MakeTestsIntersectionTbl (HTMLtools javadoc documentation)

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Class MakeTestsIntersectionTbl

java.lang.Object
  MakeTestsIntersectionTbl

public class MakeTestsIntersectionTbl
extends java.lang.Object
extends java.lang.Object

Class MakeTestsIntersectionTbl to generate a Tests Intersection Table from the set of data specified by the {test-TODO-list.txt} table. It is invoked by the

 '-makeTestsIntersectionTbl:{testsToDoFile}' switch.
 Note: that it also uses switches: 
  (required)  -inputDirectory:{input dir} 
  (required)  -outputDirectory:{output directory}
  (optional)  -mapHdrNames:{mapHdrNamesFile,fromHdrName,toHdrName}
  (optional)  -noHTML
  (optional)  -saveEditedTable2File:{outTblFile,opt. "HTML"}
  (optional)  -filterTestTestIntersection:{testTableField,d1,d2,...,dn}
  (optional)  -filterDataTestIntersection:{dataTableField,d1,d2,...,dn}
  (optional)  -addFCrangesForTestsIntersectionTable
  (optional)  -addRangeOfMeansToTItable
  (optional)  -limitMaxTableRows:{maxNbrRows,(opt.)sortByCol,(opt.)'A'or 'D'}
  
 If HTML is generated, then the usual modifiers are used:
  (required)  -addProlog:{opt. prolog file name}'
  (required)  -addEpilogue:{opt. epilogue file name}'
  (optional)  -alternateRowBackgroundColor:{c} 
  (optional)  -mapDollarsigns:{$$keyword$$,toString} 
  (optional)  -mapQuestionmarks:{??keyword??,toString}

It generates a table ftTI (Tests-Intersection) that contains data from the individual tests from the '-inputDataDir:{inputDataDir}' organized by rows of +FC genes/Feature-IDs and -FC genes/Feature-IDs. The data from the {testsToDoFile} is read into ftGTT and is use to get additional information for each test as follows. The multi-row header includes: (starting in 4th column) with data from the testsToDoFile for each test used:

    'Tissue'          (from the "Test Name")
    'FC & pValue' (from the "p-Value test thresh." & "fold-change test thresh.")
    'Test label'      (from the "HTML page label')
    "MnA/MnB"         (fixed comment indicating fold-change)
    'testName'        (from the "Test Name")

 It is derived from all of the mAdb MRR test results data and 
 used the mAdb-TestsToDo.xls data for annotation.     

  ** Each row has 3 leading params  ("Gene" "Feature ID" "Well ID") that 
     can be hyperlinked in the HTML version of the table. 
  ** This is followed by the "A-B Mean Difference" value for that test
     (for all tests).
  ** The test name, tissue, A vs B names, "MnA/MnB" are part of the 5 
     line header.
  ** The +FC and -FC data are merged (since the same gene can not be found
     in both the +FC and -FC reports).
  ** All genes found in any test are included in the table. 
  ** Where a gene does not show up in a test because the FC was below
     threshold, that cell is left blank.
  ** if adding FC ranges (-addFCrangesForTestsIntersectionTable switch)
     then add three columns "Max FC", "Min FC" and "Range FC".
     Note that we can sort on these since the sorting is done after
     the table is computed.

 The following is a (BOGUS data) example of what it might look like.

   
                                  Erythroid      Liver           . . .
                                  Stat5KO vs WT  WT+GH vs WT-GH  . . .
                                  MnA/MnB        MnA/MnB         . . .
   "Gene" "Feature ID" "Well ID"  EG1-test-1     EG2-test-1      . . .
   ------ ------------ ---------  -------------  ---------------
   Stat3  1460700_at   123456      1.234         -3.1234         . . .
   Sox9   1451538_at   234567                     2.1234         . . .
   Sox3   1455899_x_at 345678      2.5432        -4.3210         . . .
           etc...

 Data in the Test-ToDo-List Table
 Column entry    Description 
 "Affy .CEL file (16)" - The Affymetrix .CEL file name in the 
                        GSP-Inventory.xls Egxxxx worksheets
 "Simple GSP ID (10)" - The Simple GSP ID sample name in the 
                        GSP-Inventory.xls Egxxxx worksheets
 "GSP ID (9)" - The default GSP ID sample name in the GSP-Inventory.xls 
                        EGxxxx worksheets
 "Class A" - The samples in class A for the test
 "Class B" - The samples in class B for the test
 "t-Test or Fold-Change Test" - A/B indicates a fold change reported
                        as A samples / B samples.
 "Test Name" - The unique name of the test  formed from the Egxxx number.
                        E.g., EG5.1-test-3
 "p-Value test thresh" -  If there are at least 2 samples for both A 
                        and B classes, this is the p-value threshold 
                        to be used. It is empty if there are not at 
                        least 2 samples/class.
 "fold-change test thresh" -  The fold-change threshold to be used. 
                        It is shown as +/-nX since we do the test for 
                        genes > nX and genes < 1/nX and report them 
                        separately.
 "HTML page label" - Converter web page content page label
 "HTML page description" - Converter web page description content page label
 "HTML tissue name" - Converter tissue name used in the Web page and in 
                        possibly in other  areas.
 "Relative directory" - Relative subdirectory entry in the directory 
                        tree used for a) mAdb tests results (.txt & .zip 
                        files) go, b) converter input data and HTML and 
                        JTV output data, and c) the Jak-Stat Prospector Web 
                        site subdirectory tree.
 
 Test name usage:  File names generated using the 'Test Name'
 tests
 Tests for samples:     
  {testName}+FC.txt       
  {testName}-FC.txt
 
 The converter output will be a mixture of .txt, .html files, and 
 processed JTV directories and .zip files.
 The JTV .zip files have the .zip removed and an HTML file generated 
 to start up the JTV applet from the Web page.
 
 List of variables set by switch:
 -makeTestsIntersectionTbl:{testsToDoFile}
 cvt.makeTestsIntersectionTableFlag
 cvt.testsToDoTblFile
 cvt.filterTestField
 cvt.filterTestsList
 cvt.filterDataField
 cvt.filterDataList
 cvt.addFCrangesForTestsIntersectionTableFlag
 cvt.addRangeOfMeansToTItableFlag

 List of Methods

 ===================
 MakeTestsIntersectionTbl() - Constructor
 setTestFilterList() - set list of test keywords for filtering tests.
 setDataFilterList() - set list of data keywords for filtering data.
 initTestsIntersection() - initialize the input files and I/O paths
 initTblHeaderIndexes() - get TestToDo Table header idx variables
 getTestToDoRowData() - get and save row data to class 's'prefix variables.
 createTestsIntersectionTable() - create the Tests-Intersection Table.
 addAllTestsDataToTI() - add all Tests Data to ftTI Table.
 addFCdataInstanceToTI() - add gene FC data to Test-Intersection Table.
 makeUniqueRelDirList() - generate unique list of Relative Dir. entries.
 getAllTestDataForRelDir() - get list of test data for rel-dir in tdfrd.
 cvtSimpleGspId2EG() - map Simple GSP ID to an EGxxxx.y
 matchTestFilter() - test current test   tField name of ft Table
 matchDataFilter() - test the tField name of current MRR Table data.
 addFCrangesForTestsIntersectionTable() - adding FC range computations
 calcRunningMaxMinMeanABvalues() - calc row r ft max and min MeanA(B) values
 getFilterSummaryHTML() - get an HTML summary of the test/data filters used.
 
 Internal Class

 =================== 
 Class TestDataForRelDir contains lists of rows of data computed as side 
 effect for computing active lists when calling getAllTestDataForRelDir().

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: 2009/07/20 11:45:56 $ $Revision: 1.28 $
Copyright 2008, 2009 by Peter Lemkin E-Mail: lemkin@users.sourceforge.net http://lemkingroup.com/

Nested Class Summary
`(package private) class`	`MakeTestsIntersectionTbl.TestDataForRelDir` Class to contain lists of rows of data computed as side effect for computing active lists when calling getAllTestDataForRelDir().

Field Summary
`HTMLtools`	`cvt`
`private java.lang.String`	`filterDataField` Specifies the tField name of MRR Table data to test.
`private java.lang.String[]`	`filterDataList` Specifies the list of filter instances to test.
`private java.lang.String`	`filterTestField` Specifies the tField name of Tests-ToDo Table data to test.
`private java.lang.String[]`	`filterTestsList` Specifies the list of filter instances to test.
`FileTable`	`fio` Global fileTable instance
`FileTable`	`ftGTT` The FileTable created from the {test-ToDo-list.txt} file.
`FileTable`	`ftTI` The FileTable Test-Intersection Table created from the tests data that intersection the genes in the tests.
`private int`	`idx_pValueThr` The index variables for the Test-ToDo ftGTT Table instance variables.
`private int`	`idxAffyCELfile` The index variables for the Test-ToDo ftGTT Table instance variables.
`private int`	`idxClassA` The index variables for the Test-ToDo ftGTT Table instance variables.
`private int`	`idxClassB` The index variables for the Test-ToDo ftGTT Table instance variables.
`private int`	`idxFCcalc` The index variables for the Test-ToDo ftGTT Table instance variables.
`private int`	`idxFCthr` The index variables for the Test-ToDo ftGTT Table instance variables.
`private int`	`idxFeatureIDftTI` The index variables for the ftTI Tests-Intersection Table instance variables.
`private int`	`idxGeneftTI` The index variables for the ftTI Tests-Intersection Table instance variables.
`private int`	`idxGSP_ID` The index variables for the Test-ToDo ftGTT Table instance variables.
`private int`	`idxHTMLpageDescr` The index variables for the Test-ToDo ftGTT Table instance variables.
`private int`	`idxHTMLpageLabel` The index variables for the Test-ToDo ftGTT Table instance variables.
`private int`	`idxHTMLtissueName` The index variables for the Test-ToDo ftGTT Table instance variables.
`private int`	`idxMaxFCftTI` The following are computed AFTER the TI is built
`private int`	`idxMinFCftTI` The following are computed AFTER the TI is built
`private int`	`idxPercentFCftTI` The following are computed AFTER the TI is built
`private int`	`idxRangeFCftTI` The following are computed AFTER the TI is built
`private int`	`idxRangeMeanAftTI` The following are computed AFTER the TI is built
`private int`	`idxRangeMeanBftTI` The following are computed AFTER the TI is built
`private int`	`idxRelDir` The index variables for the Test-ToDo ftGTT Table instance variables.
`private int`	`idxSimpleGSP_ID` The index variables for the Test-ToDo ftGTT Table instance variables.
`private int`	`idxTestName` The index variables for the Test-ToDo ftGTT Table instance variables.
`private int`	`idxWellIDftTI` The index variables for the ftTI Tests-Intersection Table instance variables.
`private float[]`	`maxMeanA` Data accumulated while reading the individual tests and then used to compute the ranges of the means for inclusion in the final ftTI Table.
`private float[]`	`maxMeanB` Data accumulated while reading the individual tests and then used to compute the ranges of the means for inclusion in the final ftTI Table.
`private int`	`MEANS_ALLOC` Allocate xxxMeanX[] and rangeMeanX[] to MEANS_ALLOC, but then only use the data up to ftTI.tRows (before -limitMaxRows of the Table).
`private float[]`	`minMeanA` Data accumulated while reading the individual tests and then used to compute the ranges of the means for inclusion in the final ftTI Table.
`private float[]`	`minMeanB` Data accumulated while reading the individual tests and then used to compute the ranges of the means for inclusion in the final ftTI Table.
`private java.lang.String`	`s_pValueThr` The Test-ToDo ftGTT Table instance variables
`private java.lang.String`	`sAffyCELfile` The Test-ToDo ftGTT Table instance variables
`private java.lang.String`	`sClassA` The Test-ToDo ftGTT Table instance variables
`private java.lang.String`	`sClassB` The Test-ToDo ftGTT Table instance variables
`private java.lang.String`	`sFCcalc` The Test-ToDo ftGTT Table instance variables
`private java.lang.String`	`sFCthr` The Test-ToDo ftGTT Table instance variables
`private java.lang.String`	`sGSP_ID` The Test-ToDo ftGTT Table instance variables
`private java.lang.String`	`sHTMLpageDescr` The Test-ToDo ftGTT Table instance variables
`private java.lang.String`	`sHTMLpageLabel` The Test-ToDo ftGTT Table instance variables
`private java.lang.String`	`sHTMLtissueName` The Test-ToDo ftGTT Table instance variables
`private java.lang.String`	`sRelDir` The Test-ToDo ftGTT Table instance variables
`private java.lang.String`	`sSimpleGSP_ID` The Test-ToDo ftGTT Table instance variables
`private java.lang.String`	`sTestName` The Test-ToDo ftGTT Table instance variables
`private MakeTestsIntersectionTbl.TestDataForRelDir`	`tdfrd` Class to contain lists of rows of data computed as side effect for computing active lists when calling getAllTestDataForRelDir().
`java.lang.String`	`testsInputTreePath` Input tree dir path from current directory
`boolean`	`testsSizeLimitedFlag`
`private java.lang.String`	`testsToDoTblPath` The path for the tests directory from the current directory.
`java.lang.String[]`	`uniqueRelDir` Unique list of Relative Directory entries.

Constructor Summary
`MakeTestsIntersectionTbl(HTMLtools cvt)` MakeTestsIntersectionTbl() - Constructor

Method Summary
`private boolean`	`addAllTestsDataToTI(FileTable ftGTT, java.lang.String tissueName, java.lang.String relativeDir)` addAllTestsDataToTI() - add all Tests Data to ftTI Table for a Tissue.
`private boolean`	`addFCdataInstanceToTI(FileTable ftFCplus, FileTable ftFCminus, FileTable ftTI, java.lang.String tissueName, java.lang.String testName, java.lang.String pValueFCthrs, java.lang.String pageLabel, java.lang.String AsampleName, java.lang.String BsampleName)` addFCdataInstanceToTI() - add gene FC data to Test-Intersection Table.
`private boolean`	`addFCrangesForTestsIntersectionTable()` addFCrangesForTestsIntersectionTable() - adding FC range computations which expands the table and adds the three columns ("Max FC", "Min FC", "Range FC").
`private boolean`	`calcRunningMaxMinMeanABvalues(int rM, int rD, FileTable ftD, int idxMeanA_FC, int idxMeanB_FC)` calcRunningMaxMinMeanABvalues() - calc row r ftData max and min MeanA(B) values Get the data from the ft fields "A Mean" and "B Mean".
`boolean`	`createTestsIntersectionTable()` createTestsIntersectionTable() - create the Tests-Intersection Table.
`private java.lang.String`	`cvtSimpleGspId2EG(java.lang.String sgi)` cvtSimpleGspId2EG() - map Simple GSP ID to an EGxxxx.y
`private boolean`	`getAllTestDataForRelDir(java.lang.String relDir)` getAllTestDataForRelDir() - get list of test data for a relative directory in tdfrd class instance.
`java.lang.String`	`getFilterSummaryHTML(java.lang.String baseFileName)` getFilterSummaryHTML() - get an HTML summary of the test/data filters used.
`private boolean`	`getTestToDoRowData(int r)` getTestToDoRowData() - get and save row data to class 's'prefix variables.
`private boolean`	`initTblHeaderIndexes()` initTblHeaderIndexes() - get TestToDo Table header idx variables [REFACTOR] so that the ftGTT files are not hardwired.
`boolean`	`initTestsIntersection(java.lang.String testsToDoPath)` initTestsIntersection() - initialize the input files and I/O paths to make sure they are well formed and exist.
`private java.lang.String[]`	`makeUniqueRelDirList()` makeUniqueRelDirList() - generate unique list of Relative Dir.
`private boolean`	`matchDataFilter(FileTable ftMRR, int rowNbr)` matchDataFilter() - test the tField name of current MRR Table data.
`private boolean`	`matchTestFilter(FileTable ft, int rowToTest)` matchTestFilter() - test current test tField name of ft Table data to test.
`boolean`	`setDataFilterList(java.lang.String filterDataField, java.lang.String[] filterDataList)` setDataFilterList() - set list of data keywords for filtering data.
`boolean`	`setTestFilterList(java.lang.String filterTestField, java.lang.String[] filterTestsList)` setTestFilterList() - set list of test keywords for filtering tests.

Methods inherited from class java.lang.Object
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Field Detail

cvt

public HTMLtools cvt

fio

public FileTable fio

Global fileTable instance

tdfrd

private MakeTestsIntersectionTbl.TestDataForRelDir tdfrd

Class to contain lists of rows of data computed as side effect for computing active lists when calling getAllTestDataForRelDir().

uniqueRelDir

public java.lang.String[] uniqueRelDir

Unique list of Relative Directory entries.

ftGTT

public FileTable ftGTT

The FileTable created from the {test-ToDo-list.txt} file. Set with '-MakeTestsIntersectionTbl:{mAdb-TestsToDo.txt}'.

ftTI

public FileTable ftTI

The FileTable Test-Intersection Table created from the tests data that intersection the genes in the tests.

testsToDoTblPath

private java.lang.String testsToDoTblPath

The path for the tests directory from the current directory.

testsInputTreePath

public java.lang.String testsInputTreePath

Input tree dir path from current directory