Serialized Form
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Class CvtGUI extends javax.swing.JFrame implements Serializable |
serialVersionUID: 0L
gui
CvtGUI gui
- May need to define so can pass to InvokeLater methods
cvt
HTMLtools cvt
title
java.lang.String title
- string for title of frame
programName
java.lang.String programName
- The name of the program
version
java.lang.String version
- version number of the program
mbar
java.awt.MenuBar mbar
- menu bar for the frame
fileMenu
java.awt.Menu fileMenu
- "File" pull down Menu list
helpMenu
java.awt.Menu helpMenu
- "Help" pull down Menu list
ms
MenuSupport ms
- Menu support functions using Hashtables to track what is active
verboseMCB
java.awt.CheckboxMenuItem verboseMCB
- Menu checkbox item
textReport
java.lang.String textReport
- copy of text in textArea
reportFile
java.lang.String reportFile
- default SAVE AS .txt file for textReport data.
showStatusFlag
boolean showStatusFlag
textarea
javax.swing.JTextArea textarea
- Text area GUI for main report
textAreaFontSize
int textAreaFontSize
- font size
nRows
int nRows
- # of character rows to show
nCols
int nCols
- # of character cols to show
textFontFamily
java.lang.String textFontFamily
- Text area font family
processButton
javax.swing.JButton processButton
- button for "Process" button - may enable/disable button
cancelButton
javax.swing.JButton cancelButton
- button for "Cancel" button - may enable/disable button
resetButton
javax.swing.JButton resetButton
- button for "Reset" GUI button
viewHTMLchoice
java.awt.Choice viewHTMLchoice
statusLineLabel
javax.swing.JLabel statusLineLabel
- Status line label updated with UtilCM.updateReportStatusLine()
pd
ProcessData pd
- Thread for converter processing
processFlag
boolean processFlag
- "Processing" data in the GUI
processedOKflag
boolean processedOKflag
- "Process was ok" if true. Set to false if any problems.
doneFlag
boolean doneFlag
- "Done" processing data in the GUI
closeGuiFlag
boolean closeGuiFlag
- "Close" the GUI
cancelFlag
boolean cancelFlag
- "Cancel" the processing in the GUI
guiFSMstate
java.lang.String guiFSMstate
- GUI FSM state
printFSMflag
boolean printFSMflag
- print FSM debug statements in printGuiFSM()
guiBatchDoItFile
java.lang.String guiBatchDoItFile
- GUI Converter -batch DoIt file
guiParamsMapFile
java.lang.String guiParamsMapFile
- GUI Converter params map file
guiActiveHTMLfile
java.lang.String guiActiveHTMLfile
sGuiArgV
java.lang.String sGuiArgV
- Command line string created to use when running the converter
used by ProcessData
guiArgV
java.lang.String[] guiArgV
- Command line string array created to use when running the
converter used by ProcessData
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Class SearchGUI extends javax.swing.JFrame implements Serializable |
serialVersionUID: 0L
cvt
HTMLtools cvt
sGui
SearchGUI sGui
sgs
SearchGUI.SGstate sgs
- SearchGUI state variables that can be saved/imported from .sgs files.
title
java.lang.String title
- string for title of frame
programName
java.lang.String programName
- The name of the program
version
java.lang.String version
- version number of the program
mbar
java.awt.MenuBar mbar
- menu bar for the frame
fileMenu
java.awt.Menu fileMenu
- "File" pull down Menu list
viewMenu
java.awt.Menu viewMenu
- "View" pull down Menu list
listMenu
java.awt.Menu listMenu
- "List" pull down Menu list
helpMenu
java.awt.Menu helpMenu
- "Help" pull down Menu list
ms
MenuSupport ms
- Menu support functions using Hashtables to track what is active
verboseMCB
java.awt.CheckboxMenuItem verboseMCB
- Menu checkbox item for Verbose reporting
foldChangeMCB
java.awt.CheckboxMenuItem foldChangeMCB
- Menu checkbox item for "Report Fold Change of 2 sample subsets"
foldChangeThrMCB
java.awt.CheckboxMenuItem foldChangeThrMCB
- Menu checkbox item for
"Only keep genes/probes with |fold-change| >= threshold"
This pops up a dialog to enter the threshold value between 0.0 and
some large number and saves it in sgs.foldChangeThr. The associated flag
is sgs.foldChangeThrFlag.
lastRestoreSGstateMI
java.awt.MenuItem lastRestoreSGstateMI
- MenuItem "Restore previously saved search .sgs parameters from file"
restoreSGstateMI
java.awt.MenuItem restoreSGstateMI
- MenuItem "Restore previously saved search .sgs parameters from file"
saveSGstateMI
java.awt.MenuItem saveSGstateMI
- MenuItem "SaveAs current search .sgs parameters to file"
classAMI
java.awt.MenuItem classAMI
- MenuItem "Assign EG samples to Class A"
classBMI
java.awt.MenuItem classBMI
- MenuItem "Assign EG samples to Class A"
showDataHeatmapFlipTableMCB
java.awt.CheckboxMenuItem showDataHeatmapFlipTableMCB
- Menu checkbox item for "Show data heat-map in View HTML Results"
showStatusFlag
boolean showStatusFlag
textAreaFontSize
int textAreaFontSize
- font size
textFontFamily
java.lang.String textFontFamily
- Text area font family
bptv
PopupTextViewer bptv
- Optional Big popup text viewer for Report-Log
reportTextarea
javax.swing.JTextArea reportTextarea
- Text area GUI for main Report-Log. Data is also kept int textReport and
can be saved in reportFile.
searchTermTextArea
javax.swing.JTextArea searchTermTextArea
- Text area GUI for entering list of search terms
samplesList
javax.swing.JList samplesList
processButton
javax.swing.JButton processButton
- button for "Process" button - may enable/disable button
cancelButton
javax.swing.JButton cancelButton
- button for "Cancel" button - may enable/disable button
viewHTMLButton
javax.swing.JButton viewHTMLButton
- button for "ViewHTML" button - may enable/disable button
resetButton
javax.swing.JButton resetButton
- button for "Reset" converter button
statusLineLabel
javax.swing.JLabel statusLineLabel
- Status line label updated with UtilCM.updateReportStatusLine()
filterRowTextField
javax.swing.JTextField filterRowTextField
searchResultsFilenamePrefixTF
javax.swing.JTextField searchResultsFilenamePrefixTF
- SearchResults filename Prefix text field
matchGeneTermRB
javax.swing.JRadioButton matchGeneTermRB
- Exact match radio button for search-term specification,
button grouped with matchSearchStrTermRB.
Sets sgs.flipTableUseExactMatchFlag.
matchSubStrTermRB
javax.swing.JRadioButton matchSubStrTermRB
- Substring match radio button for search-term specification,
button grouped with matchGeneTermRB.
Clears sgs.flipTableUseExactMatchFlag.
andEGnamesRB
javax.swing.JRadioButton andEGnamesRB
- AND match radio button for EG sample list specification,
button grouped with orEGnamesRB.
Sets sgs.evalSearchANDbooleanFlag.
orEGnamesRB
javax.swing.JRadioButton orEGnamesRB
- OR match radio button for EG sample list specification,
button grouped with andEGnamesRB.
Clears sgs.evalSearchANDbooleanFlag.
textReport
java.lang.String textReport
- Copy of text in Report-Log reportTextarea
reportFile
java.lang.String reportFile
- Default SAVE AS .txt file for Report-Log textReport data used in
reportTextarea.
searchTermsFilterPrompt
java.lang.String searchTermsFilterPrompt
- Switch supplied search Terms filter prompt for searchTermTextArea
Set by -searchTermsFilterPrompt:{...}.
searchTermFilter
java.lang.String[][] searchTermFilter
searchTermNames
java.lang.String[] searchTermNames
nSearchTermNames
int nSearchTermNames
flipTableDataFile
java.lang.String flipTableDataFile
- Name of database Table file that we will use to verify search terms.
We get this from '-flipTableByIndexMap:{dataSet.txt,dataSet.idx}'.
flipTableIndexMapFile
java.lang.String flipTableIndexMapFile
- Name of Index Map file that we will use to verify search terms.
We get this from '-flipTableByIndexMap:{dataSet.txt,dataSet.idx}'.
This is used to read the ftIM FileTable.
ftIM
FileTable ftIM
- Index Map FileTable that we will use to verify search terms.
We get this from '-flipTableByIndexMap:{dataSet.txt,dataSet.idx}'.
ftData
FileTable ftData
- Header-only Data FileTable that we will use to get the list of
EG Samples.We get this from
'-flipTableByIndexMap:{dataSet.txt,dataSet.idx}'.
dbGSPIDlist
java.lang.String[] dbGSPIDlist
- This is the list of ftData Data Table columns starting with "EG"
and is the list of EG GSP IDs in the database.
indexMapReadyFlag
boolean indexMapReadyFlag
- The Index Map file into ftIM has been read successfully
by the ProcessLoadIndexMapData Thread.
indexMapProblemFlag
boolean indexMapProblemFlag
- There has been a problem reading the Index Map file into ftIM
by the ProcessLoadIndexMapData Thread.
searchSampleChoiceFile
java.lang.String searchSampleChoiceFile
- The name of the sample list Table file. It is a 2 column array where
used for the sample Choice GUI where the choice Object value is [][0],
and the viewable choice name is [][1].
Set by '-searchsearchSampleChoiceFile:{sample choice Table file}'.
sampleChoiceData
java.lang.String[][] sampleChoiceData
- The sample list is a 2 column array where
the Object value is [][0], and the viewable choice
name is [][1].
searchRowFilterName
java.lang.String searchRowFilterName
- Switch supplied search sample groups filter name for
sampleExprGroupsTextArea. Set by -searchRowFilterName:{...}.
searchRowFilterPrompt
java.lang.String searchRowFilterPrompt
- Switch supplied search samples group filter prompt for
sampleExprGroupsTextArea. Set by -searchRowFilterPrompt:{...}.
pds
ProcessDataSearch pds
- Thread for converter processing
processFlag
boolean processFlag
- "Processing" data in the GUI
processedOKflag
boolean processedOKflag
- "Process was ok" if true. Set to false if any problems.
doneFlag
boolean doneFlag
- "Done" processing data in the GUI
closeGuiFlag
boolean closeGuiFlag
- "Close" the GUI
cancelFlag
boolean cancelFlag
- "Cancel" the processing in the GUI
guiFSMstate
java.lang.String guiFSMstate
- GUI FSM state
dataSource
java.lang.String dataSource
- The subtitle for generated Web page by mapping to the preface
"$$DATA_SOURCE_SUBTITLE$$"
inputSearchDir
java.lang.String inputSearchDir
- Param .map default input Dir
outputSearchDir
java.lang.String outputSearchDir
- Param .map default output Dir
tableSearchDir
java.lang.String tableSearchDir
- Param .map default table Dir
guiParamsMapFile
java.lang.String guiParamsMapFile
- GUI Converter params map file
guiParamsMapDefaultPath
java.lang.String guiParamsMapDefaultPath
- GUI Converter params map default file path
guiActiveHTMLfile
java.lang.String guiActiveHTMLfile
guiActiveTXTfile
java.lang.String guiActiveTXTfile
sGuiArgV
java.lang.String sGuiArgV
- Command line string created to use when running the converter
used by ProcessDataSearch
guiArgV
java.lang.String[] guiArgV
- Command line string array created to use when running the
converter used by ProcessDataSearch