* This code is available at the HTMLtools project on SourceForge at * http://htmltools.sourceforge.net/ * 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.net/), and * Open2Dprot (http://Open2Dprot.sourceforge.net/) Table modules. *
* $Date: 2009/07/22 11:45:56 $ $Revision: 1.28 $
*
* Copyright 2008, 2009 by Peter Lemkin
* E-Mail: lemkin@users.sourceforge.net
* http://lemkingroup.com/
*
*
*
*
* List of software Development to [TODO]
* ====================================
* [ ] [TODO] add -searchGui GUI to run the program to perform an interactive
* search on an existing Table database after the user interatively
* enters search terms and sample groups. New methods SearchGUI,
* ProcessDataSearch.
* [ ] [TODO] add javascript to -exportBigCells (e.g., ExperimentGroup) which
* currently generates the "big-RC" small files. Need to keep
* copy of text in HTML along with javascript.
*
* List of changes to [TEST] or [DEBUG]
* ======================================
* [ ] [DEBUG] -jtvReZipConvertedFiles code to zip generated directory writer
* and then calling it from JTVconvert.java. Another trick might
* be to 1) copy the unzipped JTV dir to the user.dir (after checking
* that there is no dir with the same name), 2) zip it there,
* 3) copy the zipped file back to the JTVoutput dir, 4) delete
* the user.dir/{zipped dir and unzipped JTV dir).
*
* List of components [DONE]
* ================================
* [*] [DONE] add GUI to run the program with -gui switch. New methods CvtGUI,
* ProcessData.
* [*] [DONE] Add -flipTableByIndexMap:{indexMapFile,column-list} to
* generate transposed files using random access file indexing
* to create a muli-line header (1 line for each column name
* in the list) using a previously generated index map with
* the '-makeIndexMapFile:{colName1,colName2,...,colNameN}'
* command. The switches '-flipColTableList:{sourceColName,
* column-data-list}' and '-flipRowTableList:{sourceRowName,
* row-data-list}' also support this function.
* [*] [DONE] -useOnlyLastHeaderLine - reduce the number of header lines to 1
* even if there are more than 1 header line.
* [*] [DONE] If doing a set of -reorderColumn operations, sort the remaining
* columns not specified, but that are used, alphabetically. Set
* by "-reorderRemainingColumnsAlphabeticly".
* [*] [DONE] '-makeIndexMapFile:{colName1,colName2,...,colNameN}'
* 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). The index file will contain the specified
* columns in the column-list followed by the StartByte, EndByte
* 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.
* [*] [DONE] Integrated '-fastEditFile:{opt. output file}' to
* edit a subset of rows by using the Index-Map from
* '-makeIndexMapFile:{colName1,colName2,...,colNameN}'.
* [*] [DONE] added '-hdrMapName:{oldHdrColName,newHdrColName}' to map an old
* header column name {oldHdrColName} to a new name {newHdrColName}
* with multiple instances of this switch. This lets us use mappings
* from -genBatchScripts in the generated params*.map files.
* [*] [DONE] added '-joinTableFile:{joinTableFile}' adds the contents of the
* {joinTableFile} file to the table being processed. This allows us
* to add fields that can be used for sorting the new table by the
* {joinTableFile} data if it is defined. This switch can not
* (currently) be used with the -fastEditFile option.
* [*] [DONE] changed Java TreeView converter so the heatmap
* cell-focus shows the gene & Feature_ID instead of the row number.
* [*] [DONE] for Java TreeView converter, swaped order of gene data in .cdt
* file so that instead of the current order:
* WID:... WID:... || Feature_ID || MAP:... || gene -- gene_descr. ||...
* It would be
* WID:... || gene || Feature_ID -- gene_descr. || WID:... || MAP:... || ...
* [*] [DONE] automated -batchProcess batchList.doit script generation.
* Added '-genBatchScript:{...}' to generate a set of parameter
* .map files in the batchDirPath directory. These are run by a
* converter batch file called buildWebPages.doit, with a Windows
* BAT script filebuildWebPages.bat to run the converter.
* 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.
* [*] [DONE] re-did prolog/epilogue expansions using iterative -mapDollarsigns
* for more flexible keyword mappings in batch processing a large
* number of samples.
*
* List of components to [REFACTOR]
* ===================================
* [ ] [REFACTOR] Possibly REFACTOR Java TreeView converter so could popup an
* expression profile bar chart of the row data using refactored
* code from MAExplorer.
* [ ] [REFACTOR] -jtvMap etc. JTV conversions into a separate
* JTVconverter java application. The code is shared for now.
* This will make the HTMLtools focus only on Web page
* generation.
* [ ] [REFACTOR] -genBatchScripts etc. into a separate
* GenBatchScripts java application if can not generalize it.
* The code is shared for now. This will make the HTMLtools
* focus only on Web page generation.
* [ ] [REFACTOR] -makeTestsIntersections etc. into a separate
* TestsIntersections java application if can not generalize it.
* The code is shared for now. This will make the HTMLtools
* focus only on Web page generation.
* [ ] [REFACTOR] test data set so distribution is suitable for
* open-source.
* [ ] [REFACTOR] MANUAL.html with new open-source data set. Add examples
* for new switches. Split into three manuals: HTMLtools,
* JTVconverter, and GenBatchScripts, TestsIntersections (the latter
* if don't generalize it within HTMLtools).
* [ ] [REFACTOR] MANUAL.html with new open-source data set.
* [ ] [REFACTOR] batch job for use with new open-source data set.
*
*
*/
public class TODO
{
/**
* TODO() - dummy Constructor
*/
public TODO()
{ /* TODO */
} /* TODO */
} /* End of TODO documentation class TODO.java */