databionics.io
Class BMFile

java.lang.Object
  databionics.io.BaseFile
      databionics.io.ListFile
          databionics.io.MapFile
              databionics.io.BMFile

public class BMFile
extends MapFile

File that stores a list of best matches.

Field Summary

protected int	cols Number of columns from header.
protected static org.apache.log4j.Logger	log Log4j logging.
protected int	rows Number of rows from header.

Fields inherited from class databionics.io.MapFile

map

Fields inherited from class databionics.io.ListFile

data

Fields inherited from class databionics.io.BaseFile

allowEmptyLines, comment, commentPrefix, delimiter, delimiters, file, header, headerPrefix, loc, nf

Constructor Summary

BMFile()
Standard constructor

BMFile(java.lang.String filename)
Constructor with a filename

Method Summary

protected void	buildHeader() Generate header.
protected void	checkHeader() Check consistency of header information.
protected void	fillBMMatrix()
int	getBMIndexByCoordinates(int x, int y)
Bestmatch	getByIndex(int index) Get a best match by its index.
cern.colt.list.IntArrayList	getColData()
int	getCols() Get the value of cols.
static FileType	getFileType() Get the type of file.
cern.colt.list.IntArrayList	getIndices()
cern.colt.list.IntArrayList	getRowData()
int	getRows() Get the number of rows in the map
boolean	keysMatch(cern.colt.list.IntArrayList keys)
protected void	parseHeader() Parse the header.
protected void	parseLine(int row, java.lang.String line) Parse a line.
void	setCols(int v) Set the value of cols.
void	setRows(int v) Set the number of rows in the map

Methods inherited from class databionics.io.MapFile

add, getMap, remove, remove, setData, setMap

Methods inherited from class databionics.io.ListFile

buildLine, getData, getSize

Methods inherited from class databionics.io.BaseFile

checkHeaderAgainstSize, getComment, getFile, getFilename, getHeader, getLocale, getNumberFormat, init, isHeader, isNaN, isNumber, load, load, parseError, save, save, setComment, setFilename, setLocale, writeStringList, writeStringList

Methods inherited from class java.lang.Object

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

Field Detail

log

protected static org.apache.log4j.Logger log

Log4j logging.

rows

protected int rows

Number of rows from header.

cols

protected int cols

Number of columns from header.

Constructor Detail

BMFile

public BMFile()

Standard constructor

BMFile

public BMFile(java.lang.String filename)

Constructor with a filename

Parameters:

filename - Name of the file

Method Detail

parseHeader

protected void parseHeader()

Parse the header.

Overrides:

parseHeader in class BaseFile

parseLine

protected void parseLine(int row,
                         java.lang.String line)

Parse a line.

Overrides:

parseLine in class BaseFile

Parameters:

row - Number of current line.

line - Current line.

checkHeader

protected void checkHeader()

Check consistency of header information.

Overrides:

checkHeader in class BaseFile

buildHeader

protected void buildHeader()

Generate header.

Overrides:

buildHeader in class BaseFile

getByIndex

public Bestmatch getByIndex(int index)

Get a best match by its index.

Parameters:

index - Index field of item

getRows

public int getRows()

Get the number of rows in the map

Returns:

value of rows.

setRows

public void setRows(int v)

Set the number of rows in the map

Parameters:

v - Value to assign to rows.

getCols

public int getCols()

Get the value of cols.

Returns:

value of cols.

setCols

public void setCols(int v)

Set the value of cols.

Parameters:

v - Value to assign to cols.

getRowData

public cern.colt.list.IntArrayList getRowData()

getColData

public cern.colt.list.IntArrayList getColData()

getFileType

public static FileType getFileType()

Get the type of file.

getIndices

public cern.colt.list.IntArrayList getIndices()

keysMatch

public boolean keysMatch(cern.colt.list.IntArrayList keys)

getBMIndexByCoordinates

public int getBMIndexByCoordinates(int x,
                                   int y)

fillBMMatrix

protected void fillBMMatrix()