Class ReadFamilies

java.lang.Object
  |
  +--ReadFamilies

public class ReadFamilies

extends java.lang.Object

Class ReadFamilies.java - read protein families file mapping protein families to bit #s. The bits go from right to left. So that if a bit # is say 3, the corresponding bit is (1<<3).

 The tab-delimited data looks like:
  UNKNOWN   1
  Apoptosis 2
  Bcl-2 family3
  Cdk inhibition 4
       . . .
  Transport 50
  Tumor suppressor 51

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

private java.lang.String[]	defFamilies default list of protein families
long[]	familyBits list of tissue family BITS [0:nFamilies-1] return all tokens/row the familyBit[i] = 2**familyNbr[i].
java.lang.String[]	familyNames list of tissue family names [0:nFamilies-1] return all tokens/row
java.lang.String	familyNamesFile Name of the family data tab-delimited file.
int[]	familyNbrs list of tissue family Numbers [0:nFamilies-1] return all tokens/row
int	maxFamilies max # of families
int	nFamilies # of families
private ProtPlot	prp instance of ProtPlot
private char[]	tokBuf token buffer
private UtilPRP	util instance of UtilPRP

Constructor Summary

(package private)

ReadFamilies(ProtPlot prp, java.lang.String familyNamesFile, int maxFamilies, java.lang.String msg) ReadFamilies() - constructor

Method Summary

java.lang.String	cvtFamiliesStr(long fBits) cvtFamiliesStr() - lookup family strings for familyBits
long	cvtFamilyNamesToBits(java.lang.String useFamilyNames) cvtFamilyNamesToBits() - convert a String list of family names to familyBits.
private boolean	parseRows(java.lang.String sData) parseRows() - parse and save a rows of data in rd.protList[] data structures.
boolean	readFamiliesFile(java.lang.String msg) readFamiliesFile() - read list of Families into data structure

Methods inherited from class java.lang.Object

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

Field Detail

prp

private ProtPlot prp

instance of ProtPlot

util

private UtilPRP util

instance of UtilPRP

defFamilies

private java.lang.String[] defFamilies

default list of protein families

familyNamesFile

public java.lang.String familyNamesFile

Name of the family data tab-delimited file. This consists of 2 columns "FamilyName" "FamilyNbr" which is followed by the data.

maxFamilies

public int maxFamilies

max # of families

nFamilies

public int nFamilies

# of families

familyNames

public java.lang.String[] familyNames

list of tissue family names [0:nFamilies-1] return all tokens/row

familyNbrs

public int[] familyNbrs

list of tissue family Numbers [0:nFamilies-1] return all tokens/row

familyBits

public long[] familyBits

list of tissue family BITS [0:nFamilies-1] return all tokens/row the familyBit[i] = 2**familyNbr[i].

tokBuf

private char[] tokBuf

token buffer

Constructor Detail

ReadFamilies

ReadFamilies(ProtPlot prp,
             java.lang.String familyNamesFile,
             int maxFamilies,
             java.lang.String msg)

ReadFamilies() - constructor

Parameters:

prp - is instance of ProtPlot

familyNamesFile - name

maxFamilies - in file

msg - to use while reading

Method Detail

readFamiliesFile

public boolean readFamiliesFile(java.lang.String msg)

readFamiliesFile() - read list of Families into data structure

Parameters:

msg - to display while reading file.

parseRows

private boolean parseRows(java.lang.String sData)

parseRows() - parse and save a rows of data in rd.protList[] data structures.

Parameters:

sData - to parse

Returns:

true if ok.

cvtFamiliesStr

public java.lang.String cvtFamiliesStr(long fBits)

cvtFamiliesStr() - lookup family strings for familyBits

Parameters:

fBits - to lookup as string equivalent

Returns:

"Families: c1, c2, ..., cn" list

cvtFamilyNamesToBits

public long cvtFamilyNamesToBits(java.lang.String useFamilyNames)

cvtFamilyNamesToBits() - convert a String list of family names to familyBits. Allow alternate form which is a list of familyNbrs e.g. "3,25,13,10" in which case would just build the bit pattern from these

Parameters:

useFamilyNames - to convert to bits, separated by "," (CHK)

Returns:

familyBits. If no names, set to "ALL" equals 1.