Class Gene

java.lang.Object
  |
  +--Gene

class Gene

extends java.lang.Object

Field Summary

(package private) static int	C_ATCC_ID Gene property: Clone is an ATCC numbered clone
(package private) static int	C_BAD_DATA property: gene has bad data
(package private) static int	C_BAD_LOCAL_SPOT_BKGRD Gene property: bad local spot background
(package private) static int	C_BAD_MID Gene property: the gene is bad, good gene name
(package private) static int	C_BAD_SPOT Gene property: non-analyzable gene (eg.
(package private) static int	C_BAD_SPOT_GEOMETRY Gene property: bad spot geometry
(package private) static int	C_DUP_SPOT Gene property: is duplicate of another gene on array
(package private) static int	C_GOOD_MID Gene property: the gene is good, good gene name.
(package private) static int	C_IMAGE_ID Gene property: Clone is an I.M.A.G.E.
(package private) static int	C_IS_CUR_GENE Gene property: is Current Gene (not normally used)
(package private) static int	C_IS_EGL_GENE Gene property: is an E.G.
(package private) static int	C_IS_FILTERED Gene property: is a gene that did pass data Filter
(package private) static int	C_IS_KMEANS Gene property: Is a K-means node gene
(package private) static int	C_IS_NOT_FILTERED Gene property: is a gene that did not pass data Filter
(package private) static int	C_LOW_SPOT_REF_SIGNAL Gene property: low spot reference signal
(package private) static int	C_MARGINAL_SPOT Gene property: Marginal spot
(package private) static int	C_USE_GBID_FOR_CLONEID Gene property: use GenBank ID for Clone ID
private static Config	cfg link to global Config instance
(package private) java.lang.String	Clone_ID I.M.A.G.E clone id #, or "your plate", etc.
(package private) int	clusterNodeNbr if >0, then this the cluster node in K-means clustering
(package private) java.lang.String	comments --- options may or may not be used ---
(package private) float	cv optional computed coefficient of variation (CV) if doing statistical test
(package private) float	data dynamic generic data such as ratio, etc associated with this gene
(package private) float	data1 dynamic generic data for Field 1 associated with this gene
(package private) float	data2 dynamic generic data for Field 2 associated with this gene
(package private) java.lang.String	dbEST3 NCBI dbEST database 3' id
(package private) java.lang.String	dbEST5 NCBI dbEST database 5' id
(package private) java.lang.String	GenBankAcc NCBI GenBankAcc id if it exists
(package private) java.lang.String	GenBankAcc3 NCBI GenBankAcc 3' id if it exists
(package private) java.lang.String	GenBankAcc5 NCBI GenBankAcc 5' id if it exists
(package private) java.lang.String	Gene_Class opt.
(package private) java.lang.String	Gene_Name opt.
(package private) float	geneDist Opt.
(package private) java.lang.String	Generic_ID Generic Identifier - "if all else fails" the use may use some arbitrary unique ID
(package private) java.lang.String[]	GenomicID (Optional) External Genomic IDs values if specified via the MaeConfig.txt or .mae startup files.
(package private) int	gid a Grid Identifier (GID) index index corresponding to MasterID.
(package private) java.lang.String	LocusID NCBI LocusLink LocusID if it exists
private static MAExplorer	mae link to global MAExplorer instance
private static Maps	map link to global Maps instance
(package private) java.lang.String	Master_ID Master Gene Identifier (i.e.
(package private) java.lang.String	MasterGeneName Master Gene Name will be one of the gene names below ([NOTE] as of V.0.90.01)
(package private) int	mid Master gene ID index # (MID).
(package private) int[]	midList list of all mids for duplicats of this Gene [0:nMid-1] that occurs more than 2X in the in GIPO
(package private) int	nGeneClustersCnt # of genes in cluster at cluster distance threshold.
(package private) int[]	nGenomicID (Optional) If generic IDs are used this will contain the INDEX of the cfg.sGenomicMenu[] entry.
(package private) int	nMid # of genes in midList[] for this gene
(package private) java.lang.String	OmimID NCBI OMIM ID if it exists
(package private) java.lang.String	plate plate where clone was from
(package private) java.lang.String	plate_col plate where clone was from
(package private) java.lang.String	plate_row plate where clone was from
(package private) int	properties properties of the gene defined by one or more C_xxxx bits
(package private) float	pValue optional computed p-value if doing statistical test
(package private) java.lang.String	RefSeqID NCBI RefSeq ID if it exists
(package private) java.lang.String	SwissProt Swiss-Prot ID if it exists
(package private) java.lang.String	UGclusterName opt.
(package private) java.lang.String	Unigene_ID NCBI Unigene cluster if it exists

Constructor Summary

(package private)	Gene(int gid, int mid) Gene() - constructor with gid, mid and no quantified data.
(package private)	Gene(MAExplorer maE) Gene() - constructor to set up global mae instance - MUST BE CALLED FIRST!!! Note: we only need the mae instance to setup the map instance.

Method Summary

(package private) void	assignMasterGeneName(int masterGeneNameMode) assignMasterGeneName() - assign MasterGeneName using masterGeneNameMode for current database configuration.
(package private) void	assignMasterID(int masterIDmode) assignMasterID() - assign Master_ID using masterIDmode using existing data.
(package private) int	clearGeneProperty(int propToTest) clearGeneProperty() - clear C_xxxx gene properties.
(package private) boolean	isGeneProperty(int propToTest) isGeneProperty() - test if C_xxxx gene property is set.
(package private) java.lang.String	lookupIDbyName(java.lang.String idName) lookupIDbyName() - lookup the genomic gene id value given the ID name.
(package private) void	setGeneData(float data) setGeneData() - set gene quantified data
(package private) void	setGeneData(float data, float data1, float data2) setGeneData() - set quantified gene data, data1 and data2
(package private) void	setGeneData(float data, float data1, float data2, float pValue) setGeneData() - set quantified gene data, data1 and data2
(package private) void	setGeneData1AndData2(float data1, float data2) setGeneData1AndData2() - set quantified gene data1 and data2
(package private) void	setGeneDist(float geneDist) setGeneDist() - set gene cluster distance (only used if clustering).
(package private) int	setGeneProperty(int propToTest) setGeneProperty() - set C_xxxx gene properties.
(package private) void	setplateData(java.lang.String plate, java.lang.String plate_row, java.lang.String plate_col) setplateData() - set gene plate data (plate, plate_row, plate_col)
(package private) static void	sortGeneList(Gene[] cList, int nClist, boolean sortAssendingFlag) sortGeneList() - bubble sort gene list by associated gene.data field
java.lang.String	toString() toString() - generate prettyprint gene data string

Methods inherited from class java.lang.Object

, clone, equals, finalize, getClass, hashCode, notify, notifyAll, registerNatives, wait, wait, wait

Field Detail

mae

private static MAExplorer mae

link to global MAExplorer instance

map

private static Maps map

link to global Maps instance

cfg

private static Config cfg

link to global Config instance

C_IS_KMEANS

static final int C_IS_KMEANS

Gene property: Is a K-means node gene

C_GOOD_MID

static final int C_GOOD_MID

Gene property: the gene is good, good gene name. NCI/CIT mAdb: "Good" or NULL

C_BAD_MID

static final int C_BAD_MID

Gene property: the gene is bad, good gene name

C_DUP_SPOT

static final int C_DUP_SPOT

Gene property: is duplicate of another gene on array

C_BAD_SPOT

static final int C_BAD_SPOT

Gene property: non-analyzable gene (eg. marker, etc). NCI/CIT mAdb: "Not Found", "Empty"

C_IMAGE_ID

static final int C_IMAGE_ID

Gene property: Clone is an I.M.A.G.E. or numbered clone

C_ATCC_ID

static final int C_ATCC_ID

Gene property: Clone is an ATCC numbered clone

C_USE_GBID_FOR_CLONEID

static final int C_USE_GBID_FOR_CLONEID

Gene property: use GenBank ID for Clone ID

C_MARGINAL_SPOT

static final int C_MARGINAL_SPOT

Gene property: Marginal spot

C_BAD_SPOT_GEOMETRY

static final int C_BAD_SPOT_GEOMETRY

Gene property: bad spot geometry

C_BAD_LOCAL_SPOT_BKGRD

static final int C_BAD_LOCAL_SPOT_BKGRD

Gene property: bad local spot background

C_LOW_SPOT_REF_SIGNAL

static final int C_LOW_SPOT_REF_SIGNAL

Gene property: low spot reference signal

C_IS_EGL_GENE

static final int C_IS_EGL_GENE

Gene property: is an E.G. L. gene (not normally used)

C_IS_FILTERED

static final int C_IS_FILTERED

Gene property: is a gene that did pass data Filter

C_IS_NOT_FILTERED

static final int C_IS_NOT_FILTERED

Gene property: is a gene that did not pass data Filter

C_IS_CUR_GENE

static final int C_IS_CUR_GENE

Gene property: is Current Gene (not normally used)

C_BAD_DATA

static final int C_BAD_DATA

property: gene has bad data

mid

int mid

Master gene ID index # (MID). It isvalid for BOTH F1 & F2 spots. [NOTE: this used to be cid (MID)] in v0.89.41

gid

int gid

a Grid Identifier (GID) index index corresponding to MasterID. A value of -1 indicates the gid is invalid. Note: the gids are created when the GIPO database is read, but may be wrong if the mae.mp.gid2mid[] is not setup yet!

nMid

int nMid

# of genes in midList[] for this gene

midList

int[] midList

list of all mids for duplicats of this Gene [0:nMid-1] that occurs more than 2X in the in GIPO

Master_ID

java.lang.String Master_ID

Master Gene Identifier (i.e. MID) will be one of IDs below

MasterGeneName

java.lang.String MasterGeneName

Master Gene Name will be one of the gene names below ([NOTE] as of V.0.90.01)

Gene_Name

java.lang.String Gene_Name

opt. gene name if it exists

UGclusterName

java.lang.String UGclusterName

opt. UniGene cluster name if it exists

Generic_ID

java.lang.String Generic_ID

Generic Identifier - "if all else fails" the use may use some arbitrary unique ID

Clone_ID

java.lang.String Clone_ID

I.M.A.G.E clone id #, or "your plate", etc. if it exists

GenBankAcc

java.lang.String GenBankAcc

NCBI GenBankAcc id if it exists

GenBankAcc3

java.lang.String GenBankAcc3

NCBI GenBankAcc 3' id if it exists

GenBankAcc5

java.lang.String GenBankAcc5

NCBI GenBankAcc 5' id if it exists

Unigene_ID

java.lang.String Unigene_ID

NCBI Unigene cluster if it exists

OmimID

java.lang.String OmimID

NCBI OMIM ID if it exists

dbEST3

java.lang.String dbEST3

NCBI dbEST database 3' id

dbEST5

java.lang.String dbEST5

NCBI dbEST database 5' id

SwissProt

java.lang.String SwissProt

Swiss-Prot ID if it exists

RefSeqID

java.lang.String RefSeqID

NCBI RefSeq ID if it exists

LocusID

java.lang.String LocusID

NCBI LocusLink LocusID if it exists

GenomicID

java.lang.String[] GenomicID

(Optional) External Genomic IDs values if specified via the MaeConfig.txt or .mae startup files. These values IDs are only for genomic database NOT found in the default Gene ID names. The ID value data for each Gene object is obtained from the GIPO file data for this gene. The corresponding names of the Genomic databases are for the i'throws enty is cfg.sGenomicMenu[nGenomicID[i]].

nGenomicID

int[] nGenomicID

(Optional) If generic IDs are used this will contain the INDEX of the cfg.sGenomicMenu[] entry. THAT is the name of the external Genomic database.

comments

java.lang.String comments

--- options may or may not be used ---

Gene_Class

java.lang.String Gene_Class

opt. current Gene_Class (may be in several...) [TODO] may want to replace with byte[] or short[] list of GeneClass indices...

plate

java.lang.String plate

plate where clone was from

plate_row

java.lang.String plate_row

plate where clone was from

plate_col

java.lang.String plate_col

plate where clone was from

data

float data

dynamic generic data such as ratio, etc associated with this gene

data1

float data1

dynamic generic data for Field 1 associated with this gene

data2

float data2

dynamic generic data for Field 2 associated with this gene

pValue

float pValue

optional computed p-value if doing statistical test

cv

float cv

optional computed coefficient of variation (CV) if doing statistical test

geneDist

float geneDist

Opt. distance from this gene to current Gene

clusterNodeNbr

int clusterNodeNbr

if >0, then this the cluster node in K-means clustering

nGeneClustersCnt

int nGeneClustersCnt

# of genes in cluster at cluster distance threshold. This is 0 for genes which are NOT cluster nodes.

properties

int properties

properties of the gene defined by one or more C_xxxx bits

Constructor Detail

Gene

Gene(MAExplorer maE)

Gene() - constructor to set up global mae instance - MUST BE CALLED FIRST!!! Note: we only need the mae instance to setup the map instance.

Parameters:

maE - is instance of MAExplorer

Gene

Gene(int gid,
     int mid)

Gene() - constructor with gid, mid and no quantified data. Data will be stuffed later with "gene.XXXX= XXXX" etc.

Method Detail

assignMasterID

void assignMasterID(int masterIDmode)

assignMasterID() - assign Master_ID using masterIDmode using existing data.

Parameters:

masterIDmode - is current mode of the genomic ID assigned as master ID

lookupIDbyName

java.lang.String lookupIDbyName(java.lang.String idName)

lookupIDbyName() - lookup the genomic gene id value given the ID name. ID names include: "Clone ID", "GenBank", "GenBank 5'", "GenBank 3'", "UniGene ID", "dbEST 5'", "dbEST 3'", "SwissProt", "LocusID". In addition the GenomicID[] list can be used.

Parameters:

idName - is the gene name used to lookup the ID value

Returns:

the ID value or null if bad ID name.

See Also:

SimpleTable.lookupFieldIdx(java.lang.String)

assignMasterGeneName

void assignMasterGeneName(int masterGeneNameMode)

assignMasterGeneName() - assign MasterGeneName using masterGeneNameMode for current database configuration.

Parameters:

masterGeneNameMode - for this gene

setGeneData

void setGeneData(float data)

setGeneData() - set gene quantified data

Parameters:

data - is computed data for this gene

setGeneData

void setGeneData(float data,
                 float data1,
                 float data2)

setGeneData() - set quantified gene data, data1 and data2

Parameters:

data - is computed data for this gene

data1 - is data for channel 1 for this gene

data2 - is data for channel 2 for this gene

setGeneData

void setGeneData(float data,
                 float data1,
                 float data2,
                 float pValue)

setGeneData() - set quantified gene data, data1 and data2

Parameters:

data - is computed data for this gene

data1 - is data for channel 1 for this gene

data2 - is data for channel 2 for this gene

pValue - data for this gene

setGeneData1AndData2

void setGeneData1AndData2(float data1,
                          float data2)

setGeneData1AndData2() - set quantified gene data1 and data2

Parameters:

data1 - is data for channel 1 for this gene

data2 - is data for channel 2 for this gene

setGeneDist

void setGeneDist(float geneDist)

setGeneDist() - set gene cluster distance (only used if clustering).

Parameters:

geneDist - cluster distance for this gene to center of cluster

setplateData

void setplateData(java.lang.String plate,
                  java.lang.String plate_row,
                  java.lang.String plate_col)

setplateData() - set gene plate data (plate, plate_row, plate_col)

Parameters:

plate - source plate for this gene's cDNA

plate_row - source plate row for this gene's cDNA

plate_col - source plate column for this gene's cDNA

setGeneProperty

int setGeneProperty(int propToTest)

setGeneProperty() - set C_xxxx gene properties.

Parameters:

propToTest - bit or bits to test set for this gene

Returns:

the new properties bits.

clearGeneProperty

int clearGeneProperty(int propToTest)

clearGeneProperty() - clear C_xxxx gene properties.

Parameters:

propToTest - bit or bits to test set for this gene

Returns:

the new properties bits.

isGeneProperty

boolean isGeneProperty(int propToTest)

isGeneProperty() - test if C_xxxx gene property is set.

Parameters:

propToTest - bit or bits to test if any are present for this gene

sortGeneList

static void sortGeneList(Gene[] cList,
                         int nClist,
                         boolean sortAssendingFlag)

sortGeneList() - bubble sort gene list by associated gene.data field

Parameters:

cList - list of genes to be sorted [0:nClist-1]

nClist - size of gene list

sortAssendingFlag - flag to specifry assending or descending sort

toString

public java.lang.String toString()

toString() - generate prettyprint gene data string

Overrides:

toString in class java.lang.Object

Returns:

prettyprint string of gene data.