Class FieldMap

java.lang.Object
  |
  +--FieldMap

public class FieldMap

extends java.lang.Object

FieldMap maps MAE (table,field) entries to User (T,F) entries which allows user's to specify variables in terms of what they require and have it mapped to what MAExplorer requires.
This will parse a 1D array of (mT,mF,uT,uF) entries into discrete arrays that are used in the actual field name mappings. Entries with a '*' prefix mean that that entry may be repeated any number of times.

 
 Note:
 
  1. the table definitions are specified in row [0].
 
  2. entries [1:n] are tab-delimited (NOT comma-delimited). However,
     when the FieldMap associated with an ArrayLayout is saved in the .alo
     file, it is converted to a comma-delimited string since tabs are
     reserved for the .alo (N,V) data.
 

 For example (part of the Affymetrix spec):
  desiredFields[]= {"Table name\tMAE field\tUser field",  // Table def at [0]
		      "GipoTable\tLocation\tprobe set",     // entries at [1:n]
  	              "*QuantTable\tRawIntensity\tAvg Diff", 
		      "*QuantTable\tQualCheck\tAbs Call",
                    "GipoTable\tGenBankAcc\tIdentifier", 
		      "GipoTable\tClone_ID\tProbe Set",
		      "GipoTable\tGeneName\tDescription"
		      };	

This work was produced by Peter Lemkin of the National Cancer Institute, an agency of the United States Government. 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 19:22:30 $ $Revision: 1.5 $

Author:

P. Lemkin (NCI), B. Stephens(SAIC), G. Thornwall (SAIC), NCI-Frederick, Frederick, MD

See Also:

MAExplorer Home

Field Summary

private static Cvt2Mae	cvt Global link to Cvt2Mae instance
java.lang.String[]	fieldNamesGQ [0:nMapFields-1] field names read from the data file.
java.lang.String[]	fieldsOfUserFile [0:nFieldsOfUserFile-1] user fields of current file
int	fmNbr unique FieldMap instance number
int[]	idxFUmap [0:nMapFields-1] index map from userFieldMap[u] to fieldNames[f].
int[]	idxUFmap [0:nMapFields-1] index map from fieldNames[f] to userFieldMap[u].
java.lang.String[]	maeFieldMap [0:nMap-1] map of internal MAE Field name
java.lang.String[]	maeTableMap [0:nMap-1] map of internal MAE Table name
java.lang.String	mapName unique map name
static int	masterNbr master global counter for field map instances
static int	MAX_MAP_SIZE initial max map size
int	maxSize maximum size of the map
(package private) java.lang.String	newline new line character
int	nFieldsOfUserFile # of data fields in user file
int	nFieldsUsed # of data file fields found in the map and marked true in useTokFlag[].
int	nMap # of map entries
int	nMapFieldsGQ # ofentries in fieldNamesGQ
int[]	pickedGipoFields GIPO fields currently selected by user
int[]	pickedQuantFields Quant fields currently selected by user
int[]	pickedSampleFields Sample fields currently selected by user
int	remapMode sul.REMAP_GIPO, .REMAP_QUANT, .REMAP_SAMPLE 0 if no remap in progress.
boolean[]	repeatMap [0:nMap-1] map entry is repeated for each sample.
int	rowWithFields row in file where fields are found
int	tCols # of fields in table field list
java.lang.String[]	tFields [0:tCols-1] field names for table
java.lang.String[]	userFieldMap [0:nMap-1] map external user's Field name
java.lang.String	userFile full file path for file that contains field names
java.lang.String[]	userGipoFields GIPO fields selected by user
java.lang.String[]	userQuantFields Quant fields selected by user
java.lang.String[]	userSampleFields Sample fields selected by user
java.lang.String[]	userTableMap [0:nMap-1] map external user's Table name
boolean[]	useTokFlag [0:nMapFields-1] flag fields used to tokenize when parsing input table data corresponding to fieldNames[0:nMapFields-1].

Constructor Summary

FieldMap(java.lang.String mapName)
FieldMap() - constructor

Method Summary

void	addEntry(java.lang.String mT, java.lang.String mF, java.lang.String uT, java.lang.String uF) addEntry() - add an entry to the list
void	addEntry(java.lang.String mT, java.lang.String mF, java.lang.String uT, java.lang.String uF, boolean repeatFlag) addEntry() - add or replace an entry to the FieldMap list.
void	clearMap() clearMap() - clear the map and reallocate the tables
boolean[]	genUseTokFlags(java.lang.String[] fieldNamesGQ) genUseTokFlags() - generate useTokFlagGQ[0:nMapFields-1] from fieldNames[0:nMapFields-1] and FieldMap userFieldMap[0:nMap-1] data.
int	getFieldsFromUserFile(Cvt2Mae cvt, java.lang.String userFile, int rowWithFields) getFieldsFromUserFile() - get fields from user file Return the # of rows found and save the data in fieldsOfUserFile[0:nFieldsOfUserFile-1].
boolean	isDuplicateEntries(java.lang.String mT) isDuplicateEntries() - test if duplcate entries for mT entries in mT subtable.
boolean	isEntry(java.lang.String mT, java.lang.String mF) isEntry() - has an entry for (mT,mF) in the list Return true if an entry exists.
int	lookupMaeFieldToFieldNameIndex(java.lang.String mFsearch) lookupMaeFieldToFieldNameIndex() - lookup FieldName index if exists in the FieldNames[0:nMapFields-1]
int	lookupMaeIndex(java.lang.String mT, java.lang.String mF) lookupMaeIndex() - find map index given (mT, mF)
java.lang.String	lookupUserFieldFromMaeTF(java.lang.String mT, java.lang.String mF) lookupUserFieldFromMaeTF() - find map index given (mT, mF)
int	lookupUserIndex(java.lang.String uF) lookupUserIndex() - find map index given (uF)
int	lookupUserIndex(java.lang.String uT, java.lang.String uF) lookupUserIndex() - find map index given (uT, uF)
java.lang.String	lookupUserTFmapPair(java.lang.String mT, java.lang.String mF) lookupUserTFmapPair() - findUser "uT,uF" given (mT, mF) Return null if not found.
java.lang.String	lookupUTFmapPair(java.lang.String mT, java.lang.String mF) lookupUTFmapPair() - findUser "uT,uF" given (mT, mF)
boolean	rmvEntry(java.lang.String mT, java.lang.String mF) rmvEntry() - remove an entry to the list by marking it inactive.
void	setFieldList(int tCols, java.lang.String[] tFields) setFieldList() - save the tFields[0:tCols-1]
java.lang.String	toString() toString() - make prettyprint string for object.
void	useField(java.lang.String fName) useField() - set flag to true in useFieldFlag[] for fName field.

Methods inherited from class java.lang.Object

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

Field Detail

cvt

private static Cvt2Mae cvt

Global link to Cvt2Mae instance

masterNbr

public static int masterNbr

master global counter for field map instances

MAX_MAP_SIZE

public static int MAX_MAP_SIZE

initial max map size

userFile

public java.lang.String userFile

full file path for file that contains field names

fieldsOfUserFile

public java.lang.String[] fieldsOfUserFile

[0:nFieldsOfUserFile-1] user fields of current file

rowWithFields

public int rowWithFields

row in file where fields are found

nFieldsOfUserFile

public int nFieldsOfUserFile

# of data fields in user file

remapMode

public int remapMode

sul.REMAP_GIPO, .REMAP_QUANT, .REMAP_SAMPLE 0 if no remap in progress. Clear to 0 when finished mapping one of the 3 modes.

userGipoFields

public java.lang.String[] userGipoFields

GIPO fields selected by user

userQuantFields

public java.lang.String[] userQuantFields

Quant fields selected by user

userSampleFields

public java.lang.String[] userSampleFields

Sample fields selected by user

pickedGipoFields

public int[] pickedGipoFields

GIPO fields currently selected by user

pickedQuantFields

public int[] pickedQuantFields

Quant fields currently selected by user

pickedSampleFields

public int[] pickedSampleFields

Sample fields currently selected by user

fmNbr

public int fmNbr

unique FieldMap instance number

maxSize

public int maxSize

maximum size of the map

nMap

public int nMap

# of map entries

maeTableMap

public java.lang.String[] maeTableMap

[0:nMap-1] map of internal MAE Table name

maeFieldMap

public java.lang.String[] maeFieldMap

[0:nMap-1] map of internal MAE Field name

userTableMap

public java.lang.String[] userTableMap

[0:nMap-1] map external user's Table name

userFieldMap

public java.lang.String[] userFieldMap

[0:nMap-1] map external user's Field name

repeatMap

public boolean[] repeatMap

[0:nMap-1] map entry is repeated for each sample. NOTE: this is indicated in the "mT,mF,uT,uF" string by a '*' prefix so it becomes "*mT,mF,uT,uF". This means there may be 1 or more instances of this field and they will be in different columns. (eg. Affy data)

tCols

public int tCols

# of fields in table field list

mapName

public java.lang.String mapName

unique map name

tFields

public java.lang.String[] tFields

[0:tCols-1] field names for table

fieldNamesGQ

public java.lang.String[] fieldNamesGQ

[0:nMapFields-1] field names read from the data file. If a separate GIPO file is used, then this also includes the mcd.sepGIPOfields[] such that mcd.sepGIPOfieldsUsed[] fields are true.

nMapFieldsGQ

public int nMapFieldsGQ

# ofentries in fieldNamesGQ

nFieldsUsed

public int nFieldsUsed

# of data file fields found in the map and marked true in useTokFlag[]. and is less than nMapFields. This is a debugging count and is not used in any other methods.

idxUFmap

public int[] idxUFmap

[0:nMapFields-1] index map from fieldNames[f] to userFieldMap[u]. I.e. idxUFmap[f]= u, such that userFieldMap[u] data equals fieldNames[f]

idxFUmap

public int[] idxFUmap

[0:nMapFields-1] index map from userFieldMap[u] to fieldNames[f]. I.e. idxFUmap[u]= f, such that userFieldMap[u] data same as fieldNames[f]

useTokFlag

public boolean[] useTokFlag

[0:nMapFields-1] flag fields used to tokenize when parsing input table data corresponding to fieldNames[0:nMapFields-1]. This avoids having to parse tokens that are not going to be used - greatly improving the efficiency of the parser.

newline

java.lang.String newline

new line character

Constructor Detail

FieldMap

public FieldMap(java.lang.String mapName)

FieldMap() - constructor

Parameters:

mapName - name of the map

See Also:

clearMap()

Method Detail

clearMap

public void clearMap()

clearMap() - clear the map and reallocate the tables

setFieldList

public void setFieldList(int tCols,
                         java.lang.String[] tFields)

setFieldList() - save the tFields[0:tCols-1]

Parameters:

tFields - [0:tCols-1] names

tCols - number of fields in field list

useField

public void useField(java.lang.String fName)

useField() - set flag to true in useFieldFlag[] for fName field.

Parameters:

fName - field to use

isEntry

public boolean isEntry(java.lang.String mT,
                       java.lang.String mF)

isEntry() - has an entry for (mT,mF) in the list Return true if an entry exists.

Parameters:

mT - Table map

mF - Field map

Returns:

true if an entry exists

addEntry

public void addEntry(java.lang.String mT,
                     java.lang.String mF,
                     java.lang.String uT,
                     java.lang.String uF)

addEntry() - add an entry to the list

Parameters:

mT - Table map

mF - Field map

uT - user Table Map

uF - user Field Map

addEntry

public void addEntry(java.lang.String mT,
                     java.lang.String mF,
                     java.lang.String uT,
                     java.lang.String uF,
                     boolean repeatFlag)

addEntry() - add or replace an entry to the FieldMap list.

Parameters:

mT - Table map

mF - Field map

uT - user Table Map

uF - user Field Map

repeatFlag - map entry is repeated for each sample

rmvEntry

public boolean rmvEntry(java.lang.String mT,
                        java.lang.String mF)

rmvEntry() - remove an entry to the list by marking it inactive.

Parameters:

mT - Table map

mF - Field map

Returns:

true if successful

isDuplicateEntries

public boolean isDuplicateEntries(java.lang.String mT)

isDuplicateEntries() - test if duplcate entries for mT entries in mT subtable.

Parameters:

mT - Table map

Returns:

true if found

lookupMaeIndex

public int lookupMaeIndex(java.lang.String mT,
                          java.lang.String mF)

lookupMaeIndex() - find map index given (mT, mF)

Parameters:

mT - Table map

mF - Field map

Returns:

index if found, else -1 if not found

lookupUserFieldFromMaeTF

public java.lang.String lookupUserFieldFromMaeTF(java.lang.String mT,
                                                 java.lang.String mF)

lookupUserFieldFromMaeTF() - find map index given (mT, mF)

Parameters:

mT - Table map

mF - Field map

Returns:

field else null if not found.

lookupUserIndex

public int lookupUserIndex(java.lang.String uT,
                           java.lang.String uF)

lookupUserIndex() - find map index given (uT, uF)

Parameters:

mT - Table map

mF - Field map

Returns:

index else -1 if not found

lookupUserIndex

public int lookupUserIndex(java.lang.String uF)

lookupUserIndex() - find map index given (uF)

Parameters:

uF - Field map

Returns:

index else -1 if not found

lookupUserTFmapPair

public java.lang.String lookupUserTFmapPair(java.lang.String mT,
                                            java.lang.String mF)

lookupUserTFmapPair() - findUser "uT,uF" given (mT, mF) Return null if not found.

Parameters:

mT - Table map

mF - Field map

Returns:

TF pair else null if not found.

lookupUTFmapPair

public java.lang.String lookupUTFmapPair(java.lang.String mT,
                                         java.lang.String mF)

lookupUTFmapPair() - findUser "uT,uF" given (mT, mF)

Parameters:

mT - Table map

mF - Field map

Returns:

looked up pair else (mT+","+mF) if not found - effectively a no-op.

getFieldsFromUserFile

public int getFieldsFromUserFile(Cvt2Mae cvt,
                                 java.lang.String userFile,
                                 int rowWithFields)

getFieldsFromUserFile() - get fields from user file Return the # of rows found and save the data in fieldsOfUserFile[0:nFieldsOfUserFile-1].

Parameters:

cvt - is the global instance of Cvt2Mae

userFile - is the file

rowWithFields - location in file

Returns:

field if found, else 0 if can't do it.

See Also:

FileTable, FileTable.readTableFieldsFromFile(java.lang.String, int)

genUseTokFlags

public boolean[] genUseTokFlags(java.lang.String[] fieldNamesGQ)

genUseTokFlags() - generate useTokFlagGQ[0:nMapFields-1] from fieldNames[0:nMapFields-1] and FieldMap userFieldMap[0:nMap-1] data. The useTokFlag[] is used by ParseTokens getDelimTokens() to avoid having to parse tokens that are not going to be used - greatly improving the efficiency of the parser.

 This method finds pairs of (u,v)such that
     userFieldMap[u].equals(fieldNames[f])
 and sets
     useTokFlag[f]= true;
     idxUFmap[f]= u;
 

Parameters:

fieldNames - is the input table field names array.

Returns:

useTokFlag[] if found, else null if errors.

lookupMaeFieldToFieldNameIndex

public int lookupMaeFieldToFieldNameIndex(java.lang.String mFsearch)

lookupMaeFieldToFieldNameIndex() - lookup FieldName index if exists in the FieldNames[0:nMapFields-1]

Parameters:

mFsearch - string to search for

Returns:

FieldName index, else return -1.

toString

public java.lang.String toString()

toString() - make prettyprint string for object. NOTE: This is ONLY for visual consumption.

Overrides:

toString in class java.lang.Object

Returns:

pretty print string of this FieldMap instance.