addFCrangesForTestsIntersectionTable() - adding FC range computations
which expands the table and adds the three columns ("Max FC", "Min FC",
"Range FC").
addRowStatisticsToIndexMap() - add row statistics(Min,Max,Mean,StdDev)
column data to the ftIM index map table after the ftIM table
has been read into memory.
buildMapUrl() - map a cell string at [r, c] to an HTML link
string by adding the HREF if hrefIdx==c using the cvt.urlBaseLink
For the 1:1 mapping, it adds the cell value {} to the base
urlBaseLink value {}.
checkForBadTable() - verify that it is a well formed Table
with all field names present and with no null, "" or duplicate
entries, and tRows EQ tData.length.
Colormap data scale quantile TABLE HTML mapping the cvt.heatMapColors[]
quantiles to positive numeric value in range of
[cvt.glbMinRowVal, cvt.glbMaxRowVal].
concatInputFilesWithSameFields() - to create a new concatenated
tab-delimited .txt output file from the set of input text files
IFF they have exactly the same column header names.
The '-concatTables:{outputConcatenateFile.txt}' switch enables
this option by setting the switch.create a new merged
tab-delimited .txt output file from the set of input text
files IFF they have exactly the same column header names.
convertAllJTVfiles() - convert a list of sub directories of JTV
file sets by reading the three files from the each of the sub
directories in the jtvInputDir directory.
cvtJTVfileSet() - convert a sub directory JTV file set
by reading the three files from the (jtvInputDir+inputSubDir)
sub directory with (.atr,.cdt,.gtr) file extensions.
The column name for the current table keyword used
to extract the data specified with the
'-extractRow:{colName,rowNbr,resourceTblFile,htmlStyle}'
switch.
extractRowFromResourceTableAsHTML() - to get and lookup a keyword
in the table being processed at (colName,rowNbr) and then to
search a resourceTblFile for that keyword.
The row number for the current table keyword used
to extract the data specified with the
'-extractRow:{colName,rowNbr,resourceTblFile,htmlStyle}'
switch.
[20.3] Allow processing input file data line by line table that
does not buffer the data in a Table structure, but remaps each line
on the fly using '-mapLongToShortHdrNames:{L2SmapFile, opt.
This is the file that contains the list of column names to be used
when generating the flipped Table using the
'-flipTableByIndexMap:{flipDataFile,flipIndexMapFile,(opt)maxRows}' switch.
These are the list of column names to be used when generating the flipped
Table using the '-flipTableByIndexMap:{flipDataFile,flipIndexMapFile,(opt)maxRows}'
switch.
These are the list of column name values {v1,v2,...vn} to be used when
generating the flipped Table using the
'-flipTableByIndexMap:{flipDataFile,flipIndexMapFile,(opt)maxRows}'
switch.
This is the alternate output (HTML and TXT) base directory to use when
generating the flipped Table using the
'-flipTableByIndexMap:{flipDataFile,flipIndexMapFile,(opt)maxRows}'
switch.
These are the list of column names to exclude when generating the flipped
Table using the
'-flipTableByIndexMap:{flipDataFile,flipIndexMapFile,(opt)maxRows}'
switch.
If reporting fold change with reportFoldChangeFlag in flip Table
reporting, and -flipFCthreshold:{flipFCthreshold}, then
set the flipFCthrFlag and save the postive value in
flipFCthreshold.
If reporting fold change with reportFoldChangeFlag in flip Table
reporting, and -flipFCthreshold:{flipFCthreshold}, then
set the flipFCthrFlag and save the postive value in
flipFCthreshold.
These are the list of column names to be used in the flipped header
when generating the flipped Table using the
'-flipTableByIndexMap:{flipDataFile,flipIndexMapFile,(opt)maxRows}'
switch.
This is the list of row names [0:nFlipRowFilterNames-1] to be used
when generating the flipped Table using the
'-flipTableByIndexMap:{flipDataFile,flipIndexMapFile}' switch.
This is the name of the file containing the row names to be used
when generating the flipped Table using the
'-flipTableByIndexMap:{flipDataFile,flipIndexMapFile,(opt)maxRows}'.
This is the alternate output (HTML and TXT) base file name to use when
generating the flipped Table using the
'-flipTableByIndexMap:{flipDataFile,flipIndexMapFile,(opt)maxRows}'
switch.
Generate transposed files using random access file indexing to create
a multi-line header (1 line for each column name in the list) using
the list of columns previously specified when generating the index map
file with '-makeIndexMapFile:{colName1,colName2,...,colNameN}' command.
Fold-change threshold value used from the Menu checkbox item
foldChangeThrMCB for
"Only keep genes/probes with |fold-change| >= threshold"
that pops up a dialog to enter the threshold value between 0.0 and
some large number.
Menu checkbox item for
"Only keep genes/probes with |fold-change| >= threshold"
This pops up a dialog to enter the threshold value between 0.0 and
some large number and saves it in sgs.foldChangeThr.
FileTable created from the {experimentGroups.map} Table
that 'could' be used to get other experiment group data
for the summaries if we decide we want to add it.
FileTable index map where save the {colNames, "StartByte", "EndByte")
The colNames is a list with arbitrary names that can not be
either "StartByte" or "EndByte".
FileTable created from the {long2ShortHdrNamesTable.map}
Table that 'could' be used to map 'Short GSP ID's to 'GSP ID's
if we decide to list the members of the tests.
The name of the {Analyses} directory (inside of the genBatchDir)
where the generated tests HTML web files are saved when the batch
script is subsequently run.
The name of the {JTV} directory (inside of the genBatchDir)
where the generated tests HTML web files are saved when the batch
script is subsequently run.
The name of the {ParamsScripts} directory (inside of the genBatchDir)
where the generated params .map files are saved and the support .map
files are also copied.
List of Summary Templates that are used for mapping the
test-ToDo-list data so that (summaryProlog, summaryExperimental,
summaryAnalysis, summaryFurtherAnalysis, summaryEpilogue) etc.
getCleanSpaceList() - cvt str list delim by " ", ",", "\t", "\n" to " " delim str
Standardize to space delimited row of symbols
map commas, tabs, "\n" and multiple spaces to single space
This switch is used with the '-hrefData:{colHdrName,Url,
(optional)mapToken}' switch to map the data in the header row(s)
instead of the data in the Table data columns.
itemStateChanged() - handle item state changed events
NOTE: need to implement radio groups here since AWT only
implements radio groups for Checkboxes, and CheckboxMenuItems.
Name of the Long to Short array name mapping file that
contains a (L2S) Table with the array name in column 1 and one or
more alternate array names that are shorter and more descriptive.
Class JTVconvert to convert a Java Tree View (JTV) set of input
sub directories of JTV files to a remapped Array Name labels of
the .cdt files to a corresponding set of output JTV sub directories
with renamed (.atr,.cdt,.gtr) files.
If doing 'jtvHTMLgenerate', then you can use the
'-jtvCopyJTVjars:{JTV jars directory}' option to copy the
JTV jar files and plugins to the jtvOutputDir.
String set with '-jtvDescription:{prolog description}' that
may be used with '-jtvHTMLgenerate' to insert additional
text into the prolog where it replaces "$$DATA_DESCRIPTION$$".
'From' Column number used when remap the 'mAdb ID' data to data
with this column number in the jtv_mapHdrNamesFile map
and then in the "Map-Table" during the conversion.
'To' Column number used when remap the 'mAdb ID' data to data
with this column number in the jtv_mapHdrNamesFile map
and then in the "Map-Table" during the conversion.
makeColorMapScaleHTML() - make colormap data scale TABLE HTML
mapping the cvt.heatMapColors[] to positive numeric value in range of
[cvt.glbMinRowVal, cvt.glbMaxRowVal]
makeConcatTable() - create a new concatenated tab-delimited .txt
output file from the set of input text files IFF they have exactly
the same column header names.
Name of the input file (run time) used to make an index map Table
file (same name as the input file but with an .idx file extension)
of the input file (or the file output from -saveEditedTable2File
after the input table has been edited).
Make an index map Table file (same name as the input file
but with an .idx file extension) of the input file (or the file
output from -saveEditedTable2File after the input table has been
edited).
makeListOfSeekDataRowsByColumnFilters() filter rows from Index Map data
by filtering any of the flipColNameFilterData[] criteria in the
index map (which has all of the fields we need to do the filtering)
to generate a list of rows that we will actually random access read
from the input data.
The index of the map entry indexed by column for the
URL maps from "-hrefData:{colHdrName,UrlBaseLink}" switches
Each entry builds a list of nColUrlMap entries.
[HACK] If the table is sorted by sortTableRowsByField for numeric
values with the useAbsValueFlag set true, and both + and - changes
were found, it will set the needToSortTableAgainFlag so the calling
program can resort one more time if it wants to keep the data in
numeric order.
This is the number of columns and the related lists to be used
in filtering rows when generating the flipped Table using the
'-flipTableByIndexMap:{flipDataFile,flipIndexMapFile,(opt)maxRows}'
switch.
This is the number of column names to exclude when generating the flipped
Table using the
'-flipTableByIndexMap:{flipDataFile,flipIndexMapFile,(opt)maxRows}'
switch.
These are the size of the list of column names to be used in the
flipped header when generating the flipped Table using the
'-flipTableByIndexMap:{flipDataFile,flipIndexMapFile,(opt)maxRows}'
switch.
Size of the list of row names [0:nFlipRowFilterNames-1] to be used
when generating the flipped Table using the
'-flipTableByIndexMap:{flipDataFile,flipIndexMapFile}' switch.
Number of instances to copy input data tree data to batch
scripts subdirectory for copying
genTreeSrcTreeDir[0:nGenTreeCopy-1] directory trees to
genTreeDstTreeDir[0:nGenTreeCopy-1].
Size of list of Column header names
reorderColName[0:nReorderColName-1] from
'-reorderColumn:{colName,newColNbr}' to reorder this
column to the new column number in
reorderColNbr[0:nReorderColName-1].
postCopyFilesAndDirectories() - copy files post-conversion
using the set of -copyFile:{srcFile,destFile} and
-copyTree:{srcTreeFiles,destPath} switches specified.
List of Column header names [0:nReorderColName-1] from
'-reorderColumn:{colName,newColNbr}' to reorder this
column to the new column number in reorderColNbr[].
New column index of size [0:nReorderColName-1] from
'-reorderColumn:{colName,newColNbr}' to reorder the
columns in reorderColName[] to the new column number in
reorderColNbr[].
reorderColumnsInTable() - reorder Table tFields and tData by column
index of the Table based on the list of column header names
reordColName[0:nReorderColName-1] to be reordered by a corresponding
list of new column numbers in reordColNbr[].
saveIndexMapFile() - save the index map table for the edited Table
If doing '-makeIndexMapFile:{colName1,colName2,...,colNameN}'
first generate the Index-Map Table using the makeIdxMapTable().
When looking for the start of a Table in file with complex info
and possibly multiple blank lines, this switch lets the converter
search for a specific keyword as any part of the last Table header
line allowing you to specify multiple header lines using the
'-hdrLines' switch.
updateSampleList() - handle item state changed events
NOTE: need to implement radio groups here since AWT only
implements radio groups for Checkboxes, and CheckboxMenuItems.