multipurpose button that toggles between:
"Go 'Cluster gene counts' " for "allGenes" (cluster counts) and
"Go 'Cluster single genes'" for "singleGene" (similar genes).
Flag: if enabled, it first checks the /Cache directory for all http://
codebase files and if not in the cache, it saves the file in the
cache after reading it from the Web.
calcMeanAndVariance() - compute the mean and variance of dataS[]
for 1 condition and save the results inmean[conditionK] and
variance[conditionK] arrays.
calcRemCond() - compute remainder list of condition names (R = DB - Ci)
where DB is all of the Conds in the database, and Ci are the Conds
in condition Ci.
calcRemSamples() - compute remainder list of sample names (R = DB - Ci)
where DB is all of the samples in the database, and Ci are the samples
in condition Ci.
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.
copyGenesInSubtreeToEGL() - Copy terminal genes in dendrogram subtree
to E.G.L for box that was selected at (selRow,selCol) such that terminal
genes LEQ selDist GT 0.0F and dcg.drawDendroGramFlag.
createStrReportOfOCL_FstatData() - make String report of OCL F-test for mList[0:nC-1]
If the OCL F-Test filter is active, then report F-test statistics.
createTableOfHP_XYstat() - make Table of HP_XYstatistics for mList[0:nC-1]
If the t-Test filter is active, then report t-test statistics
If the KS-Test filter is active, then report KS-test statistics
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.
cvtEnvPaths2Properties() - get all system ENV variables and set them as
separate Java properties so we can get them individually from
System.getProperty(var) calls.
cvtEnvPaths2Properties() - get all system ENV variables and set them as
separate Java properties so we can get them individually from
System.getProperty(var) calls.
cvtRawQdataToMAEdata() - convert .quant data to MAE data using HP array data ms.(bkgrdQ,totQ)[]
Note: totQ is RawIntensity, or unscaled ratio
RawIntensity1/RawIntensity2.
cvtStrArrayToStr() - create(String) from String[] array with "\n" w/len
Fast method creates a tmp Character [] of required size and
stuffs it, then converts it to a string at one time instead
of repeatedly using concat(i.e.
[DEBUGGING] If debugging a plugin extending NormalizationPlugin,
you may debug it in the MAExplorer core image by temporarily including
in in the code.
genClientEpilogue() - generate epilogue R script to write data commands
to put R created data into Temp/ folder for reading by MAExplorer
when required by actions in the RLO specification.
genEpilogue() - generate epilogue R script to write data commands
to put R created data into Temp/ folder for reading by MAExplorer
when required by actions in the RLO specification.
genEpilogue() - generate epilogue R script to write data commands
to put R created data into Temp/ folder for reading by MAExplorer
when required by actions in the RLO specification.
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.
itemStateChanged() - user clicked on condtion in the condition list,
must change CondParamEditForm data, remainder and selected data,
save condForm data.
itemStateChanged() - handle check box item state changed events
NOTE: need to implement radio groups here since AWT only
implements radio groups for Checkboxes, and not for Checkbox MenuItems.
map: mid (Master Gene index) to gid (gridCoords index)
This is created by: GeneTable.setupMIDlist()
It is used for lookup by: GeneTable.getGeneListOfGeneClass()
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.
This is the name of the path for the saved R base path
in the Temp/.RbasePath file it it ever tried to prompt
for the R base path and there was no response to the\
prompt.
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.
PopupProjDirGuesser() - constructor for project director guesser
which assumes the HP menu item list is already sorted when it is created
during MAExplorer initialization.
The PopupRegistry class implements a call-back mechanism for active popup windows
It is also usable for any other objects that impelement MaeEventListeners
that are dynamicaly created and need to be notified of state changes.
preSortLists() - presort lists of Gene_Name and Master_ID for Guesser
It copies the Gene data into the working geneNameList[] and the
masterIDList[] with sizes geneNameListSize, masterIDListSize .
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.
setCy3Cy5RatiosCL() - Set GeneList of thresholded genes for Cy3/Cy5 ratio range
where the threshold for rangeType [CR1:CR2] and rangeMode
RANGE_INSIDE, RANGE_OUTSIDE.
setDefaultThreadJavaCGIBridgeTimeOut() - set communication time out
Static method sets the default communication time out in
milliseconds for the class.
updateAllPluginsJarFiles() - update all MAEPlugins from server in the /Plugins directory
This prompts for the user to verify they want to update all plugins jar files.