calcXYstat() - compute correlation statistics string for display
rSq=.., n=.., X(mn+-sd)=(..+-..), Y(mn+-sd)=(..+-..)
If propList[] is not null, then test if filtered using
IS_FILTERED property.
calcXYstat() - compute correlation statistics string for display
rSq=.., n=.., X(mn+-sd)=(..+-..), Y(mn+-sd)=(..+-..)
If propList[] is not null, then test if filtered using
fc.IS_FILTERED value.
cvs2Array() - convert String arg list "1,4,3,6,..." to String[]
If there are more than maxExpected number of args in string, ignore
them and just return what has been parsed so far.
cvs2iArray() - convert String arg list "1,4,3,6,..." to int[]
If there are more than maxExpected number of args in string, ignore
them and just return what has been parsed so far.
cvtEnvPaths2Properties() - get all system ENV variables and set them as
separate Java properties so we can get them individually from
System.getProperty(var) calls.
GenNormalizationPlugin() - constructor ONLY for use with debugging
using the mae.DBUG_GENERIC_NORM_PLUGIN flag to add
(Analysis | Normalization | Test Generic Norm Plugin [DBUG])
to the normalization menu.
get_probKS() - probability of null hypoth same distrib for
previously computed Kolmogorov-Smirnov stat d & prob of the null
hypothesis of 2 bins of data.
getAllMeanDataGeneListDataForCondition() - get all (mn,SD,prop) list Condition samples'
normalized data for genes in the specified gene list and samples in the condition
list and save in in (meanData[], stdDevData[])
for data filtered by the specified gene list.
getAllawF1F2DataAndBkgdForSample() - get all spot list raw intensity and background data
for genes and return it in the arrays pre-specified by the user.
getBottomSeparator() - Returns the bottom separator for the object
When getParsedData
method is called, the object uses the bottom separator to determine
where the rows of data inside the raw HTML output actually end.
getEPmaxMeanSampleData() - max mean normalized sample data scale factor
computed over all samples and all genes being used in a list of expression
profiles.
getF1F2dataForSample() - get filtered (f1,f2,prop) lists of Field (F1,F2) data
for sample in (f1List[], f2List[], propList[]) for FILTERED data by
the specified gene list.
getHP_XandYsamplesData() - get filtered (X,Y,prop) lists of X and Y samples data
for single samples in (Xdata[],Ydata[], propList[]) for FILTERED data
by the specified gene list.
getHP_XandYsetDataForSample() - get normalized HP-X, -Y 'sets' (X,Y,prop)
data lists for sample in (Xdata[],Ydata[], propList[] for FILTERED
data by the specified gene list.
getHPdataForSample() - get normalized filtered (data,prop) list single sample's data
for sample in (dataList[], propList[]) for FILTERED data by the
specified gene list.
getListOfGeneFieldsForMID() - get list of Gene fields for a gene by MID
DataFieldNames: "GeneName", "GenBankID", "GenBank3ID", "GenBank5ID",
"CloneID", "LocusID", "UniGeneID", "SwissProtID", "RefSeqID",
"Master_ID", "MasterGeneName", "Generic_ID"
getListsOfEPsamplesMean() - lists of normalized HP-E samples Means EPs for list of MIDs
Compute expression profiles for all of the mid's in the midList[] that are legal
(i.e.
getListsOfOrderedCondListCVs() is last conditions Coeff of Variation[] from
ordered condition list computation computed using calcOrderedCondListExprProfile().
getListsOfOrderedCondListStdDevs() is last conditions StdDev[] from ordered condition
list computation computed using calcOrderedCondListExprProfile().
getMeanDataGeneListDataForCondition() - get filtered (mn,SD,prop) list Condition samples'
normalized data for genes in the specified gene list and samples in the condition
list and save in (meanData[], stdDevData[], propList[])
for data filtered by the specified gene list.
getParsedData() - returns parsed data in form of Vector of Vectors
Returns parsed data in the form of a Vector of Vectors containing
the returned fields inside of a Vector of returned rows.
getPluginHashState() - get boolean state value from MAEPlugin hash state storage
This looks for a symbol with the name (pluginName + "." + varName) in the
global hash store.
getPluginHashState() - get byte state value from MAEPlugin hash state storage
This looks for a symbol with the name (pluginName + "." + varName) in the
global hash store.
getPluginHashState() - get double state value from MAEPlugin hash state storage
This looks for a symbol with the name (pluginName + "." + varName) in the
global hash store.
getPluginHashState() - get float state value from MAEPlugin hash state storage
This looks for a symbol with the name (pluginName + "." + varName) in the
global hash store.
getPluginHashState() - get int state value from MAEPlugin hash state storage
This looks for a symbol with the name (pluginName + "." + varName) in the
global hash store.
getPluginHashState() - get long state value from MAEPlugin hash state storage
This looks for a symbol with the name (pluginName + "." + varName) in the
global hash store.
getRawF1F2DataAndBkgdForSample() - get filtered spot list raw intensity and background data
for genes and return it in the arrays pre-specified by the user.
getAllRawHPdataForSample() - get all raw (data,prop) list single sample's
intensity data for single samples in (Xdata[],Ydata[], propList[]) for FILTERED data
by the specified gene list.
itemStateChanged() - user clicked on condtion in the condition list,
must change CondParamEditForm data, remainder and selected data,
save condForm data.
This is base class for the Application Programming Interface (API) for accessing MAExplorer data structures
This allows accessing the data structures in a uniform way that hides
the actual complexity of the internal data structures.
Class PopupCondChooser - GUI to allow users to associate conditions with samples,
define parameters of conditions and save within MAExplorer to be used in
reports/plots etc.
Class PopupOrderedCondChooser - GUI to allow users to create Ordered Condition
Lists (OCL), assign conditions, define parameters for OCLs and save within
MAExplorer to be used in reports/plots etc.
Class RevalBase is an abstract base class used to define the base
infrastructure for evaluating R scripts (using the R program) using
data supplied from a client program.
scaleIntensityData() - the gene normalization operating on gene mid
for sampleIdx where the data is ether extracted here or from the resetPipeline
pre-analysis.
scaleIntensityData() - the gene normalization operating on gene mid
for sampleIdx where the data is ether extracted here or from the resetPipeline
pre-analysis.
scaleIntensityData() - the gene normalization operating on gene mid
for sampleIdx where the data is ether extracted here or from the resetPipeline
pre-analysis.
set_nGeneClustersCnt() - set nGeneClustersCnt for specified gene, if exists
The centroid gene of a cluster is flagged by containing the # of genes
in that cluster.
setDefaultThreadJavaCGIBridgeTimeOut() - set communication time out
Static method sets the default communication time out in
milliseconds for the class.
setEPmaxMeanSampleData() - max mean normalized sample data scale factor
computed over all samples and all genes being used in a list of expression
profiles.
setRLOreportLoggingFlag() - set RLO Report logging flag
for creating subdirectory in {project}/Report/{RLOname}-yymmdd.hhmmss/
to store the RLO output files copied to Report/
setupCondData() - get remainder and selected condition data, & parameters
from MJA (indirectly from mae) and set up the oclLd[] array of ordered
condition data.