A B C D E F G H I L M N O P Q R S T U V W X Y

A

A_BG_COLOR - Static variable in class CvtGUI

Background color

aboutMenuItem - Variable in class EditMaeProjectFiles

misc

actionPerformed(ActionEvent) - Method in class CvtGUI

actionPerformed() - event handler for Buttons

actionPerformed(ActionEvent) - Method in class CvtGUI.PopupTextDialog

actionPerformed() - Handle button clicks

actionPerformed(ActionEvent) - Method in class EditMaeProjectFiles

actionPerformed() - button listener for menus and panel buttons

actionPerformed(ActionEvent) - Method in class EditWizardPanel.DialogBox

actionPerformed(ActionEvent) - Method in class FieldMapGUI

actionPerformed() - button event handler

actionPerformed(ActionEvent) - Method in class FieldMapGUI.PopupFieldMapDialog

actionPerformed() - Handle button clicks

actionPerformed(ActionEvent) - Method in class PopupDialog.MainDialog

actionPerformed() - button press handler- close window

actionPerformed(ActionEvent) - Method in class PopupEditPrjDialog

actionPerformed() - Handle button clicks

actionPerformed(ActionEvent) - Method in class PopupGetSepGIPOnamesForGridRowCol

actionPerformed() - Handle button clicks

actionPerformed(ActionEvent) - Method in class TextFrame

actionPerformed() - event handler

activeReanalyeButtonFlag - Variable in class MaeConfigData

flag: that the Reanalyze button is active (didEditALOflag && didGIPOassignFlag && didQuantFlag && hasMultDatasetsFlag).

addComponent(Component, int, int, int, int, int, int) - Method in class CvtGUI

addComponent() - add component to the GridBag layout

addComponent(Component, int, int, int, int, int, int) - Method in class TextFrame

addComponent() - add a text component to the frame

addEntry(String, String, String, String) - Method in class FieldMap

addEntry() - add an entry to the list

addEntry(String, String, String, String, boolean) - Method in class FieldMap

addEntry() - add or replace an entry to the FieldMap list.

addFinishButtonFlag - Variable in class EditMaeProjectFiles

set only for last panel

addGenomicDataFromDescr(String) - Method in class DataIO

addGenomicDataFromDescr() - setup Affy genomic ids data from Description "Cluster Incl AW208667:uo62e02.x1 Mus musculus cDNA, 3 end /clone=IMAGE-2647130 /clone_end=3 /gb=AW208667 /gi=6514607 /ug=Mm.4609 /len=474" Add field "Clone_ID" from /clone=IMAGE-2647130 Add field "GenBankAcc" from /gb=AW208667 Add field "UniGeneID from /ug=Mm.4609 Add field "LocusID" from /gb=AW208667

addGenomicFieldsNamesFromDescr() - Method in class DataIO

addGenomicFieldsNamesFromDescr() - setup genomic ids field names from Description "Cluster Incl AW208667:uo62e02.x1 Mus musculus cDNA, 3 end /clone=IMAGE-2647130 /clone_end=3 /gb=AW208667 /gi=6514607 /ug=Mm.4609 /len=474" Add field "Clone_ID" from /clone=IMAGE-2647130 Add field "GenBankAcc" from /gb=AW208667 Add field "UniGeneID from /ug=Mm.4609 Add field "LocusID" from /gb=AW208667

addLabelPanelsToMainPanel() - Method in class EditWizardPanel

addLabelPanelsToMainPanel() - add all labelPanels' to mainPanel

addMouseover(int, String) - Method in class EditWizardPanel

addMouseOver() - add current mouse over string for label[idx]

addSourceFileToList(String, String, boolean, boolean) - Method in class CvtGUI

addSourceFileToList() - add file to list and do intermediate processing.

AFFY_TMP_FILE - Static variable in class Cvt2Mae

Affy MAS-5 temp file name

affyFieldDescriptionCol - Static variable in class DataIO

Special hack for Affy files - see chkAndEditFieldNames().

alertDone - Variable in class CvtGUI.PopupTextDialog

button pressed flag

alertDone - Variable in class FieldMapGUI.PopupFieldMapDialog

button pressed flag

alertDone - Variable in class PopupEditPrjDialog

button pressed flag

alertTimeout(String) - Method in class FieldMapGUI.PopupFieldMapDialog

alertTimeout() - update the popup dialog msg - wait for CONTINUE

alertTimeout(String) - Method in class PopupEditPrjDialog

alertTimeout() - update the popup dialog msg - wait for CONTINUE

alList - Variable in class SetupLayouts

[0:maxAL-1] array layouts to choose from max of MAX_ARRAY_LAYOUTS

allowCancel - Variable in class PopupGetSepGIPOnamesForGridRowCol

allow user to cancel the interaction

allowNegQuantDataCB - Variable in class EditWizardPanel

checkbox used in data forms

allowNegQuantDataFlag - Variable in class ArrayLayout

flag: Set if .quant data has negative intensity values otherwise it clips the negative values to 0.0 (eg.

allowNegQuantDataFlag - Variable in class MaeConfigData

PARAM: "allowNegQuantDataFlag"(eg.

alNbr - Variable in class ArrayLayout

unique ArrayLayout instance number

alo_allowNegQuantDataFlag - Variable in class SetupLayouts

ALO variable: allow negative quant dat

alo_bitProps - Variable in class SetupLayouts

ALO variable: bit mcd.PROP_xxxx properties

alo_chkAndEditFieldNamesFlag - Variable in class SetupLayouts

flag: check and edit Samples and Field names data before use.

alo_colsPerGrid - Variable in class SetupLayouts

ALO variable: # of columns/grid

alo_commentToken - Variable in class SetupLayouts

ALO variable: optional comment token

alo_desiredFields - Variable in class SetupLayouts

ALO variable: list of FieldMaps for the layout

alo_expectedNbrTokens - Variable in class SetupLayouts

ALO variable: # of expected tokens

alo_geoPlatformID - Variable in class SetupLayouts

Optional GEO Platform ID

alo_hasBkgrdDataFlag - Variable in class SetupLayouts

ALO variable: has background intensity data

alo_hasMultDatasetsFlag - Variable in class SetupLayouts

ALO variable: input file has multiple samples

alo_hasQuantXYcoordsFlag - Variable in class SetupLayouts

ALO variable: has actual quant XY coordinates data

alo_initialKeyword - Variable in class SetupLayouts

ALO variable: optional initial keyword in leftmost field

alo_layoutName - Variable in class SetupLayouts

ALO variable: name of the layout

alo_maxFields - Variable in class SetupLayouts

ALO variable: number of duplicate Fields of Grids/array

alo_maxRowsExpected - Variable in class SetupLayouts

ALO variable: maximum number of spots (elements or rows)/sample

alo_nGridsPerField - Variable in class SetupLayouts

ALO variable: # of grids/field

alo_pseudoArrayFlag - Variable in class SetupLayouts

ALO variable: use generated PseudoArray image

alo_quantTool - Variable in class SetupLayouts

ALO variable: name of the quantification program

alo_rowsPerGrid - Variable in class SetupLayouts

ALO variable: # of rows/grid

alo_rowWithData - Variable in class SetupLayouts

ALO variable: # of row of FieldQ input file that contains data

alo_rowWithFields - Variable in class SetupLayouts

ALO variable: # of row of FieldQ input file that contains Field names

alo_rowWithSamples - Variable in class SetupLayouts

ALO variable: # of row of FieldQ input file that contains sample names

alo_rowWithSepGIPOData - Variable in class SetupLayouts

ALO variable: # of row of FieldG separate GIPO input file that contains data

alo_rowWithSepGIPOFields - Variable in class SetupLayouts

ALO variable: # of row of FieldG separate GIPO input file that contains Field names

alo_species - Variable in class SetupLayouts

ALO variable: species of sample

alo_specifyGeometryByNbrSpotsFlag - Variable in class SetupLayouts

ALO variable: specify (F,G,R,C) from # of spots in PseudoArray

alo_UniGeneSpeciesPrefix - Variable in class SetupLayouts

ALO variable: UniGene 2 letter prefix (eg.

alo_useRatioDataFlag - Variable in class SetupLayouts

ALO variable: data is ratio data (eg.

alo_vendor - Variable in class SetupLayouts

ALO variable: vendor making the array

ALO_VERSION - Static variable in class Cvt2Mae

Current Version number for Array layout.

aloDir - Variable in class MaeConfigData

i.e.

aloFile - Variable in class SetupLayouts

[0:nALOfilesFound-1] *.alo ALO files found the the ArrayLayout/ directory

aloFileName - Variable in class ArrayLayout

.alo file name

aloFileName - Variable in class MaeConfigData

current ArrayLayout file name

aloFileName - Variable in class SetupLayouts

ALO variable: variables for parsed .alo file

aloFileVersion - Variable in class SetupLayouts

ALO variable: Version # of .alo file

aloPanel - Variable in class CvtGUI

panel to hold "Edit Layout", "Saveas Layout" buttons

analyzeGIPOfileHeader() - Method in class CvtGUI

analyzeGIPOfileHeader() - analyze seperate GIPO file to find the list of field names, the starting row of the data and possibly determine which fields will be used when merge the data with the separate Quant file field data.

analyzeSrcFilesButton - Variable in class CvtGUI

"Analyze files" if button

answer - Variable in class PopupDialog

return if yes or no was clicked

answer - Variable in class PopupDialog.MainDialog

answer when exit dialog

appendLog(String) - Method in class TextFrame

appendLog() - save text into log area

appendLog(String, boolean) - Method in class TextFrame

appendLog() - save text into log area and set visible/invisible

area - Variable in class TextFrame

Text area for displaying the text

arrayGipoFile - Variable in class MaeConfigData

PARAM: "gipoFile" GIPO file spot print order file.

ArrayLayout - class ArrayLayout.

This class specifies vendor and user defined Array Layouts.

ArrayLayout(String, String, String, String, String, String, String, String, boolean, boolean, int, int, int, int, int, int, int, int, int, int, int, boolean, boolean, boolean, boolean, boolean, boolean, long, String[], String) - Constructor for class ArrayLayout

ArrayLayout() - constructor for Array Layouts.

arrayLayoutNamePanel_PP(int) - Method in class EditWizardPanel

arrayLayoutNamePanel_PP() - popup panel handler for array layout name and vendor.