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addStepAffyNormalization(String, String[], String, boolean, boolean, boolean, boolean, boolean) - Method in class at.tugraz.genome.R.carmaweb.axis.AxisClient

Adds a Affymetrix GeneChip preprocessing step to the analysis.

addStepTwoColorPreprocessing(String, String[], String, String, boolean, String, String, String, String, String, boolean, boolean) - Method in class at.tugraz.genome.R.carmaweb.axis.AxisClient

Adds a two color microarray preprocessing step to an analysis.

at.tugraz.genome.R.carmaweb.axis - package at.tugraz.genome.R.carmaweb.axis

AxisClient - class at.tugraz.genome.R.carmaweb.axis.AxisClient.

AxisClient() - Constructor for class at.tugraz.genome.R.carmaweb.axis.AxisClient

AxisClient(Properties) - Constructor for class at.tugraz.genome.R.carmaweb.axis.AxisClient

F

FUN_ADDFILE - Static variable in class at.tugraz.genome.R.carmaweb.axis.AxisClient

FUN_ADDSTEP_AFFY_NORMALIZATION - Static variable in class at.tugraz.genome.R.carmaweb.axis.AxisClient

FUN_ADDSTEP_TWOCOLOR_PREPROCESSING - Static variable in class at.tugraz.genome.R.carmaweb.axis.AxisClient

FUN_ERRORMESSAGE - Static variable in class at.tugraz.genome.R.carmaweb.axis.AxisClient

FUN_GENERATEID - Static variable in class at.tugraz.genome.R.carmaweb.axis.AxisClient

FUN_GET_AFFY_NORM_METHODS - Static variable in class at.tugraz.genome.R.carmaweb.axis.AxisClient

FUN_GET_AFFY_NORM_METHODS_DESCRIPTIONS - Static variable in class at.tugraz.genome.R.carmaweb.axis.AxisClient

FUN_GETFILE - Static variable in class at.tugraz.genome.R.carmaweb.axis.AxisClient

FUN_GETSTATUS - Static variable in class at.tugraz.genome.R.carmaweb.axis.AxisClient

FUN_JUSTAFFYNORMALIZATION - Static variable in class at.tugraz.genome.R.carmaweb.axis.AxisClient

FUN_LISTFILES - Static variable in class at.tugraz.genome.R.carmaweb.axis.AxisClient

FUN_PERFORM_GO_ANALYSIS - Static variable in class at.tugraz.genome.R.carmaweb.axis.AxisClient

FUN_REMOVEFILE - Static variable in class at.tugraz.genome.R.carmaweb.axis.AxisClient

FUN_START_DEFINED_ANALYSIS - Static variable in class at.tugraz.genome.R.carmaweb.axis.AxisClient

FUN_VOIDEVAL - Static variable in class at.tugraz.genome.R.carmaweb.axis.AxisClient

G

generateID() - Method in class at.tugraz.genome.R.carmaweb.axis.AxisClient

Generated a unique ID for the analysis.

getAffyNormalizationMethods() - Method in class at.tugraz.genome.R.carmaweb.axis.AxisClient

Returns the available normalization methods for Affymetrix GeneChips.

getAffyNormalizationMethodsDescriptions() - Method in class at.tugraz.genome.R.carmaweb.axis.AxisClient

Returns descriptions for the Affymetrix preprocessing methods.

getErrorMessage(String) - Method in class at.tugraz.genome.R.carmaweb.axis.AxisClient

Returns the specific error message of the analysis if one exists.

getFile(String, File, String) - Method in class at.tugraz.genome.R.carmaweb.axis.AxisClient

Downloads a file from the workspace on the server to the local filesystem.

getFile(String, String) - Method in class at.tugraz.genome.R.carmaweb.axis.AxisClient

Returns a DataHandler of a file that is stored in the workspace on the server.

getInstance() - Static method in class at.tugraz.genome.R.carmaweb.axis.AxisClient

Returns an instance of class AxisClient.

getInstance() - Static method in class at.tugraz.genome.R.carmaweb.axis.SSLAxisClient

Returns an AxisClient instance.

getInstance(Properties) - Static method in class at.tugraz.genome.R.carmaweb.axis.AxisClient

Returns an instance of class AxisClient.

getInstance(Properties) - Static method in class at.tugraz.genome.R.carmaweb.axis.SSLAxisClient

Returns an AxisClient instance.

getProperties() - Method in class at.tugraz.genome.R.carmaweb.axis.AxisClient

Returns the Properties.

getStatus(String) - Method in class at.tugraz.genome.R.carmaweb.axis.AxisClient

Returns the status of the analysis.

L

listFiles(String) - Method in class at.tugraz.genome.R.carmaweb.axis.AxisClient

Lists all files that are stored in the workspace on the server.

P

performGOAnalysis(String, String, String, String, String, String, boolean, Float, boolean, boolean, boolean) - Method in class at.tugraz.genome.R.carmaweb.axis.AxisClient

Performs a Gene Ontology analysis using the GO and GOstats packages from BioConductor.

performJustAffyNormalization(String, String, boolean, boolean, boolean, boolean, boolean) - Method in class at.tugraz.genome.R.carmaweb.axis.AxisClient

Performs just an Affymetrix GeneChip normalization.

R

removeFile(String, String) - Method in class at.tugraz.genome.R.carmaweb.axis.AxisClient

Delete a file in the workspace.

S

sendFile(String, File) - Method in class at.tugraz.genome.R.carmaweb.axis.AxisClient

Sends a file to the web service.

setProperties(Properties) - Method in class at.tugraz.genome.R.carmaweb.axis.AxisClient

Sets the Properties.

SSLAxisClient - class at.tugraz.genome.R.carmaweb.axis.SSLAxisClient.

SSLAxisClient() - Constructor for class at.tugraz.genome.R.carmaweb.axis.SSLAxisClient

SSLAxisClient(Properties) - Constructor for class at.tugraz.genome.R.carmaweb.axis.SSLAxisClient

startDefinedAnalysis(String) - Method in class at.tugraz.genome.R.carmaweb.axis.AxisClient

Starts an already defined analysis.

STATUS_ERROR - Static variable in class at.tugraz.genome.R.carmaweb.axis.AxisClient

STATUS_FINISHED - Static variable in class at.tugraz.genome.R.carmaweb.axis.AxisClient

STATUS_RUNNING - Static variable in class at.tugraz.genome.R.carmaweb.axis.AxisClient

STATUS_UNKNOWN - Static variable in class at.tugraz.genome.R.carmaweb.axis.AxisClient

V

voidEvalExpression(String, String) - Method in class at.tugraz.genome.R.carmaweb.axis.AxisClient

Evaluates the R command sent.

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