databionics.io
Class ClsFile

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

Direct Known Subclasses:

DiagnosisFile

public class ClsFile
extends MapFile

File that stores classification of data points or best matches. Attention: The list and the map store the DataClass objects retrieved from the header of the *.cls file and not the classification pairs from the body of the file. The actual classification is stored in two IntArrayLists as integer pairs (index of data points, class number). For fast access to the class number by the index value use get(int index) backed by an additional OpenIntIntMap.

Field Summary

protected cern.colt.list.IntArrayList	boldClasses Class indices to be highlighted in some display
protected ColorTable	classColors Default color table
protected cern.colt.list.IntArrayList	classes Column with class numbers
protected cern.colt.map.OpenIntIntHashMap	key2pos Column with data point keys
protected cern.colt.list.IntArrayList	keys Column with data point keys
protected static org.apache.log4j.Logger	log Log4j logging.

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

ClsFile()
Standard constructor

ClsFile(BMFile bmFile)

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

Method Summary

void	add(int index, int cls) Add an index - class number pair
void	add2bold(int i) add an single class to boldclass
void	addClass(int cls) Add a data class if it's not in the list
void	addClass(int cls, java.lang.String name) Add a data class if it's not in the list
protected void	buildHeader() Generate header.
protected java.lang.String	buildLine(int row) Construct a line for saving.
boolean	changeIndex(int from, int to) Change Index of class.
protected void	checkHeader() Check consistency of header information.
void	clear() Clear class list, set all class numbers to 0
java.lang.Object	clone() Deprecated. deprecated because incomplete. TODO: make complete
cern.colt.list.IntArrayList	getBoldClasses() Get highlighted classes.
int	getByIndex(int index) Get class number of a classification by its index
DataClass	getClass(int pos) Get a data class by its position in the list
DataClass	getClassByIndex(int index) Get a data class by its index
cern.colt.list.IntArrayList	getClasses() Get classes.
static FileType	getFileType() Get the type of file.
int	getHighestClassIndex()
cern.colt.list.IntArrayList	getKeys() Get keys.
int	getQuick(int pos) Get class number of a classification by its position in the list
int	getSize() Get the number of lines in file.
boolean	hasClass(int classnumber)
protected void	parseHeader() Parse the header.
protected void	parseLine(int row, java.lang.String line) Parse a line.
void	remove(DataClass cls) Remove a class, set all corresponding class numbers to 0
void	remove(int cls) Remove a class, set all corresponding class numbers to 0.
void	removeFromBold(int i) Remove class from boldclasses
void	removeOne(int index, int classes)
void	set(int index, int cls) Deprecated. is a wrapper to add only, wich should manage id right, check if code is still working. if yes change set to add. stammi
void	setBoldClasses(int[] classes) Set highlighted classes.
void	setBoldClasses(cern.colt.list.IntArrayList classes) Set highlighted classes.
void	setClasses(int[] classes) Set classes.
void	setClasses(cern.colt.list.IntArrayList classes) Set classes.
void	setKeys() Add automatically generated keys.
void	setKeys(int[] keys) Set keys.
void	setKeys(cern.colt.list.IntArrayList keys) Set keys.
int	size(DataClass cls) Get size of a class
int	size(int cls) Get size of a class
void	sort() Sort classifications by key number.

Methods inherited from class databionics.io.MapFile

add, getMap, remove, setData, setMap

Methods inherited from class databionics.io.ListFile

getData

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

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

Field Detail

log

protected static org.apache.log4j.Logger log

Log4j logging.

keys

protected cern.colt.list.IntArrayList keys

Column with data point keys

classes

protected cern.colt.list.IntArrayList classes

Column with class numbers

key2pos

protected cern.colt.map.OpenIntIntHashMap key2pos

Column with data point keys

classColors

protected ColorTable classColors

Default color table

boldClasses

protected cern.colt.list.IntArrayList boldClasses

Class indices to be highlighted in some display

Constructor Detail

ClsFile

public ClsFile()

Standard constructor

ClsFile

public ClsFile(java.lang.String filename)

Constructor with a filename

Parameters:

filename - Name of the file

ClsFile

public ClsFile(BMFile bmFile)

Method Detail

sort

public void sort()

Sort classifications by key number.

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

buildLine

protected java.lang.String buildLine(int row)

Construct a line for saving.

Overrides:

buildLine in class ListFile

Parameters:

row - Number of current line.

Returns:

Line with that number.

getClass

public DataClass getClass(int pos)

Get a data class by its position in the list

Parameters:

position - of data class

addClass

public void addClass(int cls,
                     java.lang.String name)

Add a data class if it's not in the list

Parameters:

cls - class number

name - class name

addClass

public void addClass(int cls)

Add a data class if it's not in the list

Parameters:

cls - class number

getClassByIndex

public DataClass getClassByIndex(int index)

Get a data class by its index

Parameters:

index - class number

getSize

public int getSize()

Get the number of lines in file.

Overrides:

getSize in class ListFile

Returns:

Number of lines in file.

add

public void add(int index,
                int cls)

Add an index - class number pair

Parameters:

index - of data point or best match

cls - class number

set

public void set(int index,
                int cls)

Deprecated. is a wrapper to add only, wich should manage id right, check if code is still working. if yes change set to add. stammi

Set an index - class number pair

Parameters:

index - of data point or best match

cls - class number

remove

public void remove(int cls)

Remove a class, set all corresponding class numbers to 0. Ignores 0 as parameter.

Overrides:

remove in class MapFile

Parameters:

cls - class number

removeOne

public void removeOne(int index,
                      int classes)

Parameters:

index -

classes -

remove

public void remove(DataClass cls)

Remove a class, set all corresponding class numbers to 0

Parameters:

cls - class

changeIndex

public boolean changeIndex(int from,
                           int to)

Change Index of class.

Parameters:

from - old Index

to - new Index

clear

public void clear()

Clear class list, set all class numbers to 0

size

public int size(int cls)

Get size of a class

Parameters:

cls - class number

Returns:

number of data points in this class

size

public int size(DataClass cls)

Get size of a class

Parameters:

cls - class

Returns:

number of data points in this class

getQuick

public int getQuick(int pos)

Get class number of a classification by its position in the list

Parameters:

position - of classification

getByIndex

public int getByIndex(int index)

Get class number of a classification by its index

Parameters:

index - index of the data point

clone

public java.lang.Object clone()

Deprecated. deprecated because incomplete. TODO: make complete

This function makes a copy of the special Instance of this class

Overrides:

clone in class java.lang.Object

Returns:

an independent copy of this

getKeys

public cern.colt.list.IntArrayList getKeys()

Get keys.

setKeys

public void setKeys(cern.colt.list.IntArrayList keys)

Set keys.

setKeys

public void setKeys(int[] keys)

Set keys.

setKeys

public void setKeys()

Add automatically generated keys.

getClasses

public cern.colt.list.IntArrayList getClasses()

Get classes.

setClasses

public void setClasses(cern.colt.list.IntArrayList classes)

Set classes.

setClasses

public void setClasses(int[] classes)

Set classes.

getBoldClasses

public cern.colt.list.IntArrayList getBoldClasses()

Get highlighted classes.

setBoldClasses

public void setBoldClasses(cern.colt.list.IntArrayList classes)

Set highlighted classes.

setBoldClasses

public void setBoldClasses(int[] classes)

Set highlighted classes.

add2bold

public void add2bold(int i)

add an single class to boldclass

Parameters:

int - i class to add

removeFromBold

public void removeFromBold(int i)

Remove class from boldclasses

Parameters:

i - position of classnumber in (IntArrayList) boldClasses

getFileType

public static FileType getFileType()

Get the type of file.

getHighestClassIndex

public int getHighestClassIndex()

Returns:

The highest classIndex

hasClass

public boolean hasClass(int classnumber)