X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Findex-files%2Findex-16.html;h=b656146aaa3099aa17ccf2b28fd7cdbe2fd08215;hb=f1bdd8da517901fe1d7957d388ea579ad1fbaa3b;hp=5c24c63d754d8af538f432a45a937dc169794d49;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git diff --git a/website/full_javadoc/index-files/index-16.html b/website/full_javadoc/index-files/index-16.html index 5c24c63..b656146 100644 --- a/website/full_javadoc/index-files/index-16.html +++ b/website/full_javadoc/index-files/index-16.html @@ -2,12 +2,12 @@ - + P-Index - + @@ -85,7 +85,7 @@ function windowTitle()
Pairwise - Class in compbio.pipeline._jpred
 
Pairwise(List<FastaSequence>) - Constructor for class compbio.pipeline._jpred.Pairwise
  -
Parameter<T> - Class in compbio.metadata
A single value containing option supported by the web service e.g.
Parameter(String, String) - +
Parameter<T> - Class in compbio.metadata
A single value containing an option supported by the web service e.g.
Parameter(String, String) - Constructor for class compbio.metadata.Parameter
 
parametersToCommandString(List<Parameter<?>>, Map<Parameter<?>, String>) - @@ -93,7 +93,7 @@ Method in class compbio.runner. 
parse(String) - Static method in class compbio.engine.conf._Key -
  +
Deprecated.  
PATH - Static variable in class compbio.engine.client.EnvVariableProcessor
Special variable keys Absolute path(s) will be merged with the content of @@ -111,6 +111,12 @@ Constructor for class compbio.data.msa.jaxws.presetAlign(List<FastaSequence>, Preset<T>) - Method in interface compbio.data.msa.MsaWS
Align a list of sequences with preset. +
presetAlign(List<FastaSequence>, Preset<T>) - +Method in class compbio.ws.server._MsaService +
  +
presetAlign(List<FastaSequence>, Preset<ClustalO>) - +Method in class compbio.ws.server.ClustalOWS +
 
presetAlign(List<FastaSequence>, Preset<ClustalW>) - Method in class compbio.ws.server.ClustalWS
  @@ -129,12 +135,36 @@ Method in class compbio.ws.server.PresetAlignResponse - Class in compbio.data.msa.jaxws
 
PresetAlignResponse() - Constructor for class compbio.data.msa.jaxws.PresetAlignResponse
  +
PresetAnalize - Class in compbio.data.msa.jaxws
 
PresetAnalize() - +Constructor for class compbio.data.msa.jaxws.PresetAnalize +
  +
presetAnalize(List<FastaSequence>, Preset<T>) - +Method in interface compbio.data.msa.SequenceAnnotation +
Analyse the sequences according to the preset settings. +
presetAnalize(List<FastaSequence>, Preset<Disembl>) - +Method in class compbio.ws.server.DisemblWS +
  +
presetAnalize(List<FastaSequence>, Preset<GlobPlot>) - +Method in class compbio.ws.server.GlobPlotWS +
  +
presetAnalize(List<FastaSequence>, Preset<IUPred>) - +Method in class compbio.ws.server.IUPredWS +
  +
presetAnalize(List<FastaSequence>, Preset<T>) - +Method in class compbio.ws.server.SequenceAnnotationService +
  +
PresetAnalizeResponse - Class in compbio.data.msa.jaxws
 
PresetAnalizeResponse() - +Constructor for class compbio.data.msa.jaxws.PresetAnalizeResponse +
 
PresetManager<T> - Class in compbio.metadata
Collection of presets and methods to manipulate them @see Preset
PresetManager() - Constructor for class compbio.metadata.PresetManager
 
Probcons - Class in compbio.runner.msa
 
Probcons() - Constructor for class compbio.runner.msa.Probcons
  +
PROBCONS_INFO - +Static variable in enum compbio.ws.client.Services +
 
ProbconsWS - Class in compbio.ws.server
 
ProbconsWS() - Constructor for class compbio.ws.server.ProbconsWS
  @@ -144,7 +174,7 @@ Static variable in class compbio.engine.local.PROC_OUT_FILE - Static variable in class compbio.engine.local.ExecutableWrapper
  -
Program - Enum in compbio.data.sequence
Programmes that can produce alignments
ProgressGetter - Class in compbio.engine
 
ProgressGetter() - +
Program - Enum in compbio.data.sequence
The list of programmes that can produce alignments
ProgressGetter - Class in compbio.engine
 
ProgressGetter() - Constructor for class compbio.engine.ProgressGetter
 
PropertyHelperManager - Class in compbio.engine.conf
 
PropertyHelperManager() - @@ -156,9 +186,6 @@ Constructor for class compbio.pipeline._jpred.PSIBlast - Class in compbio.runner._impl
 
PSIBlast(String) - Constructor for class compbio.runner._impl.PSIBlast
  -
PsiBlast - Class in compbio.runner.psiblast
 
PsiBlast() - -Constructor for class compbio.runner.psiblast.PsiBlast -
 
pull(long) - Method in class compbio.engine.FilePuller
  @@ -171,13 +198,28 @@ Constructor for class compbio.engine.PullExecStatistics - Class in compbio.data.msa.jaxws
 
PullExecStatistics() - Constructor for class compbio.data.msa.jaxws.PullExecStatistics
  -
pullExecStatistics(String, long) - -Method in interface compbio.data.msa.MsaWS +
pullExecStatistics(String, long) - +Method in interface compbio.data.msa.JManagement
Reads 1kb chunk from the statistics file which is specific to a given web - service from the position. + service from the position. +
pullExecStatistics(String, long) - +Method in class compbio.ws.server._MsaService +
  +
pullExecStatistics(String, long) - +Method in class compbio.ws.server.AAConWS +
  +
pullExecStatistics(String, long) - +Method in class compbio.ws.server.ClustalOWS +
 
pullExecStatistics(String, long) - Method in class compbio.ws.server.ClustalWS
  +
pullExecStatistics(String, long) - +Method in class compbio.ws.server.GenericMetadataService +
Assume statistics is not supported +
pullExecStatistics(String, long) - +Method in class compbio.ws.server.JronnWS +
 
pullExecStatistics(String, long) - Method in class compbio.ws.server.MafftWS
  @@ -193,15 +235,9 @@ Method in class compbio.ws.server.PullExecStatisticsResponse - Class in compbio.data.msa.jaxws
 
PullExecStatisticsResponse() - Constructor for class compbio.data.msa.jaxws.PullExecStatisticsResponse
  -
PullFile - Class in compbio.data.msa.jaxws
 
PullFile() - -Constructor for class compbio.data.msa.jaxws.PullFile -
 
pullFile(String, long) - Static method in class compbio.ws.server.WSUtil
  -
PullFileResponse - Class in compbio.data.msa.jaxws
 
PullFileResponse() - -Constructor for class compbio.data.msa.jaxws.PullFileResponse -
 
put(FilePuller) - Static method in class compbio.engine.PulledFileCache
This method allows duplicates to be added.