Class TODO

java.lang.Object
  TODO

public class TODO
extends java.lang.Object

The TODO class is a documentation-only class of things [TODO], [TEST], [DEBUG] or [REFACTOR]. It was designed so this documentation shows up in the javadocs HTML pages.

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: 2009/07/22 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.
 

Constructor Summary

TODO()
TODO() - dummy Constructor

Method Summary

Methods inherited from class java.lang.Object

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

Constructor Detail

TODO

public TODO()

TODO() - dummy Constructor