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

U

unigene_cluster_ID - Variable in class Element

GIPO data

unigene_cluster_name - Variable in class Element

GIPO data

UniGeneSpeciesPrefix - Variable in class ArrayLayout

Used with UniGene

UniGeneSpeciesPrefix - Variable in class MaeConfigData

Org=Hs or ORG=Mm, etc

uniGeneURL - Variable in class MaeConfigData

PARAM: "uniGeneURL" NCBI UNIGENE by Clone ID server.

unusedStr - Variable in class FieldMapGUI

string selected if unused

updateChipValuesGUIfromMCD() - Method in class CvtGUI

updateChipValuesGUIfromMCD() - update MCD chip layout values to text area GUI

updateCvt2MaeButton - Variable in class CvtGUI

"Update Cvt2Mae button

updateCvt2MaeJarFile() - Method in class UtilCM

updateCvt2MaeJarFile() - update MAExplorer.jar into program install area.

updateCvt2MaeProgram() - Method in class UtilCM

updateCvt2MaeProgram() - verify that want to update the Cvt2Mae.jar file from the maexplorer.sourceforge.net server.

updateInfillLocationIDs() - Method in class DataIO

updateInfillLocationIDs() - if using Location IDs, then sort datum[1:mcd.maxRowsExpected] by Location add infill spots and renumber grid coordinates.

updateMCDstateFromSrcFileData() - Method in class CvtGUI

updateMCDstateFromSrcFileData() - update MCD state from file data.

updatePopupDialog(String) - Method in class PopupEditPrjDialog

updatePopupDialog() - display/unhide popup dialog frame and set new vals.

updatePopupFieldMapDialog(String) - Method in class FieldMapGUI.PopupFieldMapDialog

updatePopupFieldMapDialog() - display/unhide popup dialog frame and set new vals.

updatePopupTextDialog(String, String) - Method in class CvtGUI.PopupTextDialog

updatePopupTextDialog() - display/unhide popup dialog frame and set new vals.

updateQuantNameList() - Method in class CvtGUI

updateQuantNameList() - update the list of samples in GUI

USE_DBUG_DIR - Static variable in class Cvt2Mae

flag: Force source and output files directories to use hardwired definitions while debugging

USE_IAM_FLAG - Static variable in class Cvt2Mae

Add Image Analysis Method GUI

USE_LOG_WINDOW - Static variable in class Cvt2Mae

flag: set if want log windows

useAffyTmpFileFlag - Variable in class MaeConfigData

flag: use the Affy tmp file to remap MAS5 data

useAL - Variable in class SetupLayouts

array layout to use, -1 means failed

useBackgroundCorrectionCB - Variable in class EditWizardPanel

checkbox used in data forms

useCy3Cy5RatioDataCB - Variable in class EditWizardPanel

checkbox used in data forms

useCy5_Cy3CB - Variable in class EditWizardPanel

checkbox used in data forms

useCy5OverCy3CB - Variable in class EditWizardPanel

checkbox used in data forms

useCy5OverCy3Flag - Variable in class MaeConfigData

PARAM: "useCy5/Cy3" switch all Cy3/Cy5 to Cy5/Cy3

useField(String) - Method in class FieldMap

useField() - set flag to true in useFieldFlag[] for fName field.

useIAM - Variable in class SetupLayouts

method to use, -1 means failed

useMaxFieldsCB - Variable in class CvtGUI

use maximum fields for mapTF gui

useMaxFieldsRequiredFlag - Variable in class Cvt2Mae

useMolDyn_NAME_GRC_specCB - Variable in class EditWizardPanel

checkbox used in data forms

useMolDyn_NAME_GRC_specFlag - Variable in class MaeConfigData

specify (grid,row,col) by Molecular Dynamics "NAME_GRC" spec

useMouseOverFlag - Variable in class MaeConfigData

PARAM: "useMouseOver" enable mouse over

usePosQuantDataCB - Variable in class EditWizardPanel

checkbox used in data forms

usePosQuantDataFlag - Variable in class MaeConfigData

PARAM: "usePosQuantDataFlag"Filter out genes where .quant file data has negative intensity values otherwise it uses the negative data

usePseudoXYcoordsCB - Variable in class EditWizardPanel

checkbox used in data forms

usePseudoXYcoordsFlag - Variable in class MaeConfigData

PARAM: "usePseudoXYcoords" generate Pseudo XY coords

useRatioDataCB - Variable in class EditWizardPanel

checkbox used in data forms

useRatioDataFlag - Variable in class ArrayLayout

flag: data is Cy3/Cy5 type fluorescent ratio data

useRatioDataFlag - Variable in class MaeConfigData

PARAM: "useRatioData" set if data is Cy3/Cy5 ratio data, else it assumes intensity data for each spot

useRatioMedianCorrectionCB - Variable in class EditWizardPanel

checkbox used in data forms

userDir - Variable in class Cvt2Mae

user directory - JVM ("user.dir")+fileSep

userDir - Variable in class MaeConfigData

startup directory

userFieldMap - Variable in class FieldMap

[0:nMap-1] map external user's Field name

userFile - Variable in class FieldMap

full file path for file that contains field names

userGipoFields - Variable in class FieldMap

GIPO fields selected by user

userQuantFields - Variable in class FieldMap

Quant fields selected by user

userSampleFields - Variable in class FieldMap

Sample fields selected by user

userTableMap - Variable in class FieldMap

[0:nMap-1] map external user's Table name

useTokFlag - Variable in class FieldMap

[0:nMapFields-1] flag fields used to tokenize when parsing input table data corresponding to fieldNames[0:nMapFields-1].

useTokFlagGQ - Variable in class DataIO

[MAX_IN_TOKENS_PER_ROW] tokens to get for FieldGQ data

util - Variable in class Cvt2Mae

Global utilities UtilCM instance

util - Variable in class CvtGUI

Utilities instance

util - Variable in class DataIO

Global utilities

util - Variable in class EditMaeProjectFiles

global link to UtilCM instance

util - Variable in class EditWizardPanel

global link to UtilCM intance

util - Variable in class SetupLayouts

Global link to UtilCM instance

UtilCM - class UtilCM.

Collection of utility functions used by various other classes.

UtilCM(boolean) - Constructor for class UtilCM

UtilCM() - constructor for setup utility pkg