Class Globals

java.lang.Object
  Globals

Direct Known Subclasses:

HTMLtools

public class Globals
extends java.lang.Object

Class Global variables used as the base class for HTMLtools. Until we [REFACTOR] the JTV (Java TreeView), TestsIntersection , and GenBatchScripts converters to separate applications, the variables reside here.

 List of Methods
 reinitGlobalSwitches() - reinitialize Global variable switches. 
 reinitGBSglobalSwitches() - reinitialize GBS Global variable switches.
 reinitTIglobalSwitches() - reinitialize TestsIntersection Global switches.
 reinitJTVglobalSwitches() - reinitialize JTV Global variable switches.
 

This code is available at the HTMLtools project on SourceForge at http://htmltools.sourceforge.org/ under the "Common Public License Version 1.0" http://www.opensource.org/licenses/cpl1.0.php.

It was derived and refactored from the open source MAExplorer (http://maexplorer.sourceforge.org/), and Open2Dprot (http://Open2Dprot.sourceforge.net/) Table modules.

$Date: 2009/12/5 11:45:56 $ $Revision: 1.40 $
Copyright 2008, 2009 by Peter Lemkin E-Mail: lemkin@users.sourceforge.net http://lemkingroup.com/

Field Summary

boolean	addFCrangesForTestsIntersectionTableFlag Add FC range computations, then expand the TI table and add the three columns ("Max FC", "Min FC", "FC Range").
java.lang.String	addOutfilePostfixName Add a postfix name to the output file before the .html.
boolean	addRangeOfMeansToTItableFlag Add the ("Range Mean A", "Range Mean B" and "FC counts %") computations to an expanded TestsIntersectionTable table.
boolean	addRowNumbersFlag Add row numbers to the preface of each row with the "-addRowNumbers" switch.
java.lang.String	addTableName The table name as a HTML header just before the table with "-addTableName:{table name to use}" switch.
boolean	addTableNameFlag Add the table name as a HTML header just before the table with "-addTableName:{table name to use}" switch.
java.lang.String	altRowBackgroundColor If set to a HTML color, then alternate the background cell colors in alternate rows in the .
static boolean	ALWAYS flag: for debugging - always TRUE
java.lang.String[]	argsV Total command list arg list originally set from main(args)
java.lang.String	batchCwd The optional directory to run the batch script in if specified, else use the current directory.
java.lang.String[]	batchParamsSpecs Is a list of batch parameter specifications from the original -batchParam list specified by the batchParamFile.
java.lang.String	batchProcessFile The batch process file containing the list of param specifications.
boolean	batchProcessFlag Do batch processing of a list of param.map type files specified in a file.
java.lang.String	batchProcessStr The contents of the batchProcessFile to process.
int	bigCellFontSize This is the big cell font size decrement used when shrinking large cells.
int	bigExportCellThr This is the big cell threshold used when exporting large cells.
int	bigShrinkCellThr This is the big cell threshold used when shrinking large cells.
int[]	colHdrIdxHmapData index of the Column header name in the tField[] data from "-hrefData:{colHdrName,UrlBaseLink}" switches.
java.lang.String[]	colHdrNameHmapData Column header name from "-hrefData:{colHdrName,UrlBaseLink,mapTokenInUrl}" switches.
java.lang.String[]	colNameIndexMap This is the list of column names to be used when generating the index map file colNameIndexMap[0:nColNameIndexMap-1].
java.lang.String	colorMapScaleHTML Colormap data scale quantile TABLE HTML mapping the cvt.heatMapColors[] quantiles to positive numeric value in range of [cvt.glbMinRowVal, cvt.glbMaxRowVal].
boolean	concatInputFilesWithSameFieldsFlag 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.
java.lang.String	concatOutputHtmlFile The output .html file name derived from '-concatTables:{outputConcatenateFile.txt}'switch.
java.lang.String	concatOutputTxtFile The output .txt file for '-concatTables:{outputConcatenateFile.txt}' switch.
Convert	convert Global Convert instance
java.lang.String[]	copyDstFile List of destination output data file paths [0:nCopyFile-1].
boolean	copyFileFlag Copy input source file to output destination file in copySrcFile[0:nCopyFile-1] to copyDstFile[0:nCopyFile-1].
java.lang.String[]	copySrcFile List of source input data file paths [0:nCopyTreeDir-1].
boolean	copyTreeDataFlag Copy input data tree files to to output directory in copyTreeSrcDir[0:nCopyTreeDir-1] to copyTreeDstDir[0:nCopyTreeDir-1].
java.lang.String[]	copyTreeDstDir List of destination output data tree paths [0:nCopyTreeDir-1].
java.lang.String[]	copyTreeSrcDir List of source input data tree paths [0:nCopyTreeDir-1].
int	curBatchJobNbr Current batch job number being processed.
int	curBatchParamsSpecs Current batch param specification being processed in the batchParamsSpecs[] list.
java.lang.String	curInputFile Current input file being analyzed (w/o full path
static HTMLtools	cvt Instance of the main module
int	dataPrecisionHTMLtable Sets the precision to use in numeric data for a generated HTML file.
java.lang.String	date date captured when this program is run
static boolean	DBUG_FLAG flag: primary debug flag - only while debugging
java.lang.String[]	dirIndexHtml List of relative directory paths [0:nDirIndexHtml-1].
boolean	dirIndexHtmlFlag Make an "index.html" file of all of the files in the specified directories in the list of directories dirIndexHtml[0:nDirIndexHtml-1].
boolean[]	dirIndexHtmlOverrideFlag List of 'O'veride (true) flags [0:nDirIndexHtml-1].
java.lang.String[]	dropColNames List of columns to drop in the output set by the '-dropColumnName:{column header name}' switch.
java.lang.String	epilogue HTML epilogue string.
java.lang.String	epilogueFile HTML epilogue file.
int	EXPORT_BIG_CELL_SIZE Size beyond which an -exportBig cell is considered to be BIG
boolean	exportBigCellsToHTMLfileFlag Set with '-exportBigCellsToHTMLfile:{opt.
java.lang.String	extractColName The column name for the current table keyword used to extract the data specified with the '-extractRow:{colName,rowNbr,resourceTblFile,htmlStyle}' switch.
java.lang.String	extractHtmlStyle The extractHtmlStyle used to process the data extracted with the '-extractRow:{colName,rowNbr,resourceTblFile,htmlStyle}' switch.
java.lang.String	extractResTblFile The resource Table file from which to extract the data specified with the '-extractRow:{colName,rowNbr,resourceTblFile,htmlStyle}' switch.
boolean	extractRowFromResTblAsHTMLflag Flag to to get and lookup a keyword in the table being processed at (colName,rowNbr) and then to search a resourceTblFile for that keyword.
int	extractRowNbr The row number for the current table keyword used to extract the data specified with the '-extractRow:{colName,rowNbr,resourceTblFile,htmlStyle}' switch.
boolean	fastEditFileFlag [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.
static java.lang.String	fileSep JVM ("file.separator")
java.lang.String	filterDataField Specifies the tField name of MRR Table data to test.
java.lang.String[]	filterDataList Specifies the list of filter instances to test.
java.lang.String	filterTestField Specifies the tField name of Tests-ToDo Table data to test.
java.lang.String[]	filterTestsList Specifies the list of filter instances to test.
FileTable	fio Global FileTable instance
java.lang.String	flipAclass If reporting fold change in flip Table reporting, then "-flipAclass:{flipAclass}" specifies the Class A samples.
java.lang.String	flipBclass If reporting fold change in flip Table reporting, then "-flipBclass:{flipBclass}" specifies the Class A samples.
java.lang.String[]	flipColumnFile 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.
java.lang.String[]	flipColumnName These are the list of column names to be used when generating the flipped Table using the '-flipTableByIndexMap:{flipDataFile,flipIndexMapFile,(opt)maxRows}' switch.
java.lang.String[][]	flipColumnValues 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.
java.lang.String	flipDataFile Name of the data file to be used when flipping a table.
java.lang.String	flipDirectory 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.
java.lang.String[]	flipExcludeColumnName These are the list of column names to exclude when generating the flipped Table using the '-flipTableByIndexMap:{flipDataFile,flipIndexMapFile,(opt)maxRows}' switch.
float	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.
boolean	flipFCthrFlag If reporting fold change with reportFoldChangeFlag in flip Table reporting, and -flipFCthreshold:{flipFCthreshold}, then set the flipFCthrFlag and save the postive value in flipFCthreshold.
java.lang.String	flipIndexMapFile Name of the Index Map file to be used when flipping a table.
java.lang.String[]	flipOrderHdrColList 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.
java.lang.String[]	flipRowFilterNames This is the list of row names [0:nFlipRowFilterNames-1] to be used when generating the flipped Table using the '-flipTableByIndexMap:{flipDataFile,flipIndexMapFile}' switch.
java.lang.String	flipRowFilterNamesFile 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}'.
java.lang.String[]	flipRowGSPIDfilters
java.lang.String	flipSaveOutputFile 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.
boolean	flipTableByIndexMapFlag 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.
boolean	flipTableUseExactMatchFlag This is the exact match filter flag.
java.lang.String[]	fromLongHdrNamesMap The long 'From_name' from the (From_name\tTo_name) data used to map long to short header names.
FileTable	ftConcat This contains the concatenated Table data for the processing with the '-concatTables:{outputConcatenateFile.txt}' switch.
FileTable	ftL2S The Long to Short mapping Table read by Switches with the '-mapLongToShortHdrNames:{long2ShortHdrNamesTable.map}'
java.lang.String	genAnalysesDir 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.
java.lang.String	genBatchDir The name of the {batchScripts} directory to put the other directories.
boolean	genBatchScriptFlag Generate a set of parameter .map files in the batchDir directory.
static java.lang.String[]	genHTMLpathList Converter generated HTML files path list.
java.lang.String	genInputTreeDir The name of the {inputTreeDir} directory (inside of the genBatchDir) where the input data to be processed by the batch params .map files are copied.
java.lang.String	genJTVDir 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.
java.lang.String	genMapEGdetails The name of the of the {EGdetailsMapFile} file to process.
java.lang.String	genMapIntroduction The name of the of the {introductionMapFile} file to process.
java.lang.String	genParamsScriptsDir 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.
java.lang.String[]	genParamTemplateFiles List of paramTemplateFileName entries when define the Param Templates.
boolean	genParamTemplateFlag List of Parameter map Templates that are used for mapping the test-ToDo-list data so that (param-MRR, param-MRR-keep, param-JTV) etc.
java.lang.String[]	genParamTemplateNames List of order numbers when define the Param Templates.
java.lang.String	genSummaryDir The name of the {Summary} directory (inside of the genBatchDir) where the generated Summary HTML web files are saved.
boolean	genSummaryTemplateFlag List of Summary Templates that are used for mapping the test-ToDo-list data so that (summaryProlog, summaryExperimental, summaryAnalysis, summaryFurtherAnalysis, summaryEpilogue) etc.
java.lang.String[]	genSummaryTemplateNames List of templateFileName entries when define the Summary Templates.
int[]	genSummaryTemplateOrderNbrs List of order numbers when define the Summary Templates.
java.lang.String[]	genSupportFilesToCopy List of support files to copy to the batchScriptsDir.
boolean	genTestsIntersectionFlag Generate Tests-Intersection params .map files and insert links into $$TEST-INTERSECTION$$ which is "" otherwise.
java.lang.String	genTestToDoListFile The name of the of the {test-ToDo-list.txt} file to process.
boolean	genTreeCopyDataFlag Copy input data tree data to batch scripts subdirectory.
java.lang.String[]	genTreeDstTreeDir Destination output data tree path to batch scripts subdirectory.
java.lang.String[]	genTreeSrcTreeDir Source input data tree data to batch scripts subdirectory.
float	glbMaxRowVal Global max value from data table computed in DataRowStatisticsIndexMap class and saved in a .sidx Table file.
float	glbMeanRowVal Global mean value from data table computed in DataRowStatisticsIndexMap class and saved in a .sidx Table file.
float	glbMinRowVal Global min value from data table computed in DataRowStatisticsIndexMap class and saved in a .sidx Table file.
float	glbStdDevRowVal Global stdDev value from data table computed in DataRowStatisticsIndexMap class and saved in a .sidx Table file.
boolean	hasEmptyLineBeforeTableFlag Set to true to look for empty line(s) BEFORE the table data.
boolean	hasStatIndexMapFileFlag Set if using the Statistics Index Map file (.sidx).
boolean	hasTableHeaderRowFlag Flag cleared if the input table does NOT have a header, default is that it has a header.
static java.lang.String[]	heatMapColors Heat-map cell color background range in 7 quantiles of colors: dark green, middle green, light green, white, light red, middle red, dark red .
boolean	hrefHeaderRowFlag 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.
boolean	ignoreDuplicateFieldsFlag Flag set if the input table MAY have duplicate fields in the header, default is no duplicates in the header.
java.lang.String	inputDataDir Input Data Path to use from "-inputDir:{inputTXTdir}" command, default is "data".
java.lang.String	inputExt Input file extension
java.lang.String[]	inputFiles List of input files (with inputExt) to convert
java.lang.String[]	inputNames List of input files (without inputExt) to convert
static boolean	isMacFlag flag: use Max list of required fields
static boolean	isSunFlag flag: true if SUNOS
static boolean	isWinPCflag flag: true if Windows PC
java.lang.String	joinTableFile
java.lang.String	jtv_mAdbArraySummaryFile Name of the mAdb Array Summary file which contains a Table with "mAdb ID" and the corresponding "Array Name" (MAS).
java.lang.String	jtv_mapHdrNamesFile 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.
java.lang.String	jtvButtonName String set with '-jtvButtonName:{button label}' that may be used with '-jtvHTMLgenerate' to label the button to activate Java TreeView.
java.lang.String	jtvCopyJTVjars If doing 'jtvHTMLgenerate', then you can use the '-jtvCopyJTVjars:{JTV jars directory}' option to copy the JTV jar files and plugins to the jtvOutputDir.
java.lang.String	jtvDescription String set with '-jtvDescription:{prolog description}' that may be used with '-jtvHTMLgenerate' to insert additional text into the prolog where it replaces "$$DATA_DESCRIPTION$$".
boolean	jtvHTMLgenerateFlag Flag set by '-jtvHTMLgenerate'.
java.lang.String	jtvInputDir Directory where to find the set of input JTV sub directories, each with (.atr,.cdt,.gtr) extension files.
boolean	jtvMapFlag Flag set if doing '-jtvNamesMap:{mAdbArraySummaryFile,mapHdrFile,fromHdrName,toHdrName}'.
java.lang.String	jtvOutputDir Directory where to write the converted JTV output file sub directories.
boolean	jtvReZipConvertedFiles Set to rezip the converted files in the output JTV directory in a file with the same name.
java.lang.String	jtvSpecificInputFileList Specific list of input files string from "-jtvFiles:f1,f2,...,fn" cmd line switch.
int	jtvUseMapFromColNbr '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.
int	jtvUseMapToColNbr '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.
java.lang.String[]	keepColNames List of columns to keep in the output set by the '-keepColumnName:{column header name}' switch.
int	limitMaxTableRows
boolean	limitMaxTableRowsFlag
boolean	limitRowsSortAscendingFlag
java.lang.String	limitRowsSortByColName
java.lang.String	logFileName Log file that is written out at the end before exiting.
int	long2ShortFromColNbr The FromColumnNbr of mapping file (From_name\tTo_name) used to map long to short header names.
int	long2ShortToColNbr The ToColumnNbr of mapping file (From_name\tTo_name) used to map long to short header names.
static boolean	MAKE_LOGGING_FILE flag: set if want logging file
boolean	makeHTMLflag Allow generation of HTML when doing a input file processing if that operation also allows HTML generation.
java.lang.String	makeIndexMapFile 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).
boolean	makeIndexMapFileFlag 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).
java.lang.String[]	makeMapColNames Ordered list of column names to be used in the map file being created.
java.lang.String	makeMapTblFileName Name of the map file to be made (only) at the same time we do a -concatTable operation.
boolean	makeOptionsListFromSemicolonListFlag Flag to map a ;; delimited cell string to an list.
boolean	makePrefaceHTMLflag Flag to make a separate preface HTML file from the input text proceeding the table data.
boolean	makeStatisticsIndexMapFlag Make a 'Statistics Index Map' Table file with the same base file name as the index map (.idx) but with a .sidx file extension.
boolean	makeTestsIntersectionTableFlag Do Tests Intersection mapping.
boolean	makeTXTflag Allow generation of TXT when doing a input file processing if that operation also allows TXT generation.
java.lang.String[]	mapDkeywords List of keywords when map prologue, epilogue and cell data of the form '$$keyword$$' to 'toString'.
boolean	mapDollarsignsFlag Map prologue, epilogue and cell data of the form '$$keyword$$' to 'toString'.
java.lang.String[]	mapDtoString List of toString words when map prologue, epilogue and cell data of the form '$$keyword$$' to 'toString'.
java.lang.String	mapHdrNamesFile Name of names mapping file (From_name\tTo_name) used to map long to short header names.
boolean	mapHdrNamesFlag Map long to short header names.
java.lang.String[]	mapQkeywords List of keywords when map prologue, epilogue and cell data of the form '??keyword??' to 'toString'.
java.lang.String[]	mapQtoString List of toString words when map prologue, epilogue and cell data of the form '??keyword??' to 'toString'.
boolean	mapQuestionmarksFlag Map prologue, epilogue and cell data of the form '??keyword??' to 'toString'.
java.lang.String[]	mapTokenInUrlHmapData Map Token name in the URL to replace with the column cell data from "-hrefData:{colHdrName,UrlBaseLink,mapTokenInUrl}" switches.
int	MAX_BATCH_SPECS The maximum number of param .map specifications in the '-batchProcess:{file of param specifications}' switch.
int	MAX_COL_EDITS The max number of columns instances that be be specified using -dropColumn and -keepColumn switches.
int	MAX_COL2URL_MAPS The max # of Columns to URL maps from "-hrefData:{colHdrName,UrlBaseLink,mapToken}" switches
int	MAX_COPY_FILES_AND_TREES The maximum number of directory tree and file specifications to copy switch.
int	MAX_IN_TOKENS_PER_ROW max # of tokens/row of an input file
int	MAX_INPUT_FILES Maximum number of input files
int	MAX_MAP_DOLLARSIGNS The max mapDollarsigns instances using -mapDollarsigns switchs.
int	MAX_MAP_QUESTIONMARKS The max mapQuestionmarks instances using -mapQuestionark switchs.
int	MAX_SORT_COLUMNS The max sort columns instances using -sortRowsByColumn switch.
int	MAX_TEMPLATES The maximum number of Summary Template specifications in the '-genSummaryTemplate:{orderNbr,templateFileName}' switch.
int	maxBatchParamsSpecs Number of batch param specs in the batch file.
int	maxFlipSeekRowsToExtract Maximum number of rows to flip from the flipDataFile
int	nbrTableHdrLines Number of lines of the Table header "-hdr:{# lines in header}" switches.
int	nColNameIndexMap Number of column names colNameIndexMap[0:nColNameIndexMap-1] to be used when generating the index map file.
int	nColUrlHmapData 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.
int	nCopyFile Number of instances of file copy specifications in copySrcFile[0:nCopyFile-1] to copyDstFile[0:nCopyFile-1].
int	nCopyTreeDir Number of instances of tree file copy specifications in copyTreeSrcDir[0:nCopyTreeDir-1] to copyTreeDstDir[0:nCopyTreeDir-1].
int	nDirIndexHtml Number of instances of tree file copy specifications in dirIndexHtml[0:nDirIndexHtml-1].
int	nDropColNames Size of the dropColNames[] list to drop from the in outout.
static boolean	NEVER flag: for debugging - always FALSE
java.lang.String[]	newHdrMapColNames List of new header map column names.
java.lang.String	newline New line separator will be CRLF or LF etc.
int	nFlipColumns 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.
int	nFlipExcludeColumns This is the number of column names to exclude when generating the flipped Table using the '-flipTableByIndexMap:{flipDataFile,flipIndexMapFile,(opt)maxRows}' switch.
int	nFlipOrderHdrColList 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.
int	nFlipRowFilterNames Size of the list of row names [0:nFlipRowFilterNames-1] to be used when generating the flipped Table using the '-flipTableByIndexMap:{flipDataFile,flipIndexMapFile}' switch.
int	nGenParamTemplates Number of Param Templates.
int	nGenSummaryTemplates Number of Summary Templates .
int	nGenSupportFilesToCopy Number of support files to copy to the batchScriptsDir.
int	nGenTreeCopy 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].
int	nHdrMapColNames Number of mappings to check when map header column names.
int	nInputFiles # of input files found in inputDataDir
int	nKeepColNames Size of the keepColNames[] list to drop from the in outout.
int	nLong2ShortHdrNamesMap The length of the (From_name\tTo_name) data used to map long to short header names.
int	nMakeMapColNames Number of entries in the ordered lList of column names makeMapColNames[] to be used in the map file being created.
int	nMapDollarsigns Number of mappings to check when map prologue, epilogue and cell data of the form '$$keyword$$' to 'toString'.
int	nMapQuestionmarks Number of mappings to check when map prologue, epilogue and cell data of the form '??keyword??' to 'toString'.
boolean	noBorderFlag Flag set if the TABLE does not have a border.
int	nReorderColName 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].
int	nSortTable The number of instances of the sort rows by column switch -sortRowsByColumn:{colName,'A'scending or 'D'escending}.
java.lang.String[]	oldHdrMapColNames List of old header map column names.
java.lang.String	oldUserDir This is the old current directory before it was changed by a new working directory set by the'-batchProcess:{file of param specs, opt.
static java.lang.String	openSourceNotice Open Source help string
static java.lang.String	osName JVM ("os.name") that we are running in
java.lang.String	outputDataDir Output Data Path to use from "-outputDir:{outputHTMLdir}" command, default is "html".
java.lang.String	outputExt Output file extension
java.lang.String[]	outputFiles List of input files (with inputExt) to convert
java.lang.String	paramMapDir Directory with the Parameter command list file.
java.lang.String	paramMapFile Parameter command list file is used.
static java.lang.String	programName Program name
static java.lang.String	programSummary program summary
java.lang.String	prolog HTML prolog string.
java.lang.String	prologFile HTML prolog file.
static java.lang.String	referenceManual Reference Manual is "MANUAL.html" for CvtTabDelim2HTML and "ReferenceManual.html" for HTMLtools.
java.lang.String[]	reorderColName List of Column header names [0:nReorderColName-1] from '-reorderColumn:{colName,newColNbr}' to reorder this column to the new column number in reorderColNbr[].
int[]	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[].
boolean	reorderRemainingColumnsFlag
boolean	reportFoldChangeFlag Flag to indicate reporting fold change in flip Table reporting, when both Class A and B are defined.
boolean	rmvTrailingBlankRowsAndColumnsFlag Flag set if remove trailing blank lines and trailing empty columns at the end of the table, default is to allow blank lines.
java.lang.String	saveEditedTable2File Make a Table file from the modified input table stream.
boolean	saveEditHTMLflag Save output HTML when doing a -saveEditedTable2File operation.
boolean	saveEditTableFlag Save edited data Table in an output file.
boolean	showDataHeatmapFlipTableFlag Flag used to generate colored heat-map data cells in a HTML conversion for a flip table using the '-flipTableByIndexMap' option.
int	SHRINK_BIG_CELL_SIZE Size beyond which a -shrinkBig cell is considered to be BIG
int	SHRINK_CELL_SIZE Decrease font size by this amount if a cell is considered to be BIG
boolean	shrinkBigCellsFlag Shrink big cells in the table with more than bigShrinkCellThr characters by decreasing the font size by bigCellFontSize for those cells.
java.lang.String	sortFlipTableByColumnName
boolean	sortRowsByColumnFlag Flag to sort the rows of the Table by values in the specified column.
boolean[]	sortTableAscendingFlag Flag to specify the sort direction of the rows of the Table by values in the specified column.
java.lang.String[]	sortTableColName Name of column to sort the rows of the Table by values in this column.
java.lang.String	sParamsStr Parameter command list string if parameter file is used.
java.lang.String	specificInputFileList Specific list of input files string from "-files:f1,f2,...,fn" cmd line switch.
java.lang.String	startTableAtKeywordLine 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.
Switches	sw Global Switches instance
java.lang.String	tableDataDir Tables Path to use for various mapping tables specified with the "-tableDir:{tablesDirectory}" command, default is "data.Table".
java.lang.String	testsToDoTblFile The ToDo tests file to use in Tests Intersection mapping.
java.lang.String	title top level GUI title
java.lang.String[]	toShortHdrNamesMap The short 'To_name' from the (From_name\tTo_name) data used to map long to short header names.
java.lang.String[]	urlBaseLinkHmapData URL base link from "-hrefData:{colHdrName,UrlBaseLink,mapTokenInUrl}" switches.
java.lang.String	useHTMLfontSize Use an HTML font size!= null, i.e.
boolean	useOnlyLastHeaderLineFlag Reduce the number of header lines to 1 even if there are more than 1 header line.
static java.lang.String	userDir user directory - JVM ("user.dir")+fileSep
UtilCM	util Global utilities UtilCM instance

Constructor Summary

Globals()

Method Summary

void	reinitGBSglobalSwitches() reinitGBSglobalSwitches() - reinitialize GBS Global variable switches.
void	reinitGlobalSwitches() reinitGlobalSwitches() - reinitialize Global variable switches.
void	reinitJTVglobalSwitches() reinitJTVglobalSwitches() - reinitialize JTV Global variable switches.
void	reinitTIglobalSwitches() reinitTIglobalSwitches() - reinitialize TestsIntersection Global switches.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

programName

public static final java.lang.String programName

Program name

See Also:

Constant Field Values

referenceManual

public static final java.lang.String referenceManual

Reference Manual is "MANUAL.html" for CvtTabDelim2HTML and "ReferenceManual.html" for HTMLtools.

See Also:

Constant Field Values

openSourceNotice

public static final java.lang.String openSourceNotice

Open Source help string

See Also:

Constant Field Values

programSummary

public static final java.lang.String programSummary

program summary

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Constant Field Values

cvt

public static HTMLtools cvt

Instance of the main module

convert

public Convert convert

Global Convert instance

fio

public FileTable fio

Global FileTable instance

sw

public Switches sw

Global Switches instance

util

public UtilCM util

Global utilities UtilCM instance

argsV

public java.lang.String[] argsV

Total command list arg list originally set from main(args)

paramMapFile

public java.lang.String paramMapFile

Parameter command list file is used.

paramMapDir

public java.lang.String paramMapDir

Directory with the Parameter command list file. Used as a base directory for other .map files.

sParamsStr

public java.lang.String sParamsStr

Parameter command list string if parameter file is used.

ALWAYS

public static boolean ALWAYS

flag: for debugging - always TRUE

NEVER

public static boolean NEVER

flag: for debugging - always FALSE

MAKE_LOGGING_FILE

public static final boolean MAKE_LOGGING_FILE

flag: set if want logging file

See Also:

Constant Field Values

DBUG_FLAG

public static boolean DBUG_FLAG

flag: primary debug flag - only while debugging

MAX_INPUT_FILES

public final int MAX_INPUT_FILES

Maximum number of input files

See Also:

Constant Field Values

EXPORT_BIG_CELL_SIZE

public final int EXPORT_BIG_CELL_SIZE

Size beyond which an -exportBig cell is considered to be BIG

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Constant Field Values

SHRINK_BIG_CELL_SIZE

public final int SHRINK_BIG_CELL_SIZE

Size beyond which a -shrinkBig cell is considered to be BIG

See Also:

Constant Field Values

SHRINK_CELL_SIZE

public final int SHRINK_CELL_SIZE

Decrease font size by this amount if a cell is considered to be BIG

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Constant Field Values

MAX_IN_TOKENS_PER_ROW

public final int MAX_IN_TOKENS_PER_ROW

max # of tokens/row of an input file

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Constant Field Values

MAX_COL2URL_MAPS

public final int MAX_COL2URL_MAPS

The max # of Columns to URL maps from "-hrefData:{colHdrName,UrlBaseLink,mapToken}" switches

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Constant Field Values

MAX_MAP_DOLLARSIGNS

public final int MAX_MAP_DOLLARSIGNS

The max mapDollarsigns instances using -mapDollarsigns switchs.

See Also:

Constant Field Values

MAX_MAP_QUESTIONMARKS

public final int MAX_MAP_QUESTIONMARKS

The max mapQuestionmarks instances using -mapQuestionark switchs.

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Constant Field Values

MAX_SORT_COLUMNS

public final int MAX_SORT_COLUMNS

The max sort columns instances using -sortRowsByColumn switch.

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Constant Field Values

MAX_COL_EDITS

public final int MAX_COL_EDITS

The max number of columns instances that be be specified using -dropColumn and -keepColumn switches.

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Constant Field Values

MAX_BATCH_SPECS

public final int MAX_BATCH_SPECS

The maximum number of param .map specifications in the '-batchProcess:{file of param specifications}' switch.

See Also:

Constant Field Values

MAX_TEMPLATES

public final int MAX_TEMPLATES

The maximum number of Summary Template specifications in the '-genSummaryTemplate:{orderNbr,templateFileName}' switch.

See Also:

Constant Field Values

MAX_COPY_FILES_AND_TREES

public final int MAX_COPY_FILES_AND_TREES

The maximum number of directory tree and file specifications to copy switch.

See Also:

Constant Field Values

title

public java.lang.String title

top level GUI title

osName

public static java.lang.String osName

JVM ("os.name") that we are running in

fileSep

public static java.lang.String fileSep

JVM ("file.separator")

userDir

public static java.lang.String userDir

user directory - JVM ("user.dir")+fileSep

date

public java.lang.String date

date captured when this program is run

isWinPCflag

public static boolean isWinPCflag

flag: true if Windows PC

isSunFlag

public static boolean isSunFlag

flag: true if SUNOS

isMacFlag

public static boolean isMacFlag

flag: use Max list of required fields

logFileName

public java.lang.String logFileName

Log file that is written out at the end before exiting. The default is programName+".log" which is overridden by the 'logName:{new log file name ending in ".log"}' switch. It is overwritten using the '-logging:{newLogFileName}'.

newline

public java.lang.String newline

New line separator will be CRLF or LF etc.

addRowNumbersFlag

public boolean addRowNumbersFlag

Add row numbers to the preface of each row with the "-addRowNumbers" switch.

addOutfilePostfixName

public java.lang.String addOutfilePostfixName

Add a postfix name to the output file before the .html. E.g., for an output file 'abc.html', with a postfix name of '-xyz', the new name is 'abc'xyz.html'. It is set with '-addOutfilePostfix:{postfix name}' switch.

useHTMLfontSize

public java.lang.String useHTMLfontSize

Use an HTML font size!= null, i.e. +1, +2, -1, -2, etc. with "-fontSizeHtml:{font Size modifier}" command line switch. Default is to decrease the size by -1.

noBorderFlag

public boolean noBorderFlag

Flag set if the TABLE does not have a border. The default is to use a 'BORDER=1'. Cleared with the "-noBorder" switch.

hasTableHeaderRowFlag

public boolean hasTableHeaderRowFlag

Flag cleared if the input table does NOT have a header, default is that it has a header. Cleared with the "-noHeader" switch.

hasEmptyLineBeforeTableFlag

public boolean hasEmptyLineBeforeTableFlag

Set to true to look for empty line(s) BEFORE the table data. Set with the "-hasEmptyLineBeforeTable"

ignoreDuplicateFieldsFlag

public boolean ignoreDuplicateFieldsFlag

Flag set if the input table MAY have duplicate fields in the header, default is no duplicates in the header. Set with the "-allowHdrDups" switch.

rmvTrailingBlankRowsAndColumnsFlag

public boolean rmvTrailingBlankRowsAndColumnsFlag

Flag set if remove trailing blank lines and trailing empty columns at the end of the table, default is to allow blank lines. Set with the "-rmvTrailingBlankRowsAndColumns" switch.

makeOptionsListFromSemicolonListFlag

public boolean makeOptionsListFromSemicolonListFlag

Flag to map a ;; delimited cell string to an list. Set with the "-mapOptionsList" switch. Default is no mapping.

altRowBackgroundColor

public java.lang.String altRowBackgroundColor

If set to a HTML color, then alternate the background cell colors in alternate rows in the . Default is no alternating of colors colors. Set with the '-alternateRowBackgroundColor:{c}' switch.

makePrefaceHTMLflag

public boolean makePrefaceHTMLflag

Flag to make a separate preface HTML file from the input text proceeding the table data. The file has the same name, but has a "preface-" string in the name. Default no preface file. Set by '-makePrefaceHTML' switch.

nbrTableHdrLines

public int nbrTableHdrLines

Number of lines of the Table header "-hdr:{# lines in header}" switches. The number of Table header lines with default of 1. If > 1 line, then the Table Fields searched for URL mapping are The last one in the header row. All header lines are bolded with TH rather than TD.

startTableAtKeywordLine

public java.lang.String startTableAtKeywordLine

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. Default no keyword search. Set by '-startTableAtKeywordLine:{keyword} switch.

useOnlyLastHeaderLineFlag

public boolean useOnlyLastHeaderLineFlag

Reduce the number of header lines to 1 even if there are more than 1 header line. Set by '-useOnlyLastHeaderLine'.

oldHdrMapColNames

public java.lang.String[] oldHdrMapColNames

List of old header map column names. List is of size nHdrMapColName and is allocated [0:MAX_COL_EDITS-1]. Set by '-hdrMapName:{oldHdrColName,newHdrColName}' switch.

newHdrMapColNames

public java.lang.String[] newHdrMapColNames

List of new header map column names. List is of size nHdrMapColName and is allocated [0:MAX_COL_EDITS-1]. Set by '-hdrMapName:{oldHdrColName,newHdrColName}' switch.

nHdrMapColNames

public int nHdrMapColNames

Number of mappings to check when map header column names. Set by number of '-hdrMapName:{oldHdrColName,newHdrColName}' switch entries.

addTableNameFlag

public boolean addTableNameFlag

Add the table name as a HTML header just before the table with "-addTableName:{table name to use}" switch.

addTableName

public java.lang.String addTableName

The table name as a HTML header just before the table with "-addTableName:{table name to use}" switch. This is added as preface text if it is defined.

mapQuestionmarksFlag

public boolean mapQuestionmarksFlag

Map prologue, epilogue and cell data of the form '??keyword??' to 'toString'. If the keyword is 'ANY', then map any keyword string to bold and red. It is set by '-mapQuestionmarks:{keyword,toString}' switch.

mapQkeywords

public java.lang.String[] mapQkeywords

List of keywords when map prologue, epilogue and cell data of the form '??keyword??' to 'toString'. List is of size nMapQuestionmarks and is allocated [0:MAX_MAP_QUESTIONMARKS-1]. See the mapQuestionmarksFlag for details.

mapQtoString

public java.lang.String[] mapQtoString

List of toString words when map prologue, epilogue and cell data of the form '??keyword??' to 'toString'. List is of size nMapQuestionmarks and is allocated [0:MAX_MAP_QUESTIONMARKS-1]. See the mapQuestionmarksFlag for details.

nMapQuestionmarks

public int nMapQuestionmarks

Number of mappings to check when map prologue, epilogue and cell data of the form '??keyword??' to 'toString'. See the mapQuestionmarksFlag for details.

mapDollarsignsFlag

public boolean mapDollarsignsFlag

Map prologue, epilogue and cell data of the form '$$keyword$$' to 'toString'. If the keyword is 'ANY', then map any keyword string to bold and red. It is set by '-mapDollarsigns:{$$keyword$$,toString}' switch.

mapDkeywords

public java.lang.String[] mapDkeywords

List of keywords when map prologue, epilogue and cell data of the form '$$keyword$$' to 'toString'. List is of size nMapDollarsigns and is allocated [0:MAX_MAP_DOLLARSIGNS-1]. See the mapDollarsignsFlag for details.

mapDtoString

public java.lang.String[] mapDtoString

List of toString words when map prologue, epilogue and cell data of the form '$$keyword$$' to 'toString'. List is of size nMapDollarsigns and is allocated [0:MAX_MAP_DOLLARSIGNS-1]. See the mapDollarsignsFlag for details.

nMapDollarsigns

public int nMapDollarsigns

Number of mappings to check when map prologue, epilogue and cell data of the form '$$keyword$$' to 'toString'. See the mapDollarsignsFlag for details.

exportBigCellsToHTMLfileFlag

public boolean exportBigCellsToHTMLfileFlag

Set with '-exportBigCellsToHTMLfile:{opt. size for big}' switch. Flag set to save the contents of big cells as separate HTML files with prefix 'bigRC-. Does not map colHdr names. Default is no exporting of big cells.

bigExportCellThr

public int bigExportCellThr

This is the big cell threshold used when exporting large cells. It is set with '-exportBigCellsToHTMLfile:{opt. size for big}' switches.

bigCellFontSize

public int bigCellFontSize

This is the big cell font size decrement used when shrinking large cells. It is set with switch '--shrinkB:{opt. size for big,opt. font size decrement}'

shrinkBigCellsFlag

public boolean shrinkBigCellsFlag

Shrink big cells in the table with more than bigShrinkCellThr characters by decreasing the font size by bigCellFontSize for those cells. with the "-shrinkB:{opt. size for big,opt. font size decrement}" switch.

bigShrinkCellThr

public int bigShrinkCellThr

This is the big cell threshold used when shrinking large cells. It is set with the '--shrinkB:{opt. size for big,opt. font size decrement}' switches.

showDataHeatmapFlipTableFlag

public boolean showDataHeatmapFlipTableFlag

Flag used to generate colored heat-map data cells in a HTML conversion for a flip table using the '-flipTableByIndexMap' option. It uses the global statistics on the (digital) data in the Statistics Index Map .sidx fileIF IT EXISTS to normalize the data and generate a cell color background range in 7 quantiles of colors: dark green, medium green, light green, white, light red, medium red, dark red. It is set by the "-showDataHeatmapFlipTable" switch.

hasStatIndexMapFileFlag

public boolean hasStatIndexMapFileFlag

Set if using the Statistics Index Map file (.sidx).

glbMinRowVal

public float glbMinRowVal

Global min value from data table computed in DataRowStatisticsIndexMap class and saved in a .sidx Table file.

glbMaxRowVal

public float glbMaxRowVal

Global max value from data table computed in DataRowStatisticsIndexMap class and saved in a .sidx Table file.

glbMeanRowVal

public float glbMeanRowVal

Global mean value from data table computed in DataRowStatisticsIndexMap class and saved in a .sidx Table file.

glbStdDevRowVal

public float glbStdDevRowVal

Global stdDev value from data table computed in DataRowStatisticsIndexMap class and saved in a .sidx Table file.

heatMapColors

public static java.lang.String[] heatMapColors

Heat-map cell color background range in 7 quantiles of colors: dark green, middle green, light green, white, light red, middle red, dark red . It is set by the "-showDataHeatmapFlipTable" switch.

colorMapScaleHTML

public java.lang.String colorMapScaleHTML

Colormap data scale quantile TABLE HTML mapping the cvt.heatMapColors[] quantiles to positive numeric value in range of [cvt.glbMinRowVal, cvt.glbMaxRowVal]. Computed by convert.makeColorMapScaleHTML() if cvt.showDataHeatmapFlipTableFlag and cvt.hasStatIndexMapFileFlag are set.

dataPrecisionHTMLtable

public int dataPrecisionHTMLtable

Sets the precision to use in numeric data for a generated HTML file. The table must be a numeric data table (such as generated using the '-flipTableByIndexMap' option. If the value is< 0, then use the full precision of the data (as supplied in the input string data). If {nbr digits precision} >= 0, then clip digits as required. Set by the '-dataPrecisionHTMLtable:{nbr digits precision}' switch.

sortFlipTableByColumnName

public java.lang.String sortFlipTableByColumnName

concatInputFilesWithSameFieldsFlag

public boolean concatInputFilesWithSameFieldsFlag

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. The -outputDir switch specifies where the file is saved. The output file is in concatOutputTxtFile. Default is not to merge the input files.

concatOutputTxtFile

public java.lang.String concatOutputTxtFile

The output .txt file for '-concatTables:{outputConcatenateFile.txt}' switch. Default is not to concatenate the input files.

concatOutputHtmlFile

public java.lang.String concatOutputHtmlFile

The output .html file name derived from '-concatTables:{outputConcatenateFile.txt}'switch. Default is not to concatenate the input files.

ftConcat

public FileTable ftConcat

This contains the concatenated Table data for the processing with the '-concatTables:{outputConcatenateFile.txt}' switch.

makeMapTblFileName

public java.lang.String makeMapTblFileName

Name of the map file to be made (only) at the same time we do a -concatTable operation. It is set with the switch -makeMapFile:{makeMapTblFileName,orderedCommaColList}. The associated map column names are in makeMapColNames[0:nMakeMapColNames-1].

makeMapColNames

public java.lang.String[] makeMapColNames

Ordered list of column names to be used in the map file being created. This is only done at the same time we do a -concatTable operation. It is set with the switch -makeMapFile:{makeMapTblFileName,orderedCommaColList}. The associated map file is makeMapTblFileName. The number of entries is nMakeMapColNames.

nMakeMapColNames

public int nMakeMapColNames

Number of entries in the ordered lList of column names makeMapColNames[] to be used in the map file being created. This is only done at the same time we do a -concatTable operation. It is set with the switch -makeMapFile:{makeMapTblFileName,orderedCommaColList}.

mapHdrNamesFlag

public boolean mapHdrNamesFlag

Map long to short header names. Default is no mapping. It is set by '-mapLongToShortHdrNames:{long2Short names map file, opt. toColumnNbr}' switch.

mapHdrNamesFile

public java.lang.String mapHdrNamesFile

Name of names mapping file (From_name\tTo_name) used to map long to short header names. Default is "mapHdrNames.map". It is set by '-mapHdrNames:{mapFile,fromFieldName,toFieldName}"' switch.

long2ShortFromColNbr

public int long2ShortFromColNbr

The FromColumnNbr of mapping file (From_name\tTo_name) used to map long to short header names. Default is 1. Ranges from 1 not 0. It is set by '-mapLongToShortHdrNames:{long2Short names map file, opt. toColumnNbr}' switch. Also set by '-mapHdrNames:{mapFile,fromHdrName,toHdrName}' switch.

long2ShortToColNbr

public int long2ShortToColNbr

The ToColumnNbr of mapping file (From_name\tTo_name) used to map long to short header names. Default is 2. Ranges from 1 not 0. It is set by '-mapLongToShortHdrNames:{long2Short names map file, opt. toColumnNbr}' switch. Also set by '-mapHdrNames:{mapFile,fromHdrName,toHdrName}' switch

fromLongHdrNamesMap

public java.lang.String[] fromLongHdrNamesMap

The long 'From_name' from the (From_name\tTo_name) data used to map long to short header names. It is set by '-mapToShortHdrNames:{long2ShortHdrNamesTable.map}'

toShortHdrNamesMap

public java.lang.String[] toShortHdrNamesMap

The short 'To_name' from the (From_name\tTo_name) data used to map long to short header names. It is set by '-mapLongToShortHdrNames:{long2ShortHdrNamesTable.map}'

nLong2ShortHdrNamesMap

public int nLong2ShortHdrNamesMap

The length of the (From_name\tTo_name) data used to map long to short header names. It is set by '-mapLongToShortHdrNames:{long2ShortHdrNamesTable.map}'

ftL2S

public FileTable ftL2S

The Long to Short mapping Table read by Switches with the '-mapLongToShortHdrNames:{long2ShortHdrNamesTable.map}'

extractRowFromResTblAsHTMLflag

public boolean extractRowFromResTblAsHTMLflag

Flag to to get and lookup a keyword in the table being processed at (colName,rowNbr) and then to search a resourceTblFile for that keyword. If it found, then it will extract the header row and the data row from the resource file and create HTML of htmlStyle. This string is then inserted into the front of the epilogue. The htmlStyles may be DL, OL, UL and and Table. Default is no row extraction. The args are specified with the '-extractRow:{colName,rowNbr,resourceTblFile,htmlStyle}' switch. It has associated variables: extractColName, extractRowNbr, extractResTblFile, extractHtmlStyle.

extractColName

public java.lang.String extractColName

The column name for the current table keyword used to extract the data specified with the '-extractRow:{colName,rowNbr,resourceTblFile,htmlStyle}' switch. See extractRowFromResTblAsHTMLflag for details.

extractRowNbr

public int extractRowNbr

The row number for the current table keyword used to extract the data specified with the '-extractRow:{colName,rowNbr,resourceTblFile,htmlStyle}' switch. See extractRowFromResTblAsHTMLflag for details.

extractResTblFile

public java.lang.String extractResTblFile

The resource Table file from which to extract the data specified with the '-extractRow:{colName,rowNbr,resourceTblFile,htmlStyle}' switch. See extractRowFromResTblAsHTMLflag for details.

extractHtmlStyle

public java.lang.String extractHtmlStyle

The extractHtmlStyle used to process the data extracted with the '-extractRow:{colName,rowNbr,resourceTblFile,htmlStyle}' switch. The htmlStyles may be DL, OL, UL and TABLE. See extractRowFromResTblAsHTMLflag for details.

sortRowsByColumnFlag

public boolean sortRowsByColumnFlag

Flag to sort the rows of the Table by values in the specified column. You can specify 'Ascending' or 'D'escending. This is done after any columns have been dropped or reordered. Default is not to sort the rows. The column name is in sortRowsByColumn and the sort direction in sortTableAscendingFlag. It is set by the -sortRowsByColumn:{colName,'A'scending or 'D'escending} switch.

sortTableColName

public java.lang.String[] sortTableColName

Name of column to sort the rows of the Table by values in this column. It is set by the -sortRowsByColumn:{colName,'A'scending or 'D'escending} switch.

sortTableAscendingFlag

public boolean[] sortTableAscendingFlag

Flag to specify the sort direction of the rows of the Table by values in the specified column. You specify 'Ascending' or 'D'escending. The sortRowsByColumnFlag is set when sorting. It is set by the -sortRowsByColumn:{colName,'A'scending or 'D'escending} switch.

nSortTable

public int nSortTable

The number of instances of the sort rows by column switch -sortRowsByColumn:{colName,'A'scending or 'D'escending}. When it does the test for the column, if one fails, it goes on to test the next etc. It uses the first one it finds.

reorderColName

public java.lang.String[] reorderColName

List of Column header names [0:nReorderColName-1] from '-reorderColumn:{colName,newColNbr}' to reorder this column to the new column number in reorderColNbr[]. You may specify multiple new columns (they must be different). Those columns not specified are moved toward the right. This is done after the list of dropped columns has been processed. Each entry builds a list of nReorderColName entries.

reorderColNbr

public int[] 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[]. empty entries are filled with -1. Each entry builds a list of nReorderColName entries.

nReorderColName

public int nReorderColName

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].

reorderRemainingColumnsFlag

public boolean reorderRemainingColumnsFlag

colHdrNameHmapData

public java.lang.String[] colHdrNameHmapData

Column header name from "-hrefData:{colHdrName,UrlBaseLink,mapTokenInUrl}" switches. Each entry builds a list of nColUrlMap entries. See also the '-hrefHeaderRow' switch.

urlBaseLinkHmapData

public java.lang.String[] urlBaseLinkHmapData

URL base link from "-hrefData:{colHdrName,UrlBaseLink,mapTokenInUrl}" switches. Each entry builds a list of nColUrlMap entries. Max size is MAX_COL2URL_MAPS.

mapTokenInUrlHmapData

public java.lang.String[] mapTokenInUrlHmapData

Map Token name in the URL to replace with the column cell data from "-hrefData:{colHdrName,UrlBaseLink,mapTokenInUrl}" switches. Each entry builds a list of nColUrlMap entries.

colHdrIdxHmapData

public int[] colHdrIdxHmapData

index of the Column header name in the tField[] data from "-hrefData:{colHdrName,UrlBaseLink}" switches. Each entry builds a list of nColUrlMap entries. Max size is MAX_COL2URL_MAPS. Note: the array must be defined, but null values are set to -1.

nColUrlHmapData

public int nColUrlHmapData

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. -1 values indicates no map for this column. Max size is MAX_IN_TOKENS_PER_ROW.

hrefHeaderRowFlag

public boolean hrefHeaderRowFlag

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. It searches the first column of the header rows to find the colHdrName to determine the row to be mapped to that colHdrName. Unlike the -hrefData option, the colHdrName can be embedded within a string. The default is not to map the header rows. Set by the '-hrefHeaderRow' switch.

dropColNames

public java.lang.String[] dropColNames

List of columns to drop in the output

set by the '-dropColumnName:{column header name}' switch. There can be multiple instances of this switch. It may be used as an alternative to -keepColumn switches as the Table may have known column names.The list size is nDropColNames.

nDropColNames

public int nDropColNames

Size of the dropColNames[] list to drop from the

in outout.

keepColNames

public java.lang.String[] keepColNames

List of columns to keep in the output

set by the '-keepColumnName:{column header name}' switch. There can be multiple instances of this switch. It specifies which columns to keep in multiple instances of the switch. Then, when the Table is processed, it drops all columns not listed. It may be used as an alternative to -dropColumn as the Table may have unknown column names. Default is not active. The list size is nKeepColNames.

nKeepColNames

public int nKeepColNames

Size of the keepColNames[] list to drop from the

in outout.

specificInputFileList

public java.lang.String specificInputFileList

Specific list of input files string from "-files:f1,f2,...,fn" cmd line switch.

inputFiles

public java.lang.String[] inputFiles

List of input files (with inputExt) to convert

curInputFile

public java.lang.String curInputFile

Current input file being analyzed (w/o full path

inputNames

public java.lang.String[] inputNames

List of input files (without inputExt) to convert

nInputFiles

public int nInputFiles

# of input files found in inputDataDir

outputFiles

public java.lang.String[] outputFiles

List of input files (with inputExt) to convert

inputExt

public java.lang.String inputExt

Input file extension

outputExt

public java.lang.String outputExt

Output file extension

joinTableFile

public java.lang.String joinTableFile

limitMaxTableRowsFlag

public boolean limitMaxTableRowsFlag

limitMaxTableRows

public int limitMaxTableRows

limitRowsSortByColName

public java.lang.String limitRowsSortByColName

limitRowsSortAscendingFlag

public boolean limitRowsSortAscendingFlag

inputDataDir

public java.lang.String inputDataDir

Input Data Path to use from "-inputDir:{inputTXTdir}" command, default is "data".

outputDataDir

public java.lang.String outputDataDir

Output Data Path to use from "-outputDir:{outputHTMLdir}" command, default is "html".

tableDataDir

public java.lang.String tableDataDir

Tables Path to use for various mapping tables specified with the "-tableDir:{tablesDirectory}" command, default is "data.Table". NOTE: this variable is also set with '-jtvTableDir' switch.

prologFile

public java.lang.String prologFile

HTML prolog file. If null indicates no file with "-addPrologFile:{file}" switch.

epilogueFile

public java.lang.String epilogueFile

HTML epilogue file. If null indicates no file with "-addEpilogueFile:{file}" switch.

prolog

public java.lang.String prolog

HTML prolog string. If null indicates no prolog

epilogue

public java.lang.String epilogue

HTML epilogue string. If null indicates no epilogue

saveEditTableFlag

public boolean saveEditTableFlag

Save edited data Table in an output file. Set by the '-saveEditedTable2File:{outTblFile,opt. "HTML"}' switch.

saveEditedTable2File

public java.lang.String saveEditedTable2File

Make a Table file from the modified input table stream. edited by -dropColumns, -keepColumns, -reorderColumns, -sortRowsByColumn. If the "saveHTML" option is set (saveEditHTMLflag), also output the HTML when doing this operation. Set by the '-saveEditedTable2File:{outTblFile,opt. "noHTML"}' switch.

saveEditHTMLflag

public boolean saveEditHTMLflag

Save output HTML when doing a -saveEditedTable2File operation. Normally don't want the HTML, just the map file. Set by the '-saveEditedTable2File:{outTblFile,opt. "HTML"}' switch.

genHTMLpathList

public static java.lang.String[] genHTMLpathList

Converter generated HTML files path list. Files added when each HTML file is successfully generated. See cvt.addNameOfHTMLfile(), cvt.clearGenHTMLpathList(), getGenHTMLpathList(). Note: this list is only used in the GUI for supplying a list of created HTML files to view, although it is created and maintained in the non-GUI processing as well.

makeTXTflag

public boolean makeTXTflag

Allow generation of TXT when doing a input file processing if that operation also allows TXT generation. This is useful if generating a HTML file from a concatenated file, but the .txt file is not desired. Set by the '-noHTML' switch.

makeHTMLflag

public boolean makeHTMLflag

Allow generation of HTML when doing a input file processing if that operation also allows HTML generation. This is useful if doing editing of large input files to generate index maps or saved files. Set by the '-noHTML' switch.

fastEditFileFlag

public boolean fastEditFileFlag

[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. toCol#}', {-dropColumns or -keepColumns} followed by -reorderColumns. Data is written immediately to a BufferedWrite stream so it can handle huge files. Because it is sequential, it can't do a -sortRowsByColumnData. This would generally be used to generate a tab-delim .txt files that can be random accessed. It is used instead of '-saveEditedTable2File:{outTblFile,opt. "noHTML"}' which overides the -saveEditedTable2File options. The filename is saved in saveEditedTable2File. This option is set by the '-fastEditFile:{opt. output file}' switch.

makeIndexMapFileFlag

public boolean makeIndexMapFileFlag

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). The index file will contain the specified columns in the column-list (i.e., colNameIndexMap[0:nColNameIndexMap-1] ) followed by the ("StartByte", "EndByte") 2-tuple for data in the input table with those column values. This file can then be used to quickly index a huge input file probably using a Hash table of the selected column names instances to lookup the (start,end) file byte pointers to random access the large file.

makeIndexMapFile

public java.lang.String makeIndexMapFile

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). Enabled by the '-makeIndexMapFile:{colName1,colName2,...,colNameN}' switch.

colNameIndexMap

public java.lang.String[] colNameIndexMap

This is the list of column names to be used when generating the index map file colNameIndexMap[0:nColNameIndexMap-1]. The default is not to save an index map file. The start of the column header occurs when find all colNames in the same row. Set by the '-makeIndexMapFile:{colName1,colName2,...,colNameN}' switch.

nColNameIndexMap

public int nColNameIndexMap

Number of column names colNameIndexMap[0:nColNameIndexMap-1] to be used when generating the index map file. The default is not to save an index map file. Set by the '-makeIndexMapFile:{colName1, colName2,...,colNameN}' switch.

makeStatisticsIndexMapFlag

public boolean makeStatisticsIndexMapFlag

Make a 'Statistics Index Map' Table file with the same base file name as the index map (.idx) but with a .sidx file extension. It is invoked after the IndexMap file is created (using the '-makeIndexMapFile' switch). Therefore, it must be specified in a subsequent command line (if using batch). Set by the "-makeStatisticsIndexMapFile" switch.

flipTableByIndexMapFlag

public boolean flipTableByIndexMapFlag

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. The processing is done in the the MakeFlipTable class. It analyzes the index map Table and then uses all columns before the ("StartByte", "EndByte") columns to define the flipped Table header. See the '-flipColumnName:{flipColumnFile,flipColumnName}' to restrict which flipped column data to use. See the '-flipRowFilterNames:{flipRowFilterNamesFile}' or See the '-flipRowFilterNames:{*LIST*,name1,name2,...,nameK}' to restrict which flipped row data to use. It is set by '-flipTableByIndexMap:{flipDataFile,flipIndexMapFile,(opt)maxRows}' switch.

flipDataFile

public java.lang.String flipDataFile

Name of the data file to be used when flipping a table. Set by '-flipTableByIndexMap:{flipDataFile,flipIndexMapFile,(opt)maxRows}' switch.

flipIndexMapFile

public java.lang.String flipIndexMapFile

Name of the Index Map file to be used when flipping a table. Set by '-flipTableByIndexMap:{flipDataFile,flipIndexMapFile,(opt)maxRows}' switch.

maxFlipSeekRowsToExtract

public int maxFlipSeekRowsToExtract

Maximum number of rows to flip from the flipDataFile

flipColumnFile

public java.lang.String[] flipColumnFile

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. Set by the '-flipColumnName:{flipColumnFile,flipColumnName}' or '-flipColumnName:{*LIST*,flipColumnName,v1,v2,...vn}' switch. The {flipColumnFile} contains a list of data to be filtered for {flipColumnNames}. Multiple switches are specified with nFlipColumns being the size of the list.

flipColumnName

public java.lang.String[] flipColumnName

These are the list of column names to be used when generating the flipped Table using the '-flipTableByIndexMap:{flipDataFile,flipIndexMapFile,(opt)maxRows}' switch. Set by the '-flipColumnName:{flipColumnFile,flipColumnName}' or '-flipColumnName:{*LIST*,flipColumnName,v1,v2,...vn}' switch. The {flipColumnFile} contains a list of data to be filtered for {flipColumnNames}. Multiple switches are specified with nFlipColumns being the size of the list. The lists are flipColumnName[0:nFlipColumns-1].

flipColumnValues

public java.lang.String[][] flipColumnValues

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. Set by the '-flipColumnName:{flipColumnFile,flipColumnName}' or '-flipColumnName:{*LIST*,flipColumnName,v1,v2,...vn}' switch. The {flipColumnFile} contains a list of data to be filtered for {flipColumnNames}. Multiple switches are specified with nFlipColumns being the size of the list. The lists are flipColumnName[0:nFlipColumns-1].

nFlipColumns

public int nFlipColumns

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. Set by the '-flipColumnName:{flipColumnFile,flipColumnName}' switch. The {flipColumnFile} contains a list of data to be filtered for {flipColumnNames}. Multiple switches are specified with nFlipColumns being the size of the list.

flipTableUseExactMatchFlag

public boolean flipTableUseExactMatchFlag

This is the exact match filter flag. If an exact match, then match flipColNameFilterData[][] exactly with equalsIgnoreCase(), otherwise do lower case IndexOf() comparison to pick up substrings. Set with the -flipUseExactColumnNameMatch:{TRUE | FALSE} switch.

flipRowFilterNamesFile

public java.lang.String flipRowFilterNamesFile

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}'. Set by '-flipRowFilterNames:{flipRowFilterNamesFile}' or '-flipRowFilterNames:{*LIST*,name1,name2,...,nameK}' switch. The contents of the file is saved in flipRowFilterNames[] used when flipping the table. If there are no names specified, then flip all rows.

flipRowFilterNames

public java.lang.String[] flipRowFilterNames

This is the list of row names [0:nFlipRowFilterNames-1] to be used when generating the flipped Table using the '-flipTableByIndexMap:{flipDataFile,flipIndexMapFile}' switch. Set by '-flipRowFilterNames:{flipRowFilterNamesFile}' or '-flipRowFilterNames:{*LIST*,name1,name2,...,nameK}' switch. The contents of the file or the list is saved in flipRowFilterNames[].

nFlipRowFilterNames

public int nFlipRowFilterNames

Size of the list of row names [0:nFlipRowFilterNames-1] to be used when generating the flipped Table using the '-flipTableByIndexMap:{flipDataFile,flipIndexMapFile}' switch. Set by '-flipRowFilterNames:{flipRowFilterNamesFile}' or '-flipRowFilterNames:{*LIST*,name1,name2,...,nameK}' switch. The contents of the file or the list is saved in flipRowFilterNames[].

flipRowGSPIDfilters

public java.lang.String[] flipRowGSPIDfilters

flipOrderHdrColList

public java.lang.String[] flipOrderHdrColList

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. Set by the '-flipOrderHdrColNames:{colHdrName1,colHdrName2,...,colHdrNameN}' switch. The lists are flipOrderHdrColList[0:nFlipOrderHdrColList-1].

nFlipOrderHdrColList

public int nFlipOrderHdrColList

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. Set by the '-flipOrderHdrColNames:{colHdrName1,colHdrName2,...,colHdrNameN}' switch. The lists are flipOrderHdrColList[0:nFlipOrderHdrColList-1].

flipExcludeColumnName

public java.lang.String[] flipExcludeColumnName

These are the list of column names to exclude when generating the flipped Table using the '-flipTableByIndexMap:{flipDataFile,flipIndexMapFile,(opt)maxRows}' switch. Set by the '-flipExcludeColumnName:{flipExcludeColumnName}' switch. Multiple switches are specified with nExcludeFlipColumns being the size of the list. The lists are flipExcludeColumnName[0:nFlipExcludeColumns-1].

nFlipExcludeColumns

public int nFlipExcludeColumns

This is the number of column names to exclude when generating the flipped Table using the '-flipTableByIndexMap:{flipDataFile,flipIndexMapFile,(opt)maxRows}' switch. Set by the '-flipExcludeColumnName:{flipExcludeColumnName}' switch. Multiple switches are specified with nExcludeFlipColumns being the size of the list. The lists are flipExcludeColumnName[0:nFlipExcludeColumns-1].

reportFoldChangeFlag

public boolean reportFoldChangeFlag

Flag to indicate reporting fold change in flip Table reporting, when both Class A and B are defined. Set by both "-flipAclass:{flipAclass}" and "-flipBclass:{flipBclass}" specified.

flipAclass

public java.lang.String flipAclass

If reporting fold change in flip Table reporting, then "-flipAclass:{flipAclass}" specifies the Class A samples. If both Class A and B are defined, the Switches() parser sets reportFoldChangeFlag.

flipBclass

public java.lang.String flipBclass

If reporting fold change in flip Table reporting, then "-flipBclass:{flipBclass}" specifies the Class A samples. If both Class A and B are defined, the Switches() parser sets reportFoldChangeFlag.

flipFCthreshold

public float 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.

flipFCthrFlag

public boolean flipFCthrFlag

If reporting fold change with reportFoldChangeFlag in flip Table reporting, and -flipFCthreshold:{flipFCthreshold}, then set the flipFCthrFlag and save the postive value in flipFCthreshold.

flipDirectory

public java.lang.String flipDirectory

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. Set by the"-flipDirectory:{flipDirectory}". If the switch is not specified, it will use the base outputDataDir name.

flipSaveOutputFile

public java.lang.String flipSaveOutputFile

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. Set by the"-flipSaveOutputFile:{flipSaveOutputFile}". If the switch is not specified, it will use the base input file name. It will add the "-search" after this base address and before the ".txt" and ".html".

batchProcessFlag

public boolean batchProcessFlag

Do batch processing of a list of param.map type files specified in a file. Set by the initial '-batchProcess:{file of param specs, opt. new working dir}' switch. If the {opt. new working dir}value is specified, it will change the current working directory to batchCwd for the CvtTabDelim2HTML when runnning -batchProcess so that you can specify it run in a particular environment. No other switches should be used with this as they will be ignored. If errors occur in any of the batch jobs, the errors are logged in the HTMLtools.log file and it aborts that particular job and continues on to do the next job in the batch list. This is parsed into the list batchParamsSpecs[0:maxBatchParamsSpecs-1]. The current batch being processed is in batchParamsSpecs[curBatchParamsSpecs].

batchProcessFile

public java.lang.String batchProcessFile

The batch process file containing the list of param specifications. Set by the '-batchProcess:{file of param specifications}' switch.

batchCwd

public java.lang.String batchCwd

The optional directory to run the batch script in if specified, else use the current directory. Set by the'-batchProcess:{file of param specs, opt. new working dir}' switch.

oldUserDir

public java.lang.String oldUserDir

This is the old current directory before it was changed by a new working directory set by the'-batchProcess:{file of param specs, opt. new working dir}' switch.

batchParamsSpecs

public java.lang.String[] batchParamsSpecs

Is a list of batch parameter specifications from the original -batchParam list specified by the batchParamFile. The list is of size maxBatchParamsSpecs

maxBatchParamsSpecs

public int maxBatchParamsSpecs

Number of batch param specs in the batch file. Set by the '-batchProcess:{file of param specifications}' switch.

curBatchParamsSpecs

public int curBatchParamsSpecs

Current batch param specification being processed in the batchParamsSpecs[] list.

curBatchJobNbr

public int curBatchJobNbr

Current batch job number being processed. This ignores comment lines starting with '#'.

batchProcessStr

public java.lang.String batchProcessStr

The contents of the batchProcessFile to process.

copyFileFlag

public boolean copyFileFlag

Copy input source file to output destination file in copySrcFile[0:nCopyFile-1] to copyDstFile[0:nCopyFile-1]. Set by -copyFile:{srcFile,destFile}.

nCopyFile

public int nCopyFile

Number of instances of file copy specifications in copySrcFile[0:nCopyFile-1] to copyDstFile[0:nCopyFile-1]. set by the '-copyFile:{srcFile,destFile}' switch. See copyFileFlag for details.

copySrcFile

public java.lang.String[] copySrcFile

List of source input data file paths [0:nCopyTreeDir-1]. Set by the '-copyFile:{srcFile,destFile}' switch. See copyFileFlag for details.

copyDstFile

public java.lang.String[] copyDstFile

List of destination output data file paths [0:nCopyFile-1]. Set by the '-copyFile:{srcFile,destFile}' switch. See copyFileFlag for details.

copyTreeDataFlag

public boolean copyTreeDataFlag

Copy input data tree files to to output directory in copyTreeSrcDir[0:nCopyTreeDir-1] to copyTreeDstDir[0:nCopyTreeDir-1]. Set by -genTreeCopy:{srcTreeFiles,destPath}.

nCopyTreeDir

public int nCopyTreeDir

Number of instances of tree file copy specifications in copyTreeSrcDir[0:nCopyTreeDir-1] to copyTreeDstDir[0:nCopyTreeDir-1]. set by the '-copyTree:{srcTreeFiles,destPath}' switch. See copyTreeDataFlag for details.

copyTreeSrcDir

public java.lang.String[] copyTreeSrcDir

List of source input data tree paths [0:nCopyTreeDir-1]. Set by the '-copyTree:{srcTreeFiles,destPath}' switch. See copyTreeDataFlag for details.

copyTreeDstDir

public java.lang.String[] copyTreeDstDir

List of destination output data tree paths [0:nCopyTreeDir-1]. Set by the '-copyTree:{srcTreeFiles,destPath}' switch. See copyTreeDataFlag for details.

dirIndexHtmlFlag

public boolean dirIndexHtmlFlag

Make an "index.html" file of all of the files in the specified directories in the list of directories dirIndexHtml[0:nDirIndexHtml-1]. This is useful when copying a set of directories on a Web server that does not show the contents of the directory if there is no index.html file. In addition, if the corresponding flag dirIndexHtmlOverrideFlag[0:nDirIndexHtml-1] is set to 'Override', then override the "index.html" file it it already exists in that directory otherwise do not generate the "index.html" file. Do this recursively on each directory. Set by '-dirIndexHtml:{dir,'O'verride}' switch.

nDirIndexHtml

public int nDirIndexHtml

Number of instances of tree file copy specifications in dirIndexHtml[0:nDirIndexHtml-1]. Set by '-dirIndexHtml:{dir,'O'verride}' switch.

dirIndexHtml

public java.lang.String[] dirIndexHtml

List of relative directory paths [0:nDirIndexHtml-1]. Set by '-dirIndexHtml:{dir,'O'verride}' switch. See dirIndexHtmlFlag for details.

dirIndexHtmlOverrideFlag

public boolean[] dirIndexHtmlOverrideFlag

List of 'O'veride (true) flags [0:nDirIndexHtml-1]. Set by '-dirIndexHtml:{dir,'O'verride}' switch. See dirIndexHtmlFlag for details.

genBatchScriptFlag

public boolean genBatchScriptFlag

Generate a set of parameter .map files in the batchDir directory. These can then be run by a converter batch file called with the same base name as the {test-ToDo-list.txt} file, but with a ".doit" file extension. The operation also creates a BAT script to start the converter on this data called {test-ToDo-list.bat} for use with Windows. The paths created in the used for the inputTreeDir and outputTreeDir base paths and use the "Relative Directory" data in the test-ToDo-list.txt within those directories. This will process a data set to generate a set of HTML pages and converted database .txt files defined by the {test-ToDo-list.txt} database. Set with -genBatchScripts:{mAdb-TestsToDo.txt,batchScripts, ParamsScripts,InputTree,Summary,Analyses,JTV} Note: (currently), DO NOT reset these variables in reinitGlobalSwitches().

genTestToDoListFile

public java.lang.String genTestToDoListFile

The name of the of the {test-ToDo-list.txt} file to process. See genBatchScriptFlag for more details. Set by -genTestFiles:{TestToDoList File} switch. // -genTestFiles:"mAdb-TestsToDo.txt"

genMapIntroduction

public java.lang.String genMapIntroduction

The name of the of the {introductionMapFile} file to process. This contains the "Introduction" paragraph index by Tissue. Set by -genMapIntroduction:{introductionMapFile} switch. //e.g. -genMapIntroduction:"CellTypeTissue.map"

genMapEGdetails

public java.lang.String genMapEGdetails

The name of the of the {EGdetailsMapFile} file to process. This contains the "Details" paragraph index by Expression Group. Set by -genMapEGdetails:{EGdetailsMapFile} switch. // e.g. -genMapEGdetails:"ExperimentGroups.map"

genBatchDir

public java.lang.String genBatchDir

The name of the {batchScripts} directory to put the other directories. See genBatchScriptFlag for more details.

genParamsScriptsDir

public java.lang.String genParamsScriptsDir

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. See genBatchScriptFlag for more details.

genInputTreeDir

public java.lang.String genInputTreeDir

The name of the {inputTreeDir} directory (inside of the genBatchDir) where the input data to be processed by the batch params .map files are copied. This is used when the batch script is subsequently run. See genBatchScriptFlag for more details.

genSummaryDir

public java.lang.String genSummaryDir

The name of the {Summary} directory (inside of the genBatchDir) where the generated Summary HTML web files are saved. See genBatchScriptFlag for more details.

genAnalysesDir

public java.lang.String genAnalysesDir

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. See genBatchScriptFlag for more details.

genJTVDir

public java.lang.String genJTVDir

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. See genBatchScriptFlag for more details.

genSummaryTemplateFlag

public boolean genSummaryTemplateFlag

List of Summary Templates that are used for mapping the test-ToDo-list data so that (summaryProlog, summaryExperimental, summaryAnalysis, summaryFurtherAnalysis, summaryEpilogue) etc. dynamically. Set by -genSummaryTemplate:{orderNbr,templateFileName} instances that can be used to generalize the currently hardwired. These are then mapped into the following keywords that may appear in any of these templates: $$TISSUE$$, "$$LIST_EXPR_GROUPS$$", $$DESCRIPTION$$, $$ANALYSIS$$, $$FURTHERANALYSIS$$, $$DATE$$. The $$INTRODUCTION$$ is extracted from the {"CellTypeTissue.map"}. Multiple instances are allowed where they are concatenenated by the orderNbr associated with each template. Note: (currently), DO NOT reset these variables in reinitGlobalSwitches().

genSummaryTemplateOrderNbrs

public int[] genSummaryTemplateOrderNbrs

List of order numbers when define the Summary Templates. List is of size nGenSummaryTemplates and is allocated [0:MAX_TEMPLATES-1]. See the genSummaryTemplateFlag for details.

genSummaryTemplateNames

public java.lang.String[] genSummaryTemplateNames

List of templateFileName entries when define the Summary Templates. List is of size nGenSummaryTemplates and is allocated [0:MAX_TEMPLATES-1]. See the genSummaryTemplateFlag for details.

nGenSummaryTemplates

public int nGenSummaryTemplates

Number of Summary Templates . See the genSummaryTemplateFlag for details.

genParamTemplateFlag

public boolean genParamTemplateFlag

List of Parameter map Templates that are used for mapping the test-ToDo-list data so that (param-MRR, param-MRR-keep, param-JTV) etc. dynamically. Set by -genParamTemplate:{name,paramTemplateFileName} instances that can be used to generalize the currently hardwired. These are then mapped into the following keywords that may appear in any of these templates: $$TISSUE$$, "$$TEST_NAME$$", "$$MRR_FILE$$", $$DESCRIPTION$$, $$PROLOG$$, $$EPILOG$$, $$DATE$$. Multiple instances are allowed where they are concatenenated by the orderNbr associated with each template. Note: (currently), DO NOT reset these variables in reinitGlobalSwitches().

genParamTemplateNames

public java.lang.String[] genParamTemplateNames

List of order numbers when define the Param Templates. List is of size nGenParamTemplates and is allocated [0:MAX_TEMPLATES-1]. See the genParamTemplateFlag for details.

genParamTemplateFiles

public java.lang.String[] genParamTemplateFiles

List of paramTemplateFileName entries when define the Param Templates. List is of size nGenParamTemplates and is allocated [0:MAX_TEMPLATES-1]. See the genParamTemplateFlag for details.

nGenParamTemplates

public int nGenParamTemplates

Number of Param Templates. See the genSummaryTemplateFlag for details.

genSupportFilesToCopy

public java.lang.String[] genSupportFilesToCopy

List of support files to copy to the batchScriptsDir. The support files are specified with a list created using multiple instances of -genCopySupportFile:{support file}. The size of the list is nSupportFilesToCopy.

nGenSupportFilesToCopy

public int nGenSupportFilesToCopy

Number of support files to copy to the batchScriptsDir. See the supportFilesToCopy for details. Set by multiple instances of -genCopySupportFile:{support file} switch.

genTreeCopyDataFlag

public boolean genTreeCopyDataFlag

Copy input data tree data to batch scripts subdirectory. Set by -genTreeCopy:{srcTreeFiles,destPath}. Note: (currently), DO NOT reset these variables in reinitGlobalSwitches().

nGenTreeCopy

public int nGenTreeCopy

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]. Set by -genTreeCopy:{srcTreeFiles,destPath}. Note: (currently), DO NOT reset these variables in reinitGlobalSwitches().

genTreeSrcTreeDir

public java.lang.String[] genTreeSrcTreeDir

Source input data tree data to batch scripts subdirectory. Copying genTreeSrcTreeDir[0:nGenTreeCopy-1] directory trees to genTreeDstTreeDir[0:nGenTreeCopy-1]. Set by -genTreeCopy:{srcTreeFiles,destPath}. See the genTreeCopyDataFlag for details.

genTreeDstTreeDir

public java.lang.String[] genTreeDstTreeDir

Destination output data tree path to batch scripts subdirectory. Copying genTreeSrcTreeDir[0:nGenTreeCopy-1] directory trees to genTreeDstTreeDir[0:nGenTreeCopy-1]. Set by -genTreeCopy:{srcTreeFiles,destPath}. See the genTreeCopyDataFlag for details.

genTestsIntersectionFlag

public boolean genTestsIntersectionFlag

Generate Tests-Intersection params .map files and insert links into $$TEST-INTERSECTION$$ which is "" otherwise. Set by -genTestsIntersection:{}. Note: (currently), DO NOT reset these variables in reinitGlobalSwitches().

makeTestsIntersectionTableFlag

public boolean makeTestsIntersectionTableFlag

Do Tests Intersection mapping. Set by -makeTestsIntersectionTbl:{testsToDoFile}

testsToDoTblFile

public java.lang.String testsToDoTblFile

The ToDo tests file to use in Tests Intersection mapping. Set by -makeTestsIntersectionTbl:{testsToDoFile}

filterTestField

public java.lang.String filterTestField

Specifies the tField name of Tests-ToDo Table data to test. It is set by setTestFilterList(). This is used when deciding which tests in Tests-ToDo Table to include. All tests are included if there is no filterTests. Otherwise, only use those that match the filter. The matchTestFilter() tests the current data against the filter data. Set by -filterTestTestIntersection:{testTableField,d1,d2,...,dn}.

filterTestsList

public java.lang.String[] filterTestsList

Specifies the list of filter instances to test. It is set by setTestFilterList(). This is used when deciding which tests in Tests-ToDo Table to include. All tests are included if there is no filterTests. Otherwise, only use those that match the filter. The matchTestFilter() tests the current data against the filter data. Set by -filterTestTestIntersection:{testTableField,d1,d2,...,dn}.

filterDataField

public java.lang.String filterDataField

Specifies the tField name of MRR Table data to test. It is set by setDataFilterList(). This is used when deciding which data rows in MRR Table to include. All tests are included if there is no filterTests. Otherwise, only use those that match the filter. The matchDataFilter() tests the current data against the filter data. Set by -filterDataTestIntersection:{dataTableField,d1,d2,...,dn}.

filterDataList

public java.lang.String[] filterDataList

Specifies the list of filter instances to test. It is set by setDataFilterList(). This is used when deciding which data rows in MRR Table to include. All tests are included if there is no filterTests. Otherwise, only use those that match the filter. The matchDataFilter() tests the current data against the filter data. Set by -filterDataTestIntersection:{dataTableField,d1,d2,...,dn}.

addFCrangesForTestsIntersectionTableFlag

public boolean addFCrangesForTestsIntersectionTableFlag

Add FC range computations, then expand the TI table and add the three columns ("Max FC", "Min FC", "FC Range"). Set by the '-addFCrangesForTestsIntersectionTable' switch.

addRangeOfMeansToTItableFlag

public boolean addRangeOfMeansToTItableFlag

Add the ("Range Mean A", "Range Mean B" and "FC counts %") computations to an expanded TestsIntersectionTable table. Set by the '-addRangeOfMeansToTItable' switch.

jtvMapFlag

public boolean jtvMapFlag

Flag set if doing '-jtvNamesMap:{mAdbArraySummaryFile,mapHdrFile,fromHdrName,toHdrName}'. Note other optional switches are '-jtvInputDir:{jtvInputSubDir}' and '-jtvOutputDir:{jtvOutputSubDir}'. [REFACTOR] to separate JTVconverter program.

jtvHTMLgenerateFlag

public boolean jtvHTMLgenerateFlag

Flag set by '-jtvHTMLgenerate'. Generate a HTML file to invoke the JTV applet for each JTV specification in the jtvInputDir. It puts the HTML file in the jtvOutputDir. Some of the non-JTV HTML modification switches are operable including: -addEpilogue, -addOutfilePostfix, -addProlog, -mapDollarsigns, -mapQuestionmarks. Also the -jtvDescription may be used to insert additional text into the prolog where it replaces "$$DATA_DESCRIPTION$$". [REFACTOR] to separate JTVconverter program.

jtvDescription

public java.lang.String jtvDescription

String set with '-jtvDescription:{prolog description}' that may be used with '-jtvHTMLgenerate' to insert additional text into the prolog where it replaces "$$DATA_DESCRIPTION$$". [REFACTOR] to separate JTVconverter program.

jtvButtonName

public java.lang.String jtvButtonName

String set with '-jtvButtonName:{button label}' that may be used with '-jtvHTMLgenerate' to label the button to activate Java TreeView. [REFACTOR] to separate JTVconverter program.

jtvCopyJTVjars

public java.lang.String jtvCopyJTVjars

If doing 'jtvHTMLgenerate', then you can use the '-jtvCopyJTVjars:{JTV jars directory}' option to copy the JTV jar files and plugins to the jtvOutputDir. [REFACTOR] to separate JTVconverter program.

jtvSpecificInputFileList

public java.lang.String jtvSpecificInputFileList

Specific list of input files string from "-jtvFiles:f1,f2,...,fn" cmd line switch. [REFACTOR] to separate JTVconverter program.

jtvInputDir

public java.lang.String jtvInputDir

Directory where to find the set of input JTV sub directories, each with (.atr,.cdt,.gtr) extension files. This is parsed with the optional '-jtvInputDir:{jtvInputDir}' with a default value of "JTVinput". [REFACTOR] to separate JTVconverter program.

jtvOutputDir

public java.lang.String jtvOutputDir

Directory where to write the converted JTV output file sub directories. This is parsed with the optional '-jtvOutputDir:{jtvOutputDir}' with a default value of "JTVoutput". [REFACTOR] to separate JTVconverter program.

jtvUseMapFromColNbr

public int jtvUseMapFromColNbr

'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. Set by '-jtvNamesMap:{mAdbArraySummaryFile,mapHdrFile,fromHdrName,toHdrName}'. [REFACTOR] to separate JTVconverter program.

jtvUseMapToColNbr

public int jtvUseMapToColNbr

'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. Set by '-jtvNamesMap:{mAdbArraySummaryFile,mapHdrFile,fromHdrName,toHdrName}'. [REFACTOR] to separate JTVconverter program.

jtv_mAdbArraySummaryFile

public java.lang.String jtv_mAdbArraySummaryFile

Name of the mAdb Array Summary file which contains a Table with "mAdb ID" and the corresponding "Array Name" (MAS). Set by '-jtvNamesMap:{mAdbArraySummaryFile,mapHdrFile,fromHdrName,toHdrName}'. [REFACTOR] to separate JTVconverter program.

jtv_mapHdrNamesFile

public java.lang.String jtv_mapHdrNamesFile

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. Set by '-jtvNamesMap:{mAdbArraySummaryFile,mapHdrFile,fromHdrName,toHdrName}'. [REFACTOR] to separate JTVconverter program.

jtvReZipConvertedFiles

public boolean jtvReZipConvertedFiles

Set to rezip the converted files in the output JTV directory in a file with the same name. Set by the 'jtvReZipConvertedFiles' switch. [REFACTOR] to separate JTVconverter program.

Constructor Detail

Globals

public Globals()

Method Detail

reinitGlobalSwitches

public void reinitGlobalSwitches()

reinitGlobalSwitches() - reinitialize Global variable switches. This is invoked for each batch job before the switches are parsed. Note: this must NOT be called before cvt.init() since some of the OS variables will not be set.

reinitGBSglobalSwitches

public void reinitGBSglobalSwitches()

reinitGBSglobalSwitches() - reinitialize GBS Global variable switches. This is invoked for each batch job before the switches are parsed. Note: this must NOT be called before cvt.init() since some of the OS variables will not be set. It should only be called once at top level. [REFACTOR] to separate GenBatchScripts program.

reinitTIglobalSwitches

public void reinitTIglobalSwitches()

reinitTIglobalSwitches() - reinitialize TestsIntersection Global switches. This is invoked for each batch job before the switches are parsed. Note: this must NOT be called before cvt.init() since some of the OS variables will not be set. [REFACTOR] to separate TestsIntersection program.

reinitJTVglobalSwitches

public void reinitJTVglobalSwitches()

reinitJTVglobalSwitches() - reinitialize JTV Global variable switches. This is invoked for each batch job before the switches are parsed. Note: this must NOT be called before cvt.init() since some of the OS variables will not be set. [REFACTOR] to separate JTVconverter program.