Class ReadTissues

java.lang.Object
  |
  +--ReadTissues

public class ReadTissues

extends java.lang.Object

Class ReadTissues.java - read tissues file mapping tissues 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 the following (the values may change):
   uncharacterized tissue	1
   heart	2
   lung	3
   vascular	4
   liver	5
   eye	6
   testis	7
   brain	8
   . . .
   adrenal medulla	50
   nervous	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[]	defTissues Default list of tissues
int	maxTissues max # of families
int	nTissues # of families
private ProtPlot	prp instance of ProtPlot
long[]	tissueBits list of tissue tissue BITS [0:nFamilies-1] return all tokens/row the tissueBit[i] = 2**tissueNbr[i].
java.lang.String[]	tissueNames List of tissue names [0:nTissues-1] return all tokens/row
java.lang.String	tissueNamesFile Name of the tissue data tab-delimited file.
int[]	tissueNbrs list of tissue tissue Numbers [0:nFamilies-1] return all tokens/row
private char[]	tokBuf token buffer
private UtilPRP	util instance of UtilPRP

Constructor Summary

(package private)

ReadTissues(ProtPlot prp, java.lang.String tissueNamesFile, int maxTissues, java.lang.String msg) ReadTissues() - constructor

Method Summary

long	cvtTissueNamesToBits(java.lang.String useTissueNames) cvtTissueNamesToBits() - convert tissue names to tissueBits Eg.
java.lang.String	cvtTissuesStr(long tBits) cvtTissuesStr() - lookup tissues from the tissueBits
private boolean	parseRows(java.lang.String sData) parseRows() - parse and save a rows of data in rd.protList[] data structures.
boolean	readTissuesFile(java.lang.String msg) readTissuesFile() - read list of tissues 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

defTissues

private java.lang.String[] defTissues

Default list of tissues

tissueNamesFile

public java.lang.String tissueNamesFile

Name of the tissue data tab-delimited file. This consists of 2 columns "TissueName" "TissueNbr" which is followed by the data.

maxTissues

public int maxTissues

max # of families

nTissues

public int nTissues

# of families

tissueNames

public java.lang.String[] tissueNames

List of tissue names [0:nTissues-1] return all tokens/row

tissueNbrs

public int[] tissueNbrs

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

tissueBits

public long[] tissueBits

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

tokBuf

private char[] tokBuf

token buffer

Constructor Detail

ReadTissues

ReadTissues(ProtPlot prp,
            java.lang.String tissueNamesFile,
            int maxTissues,
            java.lang.String msg)

ReadTissues() - constructor

Parameters:

prp - is instance of ProtPlot

tissueNamesFile - name

maxTissues - in file

msg - to use while reading

Method Detail

readTissuesFile

public boolean readTissuesFile(java.lang.String msg)

readTissuesFile() - read list of tissues 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.

cvtTissuesStr

public java.lang.String cvtTissuesStr(long tBits)

cvtTissuesStr() - lookup tissues from the tissueBits

Parameters:

tBits - is the tissue bits to lookup as string equivalent

Returns:

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

cvtTissueNamesToBits

public long cvtTissueNamesToBits(java.lang.String useTissueNames)

cvtTissueNamesToBits() - convert tissue names to tissueBits Eg. "Tissues: c1,c2,...,cn" list Allow alternate form which is a list of tissueNbrs e.g. "3,25,13,10" in which case would just build the bit pattern from these

Parameters:

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

Returns:

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