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

I

iam - Variable in class SetupLayouts

[0:nIAused-1] image analysis methods to choose from max of MAX_IMG_ANALY_METHODS

identifier - Variable in class Element

generic Genomic ID

idxClone_ID - Variable in class DataIO

GIPO index for clone ID

idxDatabase_File - Variable in class MaeSampleData

idx of "Database_File" field

idxDbEst3 - Variable in class DataIO

GIPO index 'dbEST' identifier data.

idxDbEst5 - Variable in class DataIO

GIPO index 'dbEST' identifier data.

idxDetValue - Variable in class DataIO

GIPO index for Spot Detection value

idxDiffCall - Variable in class DataIO

GIPO index for Affy Diff Call

idxField - Variable in class DataIO

GIPO index

idxFoldChange - Variable in class DataIO

GIPO index for Fole Change

idxFUmap - Variable in class FieldMap

[0:nMapFields-1] index map from userFieldMap[u] to fieldNames[f].

idxGenBankAcc - Variable in class DataIO

GIPO index 'GenBank' identifier data.

idxGenBankAcc3 - Variable in class DataIO

GIPO index 'GenBank' identifier data.

idxGenBankAcc5 - Variable in class DataIO

GIPO index 'GenBank' identifier data.

idxGeneName - Variable in class DataIO

GIPO index for gene name

idxGrid - Variable in class DataIO

GIPO index for Grid

idxGridCol - Variable in class DataIO

GIPO index for grid column

idxGridRow - Variable in class DataIO

GIPO index for grid row

idxIdentifier - Variable in class DataIO

generic Genomic ID - used when no other ids

idxLocation - Variable in class DataIO

GIPO index fields for fieldNames[]

idxLocusLinkID - Variable in class DataIO

GIPO index

idxNAME_GRC - Variable in class DataIO

GIPO index for NAME_GRC; (Molecular Dynamics "NAME_GRC" spec )

idxParameter - Variable in class EditMaeProjectFiles

index for Parameter for getValueByName methods

idxPlate - Variable in class DataIO

GIPO index for plate

idxPlateCol - Variable in class DataIO

GIPO index for plate column

idxPlateRow - Variable in class DataIO

GIPO index for plate row

idxProject - Variable in class MaeSampleData

idx of "Project" field

idxQualCheck - Variable in class DataIO

GIPO index

idxQualCheckGIPO - Variable in class DataIO

GIPO index for 'GIPO' QualCheck data

idxRawBackground - Variable in class DataIO

GIPO index

idxRawBackground1 - Variable in class DataIO

GIPO index

idxRawBackground2 - Variable in class DataIO

GIPO index

idxRawIntensity - Variable in class DataIO

GIPO index

idxRawIntensity1 - Variable in class DataIO

GIPO index

idxRawIntensity2 - Variable in class DataIO

GIPO index

idxSample_ID - Variable in class MaeSampleData

idx of "Sample_ID" field

idxSwissProtID - Variable in class DataIO

GIPO index SwissProtID

idxUFmap - Variable in class FieldMap

[0:nMapFields-1] index map from fieldNames[f] to userFieldMap[u].

idxUnigene_cluster_ID - Variable in class DataIO

GIPO index Unigene cluster ID

idxUnigene_cluster_name - Variable in class DataIO

GIPO index Unigene cluster name

idxValue - Variable in class EditMaeProjectFiles

index for Value for getValueByName methods

idxX - Variable in class DataIO

Quant index fields are for fieldNames[]

idxY - Variable in class DataIO

GIPO index

ignoreExtraFIELDS - Variable in class MaeConfigData

PARAM: "ignoreExtraFields" ignore extra fields in .quant

ignoreExtraFIELDSCB - Variable in class EditWizardPanel

checkbox used in data forms

iLocation - Variable in class Element

int value of Location

IMAGE2GenBankURL - Variable in class MaeConfigData

PARAM: "IMAGE2GenBankURL" lookup GenBank entry from CloneID server.

IMAGE2GidURL - Variable in class MaeConfigData

PARAM: "IMAGE2GIDURL" NCI/CIT lookup GenBank GID from CloneID server.

IMAGE2unigeneURL - Variable in class MaeConfigData

PARAM: "IMAGE2unigeneURL" NCI/CIT lookup UNIGENE from CloneID server.

ImageAnalysisMethod - class ImageAnalysisMethod.

This class specifies segmentation software tool used in quantifying the image spot data.

ImageAnalysisMethod(String, String, String, String, String, String, String) - Constructor for class ImageAnalysisMethod

ImageAnalysisMethod() - constructor

imgAnalyLabel - Variable in class CvtGUI

1.1 Select Quant.

imgAnalysisChoice - Variable in class CvtGUI

choice of image analysis pkg used to generate quantification files if they are NOT part of the input file.

imgAnalySoftware - Variable in class MaeConfigData

image quant program

indexToLongestStr(String[]) - Method in class FieldMapGUI

indexToLongestStr() - find max size of str in array and return its array index (location within array).

inFilesList - Variable in class CvtGUI

list for showing input files...

infillCnt - Variable in class DataIO

# of infill spots generated

init() - Method in class Cvt2Mae

init() - initialize data structures and create and start the GUI.

initFieldMapGUI() - Method in class FieldMapGUI

initFieldMapGUI() - initialize GUI list method

initFM() - Method in class FieldMapGUI

initFM() - initialize non-GUI objects

initialKeyword - Variable in class ArrayLayout

initial keyword if any for chip

initialKeyword - Variable in class MaeConfigData

initial keyword if not ""

initMCD() - Method in class MaeConfigData

initMCD() - init data structures

InputFileRowsPanel_PP(int) - Method in class EditWizardPanel

InputFileRowsPanel_PP() - popup panel handler for input file rows data.

inSamplesList - Variable in class CvtGUI

input samples (i.e.

isDuplicateEntries(String) - Method in class FieldMap

isDuplicateEntries() - test if duplcate entries for mT entries in mT subtable.

isEntry(String, String) - Method in class FieldMap

isEntry() - has an entry for (mT,mF) in the list Return true if an entry exists.

isIntensityOrBackground(String) - Method in class FieldMapGUI

isIntensityOrBackground() - test if it is a legal intensity or background MAE Quant names.

isMacFlag - Variable in class Cvt2Mae

flag: use Max list of required fields

isSunFlag - Variable in class Cvt2Mae

flag: true if SUNOS

isWinPCflag - Variable in class Cvt2Mae

flag: true if Windows PC

isWinPCflag - Variable in class FieldMapGUI

os type flag

itemStateChanged(ItemEvent) - Method in class CvtGUI

itemStateChanged() - event handler for Choices

itemStateChanged(ItemEvent) - Method in class EditWizardPanel

itemStateChanged() - handler if check box state was changed

itemStateChanged(ItemEvent) - Method in class FieldMapGUI

itemStateChanged() - event handler for Choice list.

itemStateChanged(ItemEvent) - Method in class PopupGetSepGIPOnamesForGridRowCol

itemStateChanged() - event handler for Choices