X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Fdm_javadoc%2Findex-files%2Findex-1.html;h=ea7a39ca25c81ce499d1c41c0fbbb09f05fe718f;hb=faac303bf9ad8c17b71a55d23b7a2c0a9e6e2efa;hp=70eb3805049734cecb85f93d33489080f90e8458;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git diff --git a/website/dm_javadoc/index-files/index-1.html b/website/dm_javadoc/index-files/index-1.html index 70eb380..ea7a39c 100644 --- a/website/dm_javadoc/index-files/index-1.html +++ b/website/dm_javadoc/index-files/index-1.html @@ -2,12 +2,12 @@ - + A-Index - + @@ -85,9 +85,12 @@ function windowTitle()
AA - Static variable in class compbio.data.sequence.SequenceUtil
Valid Amino acids -
addOption(Option<T>) - -Method in class compbio.metadata.RunnerConfig +
AACON_INFO - +Static variable in enum compbio.ws.client.Services
  +
AAConClient - Class in compbio.ws.client
A command line client for AACon web service
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 @@ -96,10 +99,16 @@ Method in class compbio.metadata. 
addParameter(Parameter<T>) - Method in class compbio.metadata.RunnerConfig -
  +
Adds parameter to the internal parameter list
addPossibleValues(String...) - Method in class compbio.metadata.Parameter
  +
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.
Alignment - Class in compbio.data.sequence
Multiple sequence alignment.
Alignment(List<FastaSequence>, Program, char) - Constructor for class compbio.data.sequence.Alignment
  @@ -109,14 +118,32 @@ Constructor for class compbio.data.sequence.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. +
AnalizeResponse - Class in compbio.data.msa.jaxws
 
AnalizeResponse() - +Constructor for class compbio.data.msa.jaxws.AnalizeResponse +
 
Argument<T> - Interface in compbio.metadata
An unmodifiable view for the options and parameters, with one exception - it - allows to set a value + allows to set a value
asMap() - +Method in class compbio.data.sequence.ScoreManager +
  +
asSet() - +Method in class compbio.data.sequence.ScoreManager +
  +