+A-Index +

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Findex-files%2Findex-1.html;fp=website%2Ffull_javadoc%2Findex-files%2Findex-1.html;h=f2619ab5d84bbc133de6cd273ac22e6efe0e5117;hb=da8c820a7fb2edecb190589f3dc9c362e57a2f24;hp=0000000000000000000000000000000000000000;hpb=0bbebf27d045b1345bc042bdf24ef2e6808df251;p=jabaws.git diff --git a/website/full_javadoc/index-files/index-1.html b/website/full_javadoc/index-files/index-1.html new file mode 100644 index 0000000..f2619ab --- /dev/null +++ b/website/full_javadoc/index-files/index-1.html @@ -0,0 +1,290 @@ + + + + + + +A-Index + + + + + + + + + + + + +

+ + + + + + + + + + + + + + + +

+ + + + + + + + + + + + +

Overview

Package

Class

Use

Tree

Deprecated

Index

Help

+ +

+ PREV LETTER + NEXT LETTER

+ FRAMES + NO FRAMES + + + + +

+ + + +A B C D E F G H I J K L M N O P R S T U V W _

+A

AA - +Static variable in class compbio.data.sequence.SequenceUtil +: Valid Amino acids +
AACon - Class in compbio.runner.conservation: Command line + + java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out
AACon() - +Constructor for class compbio.runner.conservation.AACon +: +
AACON_INFO - +Static variable in enum compbio.ws.client.Services +: +
AAConClient - Class in compbio.ws.client: A command line client for AACon web service
AAConWS - Class in compbio.ws.server
AAConWS() - +Constructor for class compbio.ws.server.AAConWS +: +
addOption(Option<T>) - +Method in class compbio.metadata.RunnerConfig +: Adds Option to the internal list of options +
addOptionNames(String...) - +Method in class compbio.metadata.Option +: Adds an option to the optionName list +
addOptionNames(String...) - +Method in class compbio.metadata.Parameter +: +
addParameter(Parameter<T>) - +Method in class compbio.metadata.RunnerConfig +: Adds parameter to the internal parameter list +
addParameter(String) - +Method in class compbio.runner._SkeletalCommandBuilder +: Deprecated. +
addParameters(List<String>) - +Method in class compbio.engine.client.ConfExecutable +: +
addParameters(List<String>) - +Method in interface compbio.engine.client.Executable +: Adds parameter to the list of parameters for a native executable +
addParameters(List<String>) - +Method in class compbio.engine.client.SkeletalExecutable +: +
addParameters(List<String>) - +Method in class compbio.runner._impl.NetNglyc +: +
addParameters(String[]) - +Method in class compbio.runner._SkeletalCommandBuilder +: Deprecated. +
addParameters(List<String>) - +Method in class compbio.runner._SkeletalCommandBuilder +: Deprecated. +
addParameters(List<String>) - +Method in class compbio.runner.msa.Mafft +: Mafft input must always be the last parameter! +
addParams(List<String>) - +Method in class compbio.engine.client.CommandBuilder +: +
addPossibleValues(String...) - +Method in class compbio.metadata.Parameter +: +
addTask(ConfiguredExecutable<?>, Future<ConfiguredExecutable<?>>) - +Static method in class compbio.engine.SubmissionManager +: +
Align - Class in compbio.data.msa.jaxws
Align() - +Constructor for class compbio.data.msa.jaxws.Align +: +
align(List<FastaSequence>) - +Method in interface compbio.data.msa.MsaWS +: Align a list of sequences with default settings. +
align(List<FastaSequence>) - +Method in class compbio.ws.server._MsaService +: +
align(List<FastaSequence>) - +Method in class compbio.ws.server.ClustalOWS +: +
align(List<FastaSequence>) - +Method in class compbio.ws.server.ClustalWS +: +
align(List<FastaSequence>) - +Method in class compbio.ws.server.MafftWS +: +
align(List<FastaSequence>) - +Method in class compbio.ws.server.MuscleWS +: +
align(List<FastaSequence>) - +Method in class compbio.ws.server.ProbconsWS +: +
align(List<FastaSequence>) - +Method in class compbio.ws.server.TcoffeeWS +: +
align(List<FastaSequence>, ConfiguredExecutable<T>, Logger, String, Limit<T>) - +Static method in class compbio.ws.server.WSUtil +: +
Alignment - Class in compbio.data.sequence: Multiple sequence alignment.
Alignment(List<FastaSequence>, Program, char) - +Constructor for class compbio.data.sequence.Alignment +: +
Alignment(List<FastaSequence>, AlignmentMetadata) - +Constructor for class compbio.data.sequence.Alignment +: +
AlignmentMetadata - Class in compbio.data.sequence: Alignment metadata e.g.
AlignmentMetadata(Program, char) - +Constructor for class compbio.data.sequence.AlignmentMetadata +: +
AlignResponse - Class in compbio.data.msa.jaxws
AlignResponse() - +Constructor for class compbio.data.msa.jaxws.AlignResponse +: +
AMBIGUOUS_AA - +Static variable in class compbio.data.sequence.SequenceUtil +: Same as AA pattern but with two additional letters - XU +
AMBIGUOUS_NUCLEOTIDE - +Static variable in class compbio.data.sequence.SequenceUtil +: Ambiguous nucleotide +
Analize - Class in compbio.data.msa.jaxws
Analize() - +Constructor for class compbio.data.msa.jaxws.Analize +: +
analize(List<FastaSequence>) - +Method in interface compbio.data.msa.SequenceAnnotation +: Analyse the sequences. +
analize(List<FastaSequence>) - +Method in class compbio.ws.server.AAConWS +: +
analize(List<FastaSequence>) - +Method in class compbio.ws.server.SequenceAnnotationService +: +
analize(List<FastaSequence>, ConfiguredExecutable<T>, Logger, String, Limit<T>) - +Static method in class compbio.ws.server.WSUtil +: +
AnalizeResponse - Class in compbio.data.msa.jaxws
AnalizeResponse() - +Constructor for class compbio.data.msa.jaxws.AnalizeResponse +: +
AnnualStat - Class in compbio.stat.servlet
AnnualStat() - +Constructor for class compbio.stat.servlet.AnnualStat +: +
Argument<T> - Interface in compbio.metadata: An unmodifiable view for the options and parameters, with one exception - it + allows to set a value
argumentsToCommandString(List<? extends Option<?>>) - +Method in class compbio.runner.OptionCombinator +: +
argumentsToCommandString(List<? extends Option<?>>, RunnerConfig<? extends Executable<?>>) - +Static method in class compbio.runner.OptionCombinator +: +
asMap() - +Method in class compbio.data.sequence.ScoreManager +: +
asSet() - +Method in class compbio.data.sequence.ScoreManager +: +
AsyncExecutor - Interface in compbio.engine: An asynchronous executor engine, capable of running, cancelling, + obtaining results calculated by a native executable wrapper in Executable interface.
AsyncJobRunner - Class in compbio.engine.cluster.drmaa: Single cluster job runner class
AsyncJobRunner() - +Constructor for class compbio.engine.cluster.drmaa.AsyncJobRunner +: +
AsyncLocalRunner - Class in compbio.engine.local
AsyncLocalRunner() - +Constructor for class compbio.engine.local.AsyncLocalRunner +: +