Class ReadPRP

java.lang.Object
  |
  +--ReadPRP

public class ReadPRP

extends java.lang.Object

Class ReadPRP.java - read a .prp file and set up data structures. 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

java.lang.String	dataFile full name of data file to use
java.lang.String[]	field fields [0:nFields]
int	idx_estExpr index for field name max EST expression
int	idx_FamilyName index for field name Family Name
int	idx_GenBankID index for field name GenBank ID
int	idx_MW index for field name MW
int	idx_pI index for field name pI
int	idx_SwissProtAcc index for field name SwissProt Acc
int	idx_SwissProtId index for field name SwissProt ID
int	idx_TissueName index for field name Tissue Name
static int	MAX_COLS max # cols in data file
int	maxCols max size of token array
float	maxData_MW range of MW data
float	maxData_pI range of pI data
int	maxProteins max # of proteins
float	minData_MW range of MW data
float	minData_pI range of pI data
int	nCols actual # of tokens found
int	nFields # of fields in actual data file
int	nProteins actual # of proteins found
Protein[]	protList [0:nProteins-1] list of all proteins
private ProtPlot	prp instance of ProtPlot
java.lang.String	prpDir Directory of the .prp data file to use
java.lang.String	prpFile File of the .prp data file to use
java.lang.String	prpName Name of the .prp data file without .prp and cvt '_' to " "
int	sampleNbr The sampleNbr for the sample being read
boolean	strictDataFormatFlag Flag determines whether strict parsing is used.
private java.lang.String[]	tokArray token parse array [0:nCols-1] return all tokens/row
private char[]	tokBuf token buffer for parsing a line
private UtilPRP	util instance of UtilPRP

Constructor Summary

(package private)

ReadPRP(ProtPlot prp, java.lang.String prpDir, java.lang.String prpFile, int sampleNbr, int maxProteins, java.lang.String msg, boolean strictDataFormatFlag) ReadPRP() - constructor to read and build a sample data structure.

Method Summary

int	getArrayOfTabDelimTokens(char[] lineBuf, int bufSize, java.lang.String[] tokArray) getArrayOfTabDelimTokens() - get array of tab-delim tokens The number of expected columns is specified and if there is no more data, it will leave those cells null.
int	lookupPIDfromMPID(int mPid) lookupPIDfromMPID() - lookup the pid given the mPid
private boolean	parseRows(java.lang.String sData, int nCols) parseRows() - parse & save a rows of data in rd.protList[] data structures.
boolean	readDataFile(java.lang.String msg) readDataFile() - read (pI,mw,SP-ID) into data structure

Methods inherited from class java.lang.Object

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

Field Detail

MAX_COLS

public static final int MAX_COLS

max # cols in data file

prp

private ProtPlot prp

instance of ProtPlot

util

private UtilPRP util

instance of UtilPRP

prpDir

public java.lang.String prpDir

Directory of the .prp data file to use

prpFile

public java.lang.String prpFile

File of the .prp data file to use

prpName

public java.lang.String prpName

Name of the .prp data file without .prp and cvt '_' to " "

dataFile

public java.lang.String dataFile

full name of data file to use

strictDataFormatFlag

public boolean strictDataFormatFlag

Flag determines whether strict parsing is used. If the strictDataFormatFlag is true it requires the following fields: (pI, Mw, SP-ID, SP-ACC, expression, tissue). If it is false, it only requires (SP-ID, expression) since it will get the rest of the missing data from Master Protein Index entry.

field

public java.lang.String[] field

fields [0:nFields]

maxCols

public int maxCols

max size of token array

nCols

public int nCols

actual # of tokens found

sampleNbr

public int sampleNbr

The sampleNbr for the sample being read

maxProteins

public int maxProteins

max # of proteins

nProteins

public int nProteins

actual # of proteins found

protList

public Protein[] protList

[0:nProteins-1] list of all proteins

minData_pI

public float minData_pI

range of pI data

maxData_pI

public float maxData_pI

range of pI data

minData_MW

public float minData_MW

range of MW data

maxData_MW

public float maxData_MW

range of MW data

nFields

public int nFields

# of fields in actual data file

idx_pI

public int idx_pI

index for field name pI

idx_MW

public int idx_MW

index for field name MW

idx_SwissProtAcc

public int idx_SwissProtAcc

index for field name SwissProt Acc

idx_SwissProtId

public int idx_SwissProtId

index for field name SwissProt ID

idx_GenBankID

public int idx_GenBankID

index for field name GenBank ID

idx_FamilyName

public int idx_FamilyName

index for field name Family Name

idx_TissueName

public int idx_TissueName

index for field name Tissue Name

idx_estExpr

public int idx_estExpr

index for field name max EST expression

tokArray

private java.lang.String[] tokArray

token parse array [0:nCols-1] return all tokens/row

tokBuf

private char[] tokBuf

token buffer for parsing a line

Constructor Detail

ReadPRP

ReadPRP(ProtPlot prp,
        java.lang.String prpDir,
        java.lang.String prpFile,
        int sampleNbr,
        int maxProteins,
        java.lang.String msg,
        boolean strictDataFormatFlag)

ReadPRP() - constructor to read and build a sample data structure. It will merge the data into the Master Protein Index. If the strictDataFormatFlag is true it requires the following fields: (pI, Mw, SP-ID, SP-ACC, expression, tissue). If it is false, it only requires (SP-ID, expression) since it will get the rest of the missing data from Master Protein Index entry.

Parameters:

prp - instance of ProtPlot

prpDir - is the directory for the .prp file to read

prpFile - for the .prp file to read

sampleNbr - for the current sample

maxProteins - to read

msg - to display while reading

strictDataFormatFlag - to perform strict parsing (see above)

Method Detail

readDataFile

public boolean readDataFile(java.lang.String msg)

readDataFile() - read (pI,mw,SP-ID) into data structure

Parameters:

msg - to display while reading

Returns:

true if succeed

getArrayOfTabDelimTokens

public int getArrayOfTabDelimTokens(char[] lineBuf,
                                    int bufSize,
                                    java.lang.String[] tokArray)

getArrayOfTabDelimTokens() - get array of tab-delim tokens The number of expected columns is specified and if there is no more data, it will leave those cells null. If the token is "", it returns "" not null. Store the data in tokArray[].

Parameters:

lineBuf - is the source data

bufSize - is the # chars

tokArray - where data is teturned

Returns:

number of tokens/row else 0 if there is no more data.

parseRows

private boolean parseRows(java.lang.String sData,
                          int nCols)

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

Parameters:

sData - to parse

nCols - to look for in data

Returns:

true if ok.

lookupPIDfromMPID

public int lookupPIDfromMPID(int mPid)

lookupPIDfromMPID() - lookup the pid given the mPid

Parameters:

mPid - to lookup

Returns:

-1 if failed, else the corresponding pid if it exists.