programs.
blastx - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
BLOSUM45 - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
BLOSUM50 - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
BLOSUM62 - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
BLOSUM80 - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
BLOSUM90 - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum

C

CDD_SEARCH - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
CMD - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
compareTo(HmmerDomain) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
compareTo(HmmerResult) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
COMPOSITION_BASED_STATISTICS - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

D

DATABASE - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
DATABASE_PREFIX - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
DATABASE_SORT - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
DB_GENETIC_CODE - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
demo - package demo
DESCRIPTIONS - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
DESCRIPTIONS - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
DISPLAY_SORT - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

E

EMAIL - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
ENTREZ_QUERY - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
EXPECT - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
EXPECT_HIGH - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
EXPECT_LOW - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

F

FILTER - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
FIRST_QUERY_NUM - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
FlatQueryAnchored - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
FlatQueryAnchoredNoIdentities - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
FORMAT_ENTREZ_QUERY - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
FORMAT_OBJECT - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
FORMAT_TYPE - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

G

GAPCOSTS - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
GENETIC_CODE - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
getAcc() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
getAlignmentNumber() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
getAlignmentOption(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: This method forwards to NCBIQBlastAlignmentProperties.getAlignmentOption(BlastAlignmentParameterEnum).
getAlignmentOption(String) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentProperties: Method that returns the value associated with the key given in parameter.
getAlignmentOption(BlastAlignmentParameterEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: Gets the value of specified parameter or null if it is not set.
getAlignmentOptions() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: Gets parameters, which are currently set
getAlignmentOptions() - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentProperties: Method to get all keys to the information stored in this object.
getAlignmentOutputFormat() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
getAlignmentResults(String, RemotePairwiseAlignmentOutputProperties) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService: Extracts the actual Blast report for given request id according to options provided in outputProperties argument.
getAlignmentResults(String, RemotePairwiseAlignmentOutputProperties) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentService: Getting the actual alignment results from this instantiated service for a given ID with specific formatting parameters held in a RemotePairwiseAlignmentOutputProperties-implemented object.
getAliLenth() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
getBlastAdvancedOptions() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
getBlastDatabase() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
getBlastExpect() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
getBlastFromPosition() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
getBlastGapCosts() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: Returns the actual string for the GAPCOSTS parameter which is used to build the URL
getBlastGapCreation() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: Returns the value for the GAP_CREATION parameter (first half of GAPCOSTS parameter)
getBlastGapExtension() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: Returns the value for the gap extension parameter (second half of GAPCOSTS parameter)
getBlastMatrix() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: Returns the value of the specified substitution matrix
getBlastProgram() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
getBlastToPosition() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
getBlastWordSize() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: Returns the value of the WORD_SIZE parameter used for this blast run
getDcl() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
getDesc() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
getDescriptionNumber() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
getDomains() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
getEmail() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService: Get the email for QBlast.
getEvalue() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
getEvalue() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
getExpectedExecutionTime() - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob
getHmmAcc() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
getHmmDesc() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
getHmmFrom() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
getHmmName() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
getHmmTo() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
getId() - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob: Request id (RID) as received from QBlast server
getMappingSequence() - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
getName() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
getNdom() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
getNreported() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
getNullValue() - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
getOutputFormat() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties
getOutputOption(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties: This method forwards to NCBIQBlastOutputProperties.getOutputOption(BlastOutputParameterEnum).
getOutputOption(String) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentOutputProperties: Method that returns the value associated with the key given in parameter.
getOutputOption(BlastOutputParameterEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties: Gets the value of specified parameter or null if it is not set
getOutputOptions() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties: Gets output parameters, which are currently set
getOutputOptions() - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentOutputProperties: Method to get all keys to the information stored in this object.
getOverlapLength(HmmerResult) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult: Get the overlap between two HmmerResult objects
getPvalue() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
getRemoteBlastInfo() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService: A simple method to check the availability of the QBlast service.
getScore() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
getSeparatorSequence() - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
getSimCount() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
getSqFrom() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
getSqTo() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
getStartTimestamp() - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob
getTool() - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService: Get the tool identifier for QBlast.

H

HITLIST_SIZE - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
HMMER_SERVICE - Static variable in class org.biojava.nbio.ws.hmmer.RemoteHmmerScan
HmmerDemo - Class in demo: The cookbook recipe for how to request Pfam annotations for a protein sequence using the Hmmer3 service
HmmerDemo() - Constructor for class demo.HmmerDemo
HmmerDomain - Class in org.biojava.nbio.ws.hmmer: Provides the details of a domain hit
HmmerDomain() - Constructor for class org.biojava.nbio.ws.hmmer.HmmerDomain
HmmerResult - Class in org.biojava.nbio.ws.hmmer: The results of a Hmmer search for a single sequence
HmmerResult() - Constructor for class org.biojava.nbio.ws.hmmer.HmmerResult
HmmerScan - Interface in org.biojava.nbio.ws.hmmer: Interface for performing Hmmscans on sequences.
HSP_SORT - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
HTML - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputFormatEnum

I

I_THRESH - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
I_THRESH - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
isReady(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService: Wrapper method for NCBIQBlastService.isReady(String, long), omitting unnecessary present property.
isReady(String, long) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService: Checks for completion of request.
isReady(String, long) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentService: Simple method to check if the specified request has been completed by the service used.

L

LCASE_MASK - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

M

main(String[]) - Static method in class demo.HmmerDemo
main(String[]) - Static method in class demo.NCBIQBlastServiceDemo
MapToStringTransformer - Class in org.biojava.nbio.ws.alignment.qblast: Transforms Map to String.
MapToStringTransformer() - Constructor for class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer: Creates MapToStringTransformer with defaults:
MapToStringTransformer(String, String, String) - Constructor for class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer: Creates MapToStringTransformer with given values
MASK_CHAR - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
MASK_COLOR - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
MATCH_SCORES - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
MATRIX_NAME - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
MAX_NUM_SEQ - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
megablast - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
MEGABLAST - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

N

NCBI_GI - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
NCBIQBlastAlignmentProperties - Class in org.biojava.nbio.ws.alignment.qblast: This class wraps a QBlast search request parameter Map by adding several convenient parameter addition methods.
NCBIQBlastAlignmentProperties() - Constructor for class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties
NCBIQBlastOutputProperties - Class in org.biojava.nbio.ws.alignment.qblast: This class wraps a QBlast output parameter Map by adding several convenient parameter addition methods.
NCBIQBlastOutputProperties() - Constructor for class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties: This constructor builds the parameters for the output of the GET command sent to the QBlast service with default values:
NCBIQBlastService - Class in org.biojava.nbio.ws.alignment.qblast: Provides a simple way of submitting BLAST request to the QBlast service at NCBI.
NCBIQBlastService() - Constructor for class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService: Constructs a service object that targets the public NCBI BLAST network service.
NCBIQBlastService(String) - Constructor for class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService: Constructs a service object which targets a custom NCBI BLAST network service (e.g.: an instance of BLAST in the cloud).
NCBIQBlastServiceDemo - Class in demo: A simple demo showing NCBIQBlastService usage
NCBIQBlastServiceDemo() - Constructor for class demo.NCBIQBlastServiceDemo
NOHEADER - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
NUM_OVERVIEW - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
NUM_OVERVIEW - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

O

org.biojava.nbio.ws.alignment - package org.biojava.nbio.ws.alignment: This package contains the interfaces that need to be implemented by discrete alignment services.
org.biojava.nbio.ws.alignment.qblast - package org.biojava.nbio.ws.alignment.qblast
org.biojava.nbio.ws.hmmer - package org.biojava.nbio.ws.hmmer
OTHER_ADVANCED - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

P

Pairwise - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
PAM250 - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
PAM30 - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
PAM70 - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum
PERC_IDENT - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
PHI_PATTERN - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
PROGRAM - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
PSSM - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

Q

QUERY - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
QUERY_BELIEVE_DEFLINE - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
QUERY_FROM - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
QUERY_TO - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
QueryAnchored - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
QueryAnchoredNoIdentities - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum

R

RemoteHmmerScan - Class in org.biojava.nbio.ws.hmmer: Makes remote calls to the HMMER web service at the EBI web site and returns Pfam domain annotations for an input protein sequence.
RemoteHmmerScan() - Constructor for class org.biojava.nbio.ws.hmmer.RemoteHmmerScan
RemotePairwiseAlignmentOutputProperties - Interface in org.biojava.nbio.ws.alignment: RemotePairwiseAlignmentOutputProperties: the simplest representation of an object capable of holding output formatting informations to be fed to a RemotePairwiseAlignmentService-implemented object.
RemotePairwiseAlignmentProperties - Interface in org.biojava.nbio.ws.alignment: RemotePairwiseAlignmentProperties is a interface that contains the barest of methods for setting and getting Alignment properties.
RemotePairwiseAlignmentService - Interface in org.biojava.nbio.ws.alignment: This interface specifies minimal information needed to execute a pairwise alignment on a remote service.
removeAlignmentOption(BlastAlignmentParameterEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: Removes given parameter
removeOutputOption(BlastOutputParameterEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties: Removes given parameter
REPEATS - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
RID - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

S

scan(ProteinSequence) - Method in interface org.biojava.nbio.ws.hmmer.HmmerScan
scan(ProteinSequence) - Method in class org.biojava.nbio.ws.hmmer.RemoteHmmerScan
scan(ProteinSequence, URL) - Method in class org.biojava.nbio.ws.hmmer.RemoteHmmerScan: Scans a protein sequence for Pfam profile matches.
SEARCHSP_EFF - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
sendAlignmentRequest(int, RemotePairwiseAlignmentProperties) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService: Converts given GenBank GID to String and calls NCBIQBlastService.sendAlignmentRequest(String, RemotePairwiseAlignmentProperties)
sendAlignmentRequest(String, RemotePairwiseAlignmentProperties) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService: Sends the Blast request via the Put command of the CGI-BIN interface.
sendAlignmentRequest(String, RemotePairwiseAlignmentProperties) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentService: Doing the actual analysis on the instantiated service using specified parameters on the string representation of the Sequence object
sendAlignmentRequest(Sequence<Compound>, RemotePairwiseAlignmentProperties) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService: Converts given sequence to String and calls NCBIQBlastService.sendAlignmentRequest(String, RemotePairwiseAlignmentProperties)
sendAlignmentRequest(Sequence<Compound>, RemotePairwiseAlignmentProperties) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentService: Doing the actual analysis on the instantiated service using specified parameters and the RichSequence object
sendDeleteRequest(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService: Sends a delete request for given request id.
serialVersionUID - Static variable in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentOutputProperties
serialVersionUID - Static variable in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentProperties
setAcc(String) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
setAlignementOption(String, String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: This method forwards to NCBIQBlastAlignmentProperties.setAlignmentOption(BlastAlignmentParameterEnum, String).
setAlignementOption(String, String) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentProperties: Method to set the value for a specific alignment parameter using a key to store in a map.
setAlignmentNumber(int) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties: Set the number of alignments to fetch
setAlignmentOption(BlastAlignmentParameterEnum, String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: Sets the value of specified parameter
setAlignmentOutputFormat(BlastOutputAlignmentFormatEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties: Sets the alignment output format to get from the QBlast service
setAliLenth(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
setBlastAdvancedOptions(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: This method is to be used if a request is to use non-default values at submission.
setBlastDatabase(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: Sets the database to be used with blastall
setBlastExpect(double) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: Sets the EXPECT parameter to be use with blastall
setBlastFromToPosition(int, int) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: Sets the QUERY_FROM and QUERY_TO parameters to be use by blast.
setBlastGapCosts(int, int) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: Sets the GAPCOSTS parameter
setBlastMatrix(BlastMatrixEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: Sets the value for the MATRIX parameter to use for blastall
setBlastProgram(BlastProgramEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: Sets the program to be used with blastall
setBlastWordSize(int) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastAlignmentProperties: Sets the WORD_SIZE parameter to be use with blastall
setDcl(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
setDesc(String) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
setDescriptionNumber(int) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties: Sets the number of descriptions to fetch
setDomains(SortedSet<HmmerDomain>) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
setEmail(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService: Set the email for QBlast.
setEvalue(Float) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
setEvalue(Float) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
setExpectedExecutionTime(long) - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob
setHmmAcc(String) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
setHmmDesc(String) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
setHmmFrom(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
setHmmName(String) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
setHmmTo(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
setId(String) - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob
setMappingSequence(String) - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
setName(String) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
setNdom(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
setNreported(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
setNullValue(String) - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
setOutputFormat(BlastOutputFormatEnum) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties: Sets the stream output format to get from the QBlast service
setOutputOption(String, String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties: This method forwards to NCBIQBlastOutputProperties.setOutputOption(BlastOutputParameterEnum, String).
setOutputOption(String, String) - Method in interface org.biojava.nbio.ws.alignment.RemotePairwiseAlignmentOutputProperties: Method to set the value for a specific output parameter using a key to store in a map.
setOutputOption(BlastOutputParameterEnum, String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastOutputProperties: Sets the value of specified output parameter
setPvalue(Double) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
setScore(Float) - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
setSeparatorSequence(String) - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer
setSimCount(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
setSqFrom(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
setSqTo(Integer) - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
setStartTimestamp(long) - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob
setTool(String) - Method in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService: Set the tool identifier for QBlast.
SHORT_QUERY_ADJUST - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
SHOW_CDS_FEATURE - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
SHOW_LINKOUT - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum
SHOW_OVERVIEW - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum

T

Tabular - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum
tblastn - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
tblastx - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum
TEMPLATE_LENTH - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
TEMPLATE_TYPE - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
Text - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputFormatEnum
THRESHOLD - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
TOOL - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
toString() - Method in class org.biojava.nbio.ws.alignment.qblast.BlastJob
toString() - Method in class org.biojava.nbio.ws.hmmer.HmmerDomain
toString() - Method in class org.biojava.nbio.ws.hmmer.HmmerResult
transform(Map<?, ?>) - Method in class org.biojava.nbio.ws.alignment.qblast.MapToStringTransformer: Transforms Map to String, representing every entry as key mappingSequence value , joined by separatorSequence
TWO_HITS - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

V

valueOf(String) - Static method in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputFormatEnum: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum: Returns the enum constant of this class with the specified name.
values() - Static method in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.biojava.nbio.ws.alignment.qblast.BlastMatrixEnum: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputAlignmentFormatEnum: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputFormatEnum: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputParameterEnum: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class org.biojava.nbio.ws.alignment.qblast.BlastProgramEnum: Returns an array containing the constants of this enum class, in the order they are declared.

W

WAIT_INCREMENT - Static variable in class org.biojava.nbio.ws.alignment.qblast.NCBIQBlastService: Number of milliseconds by which expected job execution time is incremented if it is not finished yet.
WORD_SIZE - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum
WWW_BLAST_TYPE - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastAlignmentParameterEnum

X

XML - Enum constant in enum class org.biojava.nbio.ws.alignment.qblast.BlastOutputFormatEnum

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