Class Protein

java.lang.Object
  |
  +--Protein

public class Protein

extends java.lang.Object

Class Protein represents an individual Protein spot entry. This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government and Djamel Medjahed (SAIC-Frederick). As a work of the United States Government there is no associated copyright. It is offered as open source software under the Mozilla Public License (version 1.1) subject to the limitations noted in the accompanying LEGAL file.

Version:

$Date: 2002/10/14 20:17:17 $ $Revision: $

Author:

P. Lemkin (NCI), Djamel Medjahed (SAIC), NCI-Frederick, Frederick, MD

See Also:

ProtPlot Home

This work was derived from MAExplorer under the Mozilla 1.1 Open Source Public License by Peter Lemkin of the National Cancer Institute, an agency of the United States Government subject to the limitations noted in the accompanying LEGAL file. See licence info on http://maexplorer.sourceforge.org/

Field Summary

int	clusterNbr Cluster number used with K-means and other divisive clustering methods NOTE: ONLY used with Master Protein List, it is -1 otherwise.
float	estExpr Normalized EST expression from CGAP/UniGene library expression value
long	familyBits bits corresponding to familyList[] names
java.lang.String	genBankID GenBank ID
float[]	mExprVect Master expression list vector [0:nPRPs-1] for this protein NOTE: ONLY used with Master Protein List, it is Null otherwise.
int	mPid Master PID cross reference to global list of proteins index kept in prp.mPidList[].
float	mw molecular mass
static int	nextPid id of this protein instance
int	nFamilies prc.rc.nFamilies
int	nSamples # of samples with this protein - ONLY used by master list
int	nTissues prc.rt.nTissues
float	pI isoelectric point
int	pid local index
private static ProtPlot	prp instance of ProtPlot
java.lang.String	swissProtAcc SwissProt Acc (accession number)
java.lang.String	swissProtId SwissProt ID (name of the protein)
long	tissueBits bits corresponding to tissueList[] names

Constructor Summary

(package private)	Protein() Protein() - constructor tomake an empy instance
(package private)	Protein(float pI, float mw, java.lang.String swissProtAcc, java.lang.String swissProtId, java.lang.String genBankID, long familyBits, long tissueBits, float estExpr) Protein() - constructor for new instance.
(package private)	Protein(ProtPlot prP) Protein() - constructor to set prp - MUST BE CALLED FIRST!!!

Method Summary

Protein	newProteinCopy() newProteinCopy() - make a new copy of this Protein instance.
static void	resetNextPID() resetNextPID() - clear the next PID counter.
java.lang.String	toString() toString() - prettyprint Protein data

Methods inherited from class java.lang.Object

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

Field Detail

prp

private static ProtPlot prp

instance of ProtPlot

nextPid

public static int nextPid

id of this protein instance

pid

public int pid

local index

mPid

public int mPid

Master PID cross reference to global list of proteins index kept in prp.mPidList[]. -1 means that it does not exist.

nSamples

public int nSamples

# of samples with this protein - ONLY used by master list

nFamilies

public int nFamilies

prc.rc.nFamilies

nTissues

public int nTissues

prc.rt.nTissues

estExpr

public float estExpr

Normalized EST expression from CGAP/UniGene library expression value

mExprVect

public float[] mExprVect

Master expression list vector [0:nPRPs-1] for this protein NOTE: ONLY used with Master Protein List, it is Null otherwise. NOTE: this is a link to prp.mExprVector[p.mPid].

clusterNbr

public int clusterNbr

Cluster number used with K-means and other divisive clustering methods NOTE: ONLY used with Master Protein List, it is -1 otherwise. [NOT USED YET]

pI

public float pI

isoelectric point

mw

public float mw

molecular mass

swissProtId

public java.lang.String swissProtId

SwissProt ID (name of the protein)

swissProtAcc

public java.lang.String swissProtAcc

SwissProt Acc (accession number)

genBankID

public java.lang.String genBankID

GenBank ID

familyBits

public long familyBits

bits corresponding to familyList[] names

tissueBits

public long tissueBits

bits corresponding to tissueList[] names

Constructor Detail

Protein

Protein(ProtPlot prP)

Protein() - constructor to set prp - MUST BE CALLED FIRST!!!

Protein

Protein(float pI,
        float mw,
        java.lang.String swissProtAcc,
        java.lang.String swissProtId,
        java.lang.String genBankID,
        long familyBits,
        long tissueBits,
        float estExpr)

Protein() - constructor for new instance.

Parameters:

pI -

mw -

swissProtAcc -

swissProtId -

genBankID -

familyBits -

tissueBits -

estExpr -

Protein

Protein()

Protein() - constructor tomake an empy instance

Method Detail

newProteinCopy

public Protein newProteinCopy()

newProteinCopy() - make a new copy of this Protein instance. This is ONLY used in creating the master list.

Returns:

the new instance

resetNextPID

public static void resetNextPID()

resetNextPID() - clear the next PID counter. This is called when read in a new list of proteins.

toString

public java.lang.String toString()

toString() - prettyprint Protein data

Overrides:

toString in class java.lang.Object