databionics.io
Class DiagnosisFile

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

public class DiagnosisFile
extends ClsFile

File that stores possibly multiple classification of data points or best matches.

Field Summary

protected java.util.List	allClasses Column with class numbers
protected static org.apache.log4j.Logger	log Log4j logging.

Fields inherited from class databionics.io.ClsFile

boldClasses, classColors, classes, key2pos, keys

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

DiagnosisFile()
Standard constructor

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

Method Summary

void	add(int index, int cls) Add an index - class number pair
void	add(int index, java.lang.String cls) Add an index - class number pair
protected java.lang.String	buildLine(int row) Construct a line for saving.
protected void	checkHeader() Check consistency of header information.
cern.colt.list.IntArrayList	getAll(int pos) Get all class numbers of a classification by its position in the list
cern.colt.list.IntArrayList	getAllByIndex(int index) Get all class numbers of a classification by its index
java.util.List	getAllClasses() Get list of IntArrayLists with all class numbers.
static FileType	getFileType() Get the type of file.
protected void	parseLine(int row, java.lang.String line) Parse a line.
void	setAllClasses(java.util.List allClasses) Set list of IntArrayLists with all class numbers.

Methods inherited from class databionics.io.ClsFile

add2bold, addClass, addClass, buildHeader, changeIndex, clear, clone, getBoldClasses, getByIndex, getClass, getClassByIndex, getClasses, getHighestClassIndex, getKeys, getQuick, getSize, hasClass, parseHeader, remove, remove, removeFromBold, removeOne, set, setBoldClasses, setBoldClasses, setClasses, setClasses, setKeys, setKeys, setKeys, size, size, sort

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.

allClasses

protected java.util.List allClasses

Column with class numbers

Constructor Detail

DiagnosisFile

public DiagnosisFile()

Standard constructor

DiagnosisFile

public DiagnosisFile(java.lang.String filename)

Constructor with a filename

Parameters:

filename - Name of the file

Method Detail

parseLine

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

Parse a line.

Overrides:

parseLine in class ClsFile

Parameters:

row - Number of current line.

line - Current line.

checkHeader

protected void checkHeader()

Check consistency of header information.

Overrides:

checkHeader in class ClsFile

buildLine

protected java.lang.String buildLine(int row)

Construct a line for saving.

Overrides:

buildLine in class ClsFile

Parameters:

row - Number of current line.

Returns:

Line with that number.

add

public void add(int index,
                int cls)

Add an index - class number pair

Overrides:

add in class ClsFile

Parameters:

index - of data point or best match

cls - class number

add

public void add(int index,
                java.lang.String cls)
         throws java.lang.NumberFormatException

Add an index - class number pair

Parameters:

index - of data point or best match

cls - class number

Throws:

java.lang.NumberFormatException

getAll

public cern.colt.list.IntArrayList getAll(int pos)

Get all class numbers of a classification by its position in the list

Parameters:

position - of classification

getAllByIndex

public cern.colt.list.IntArrayList getAllByIndex(int index)

Get all class numbers of a classification by its index

Parameters:

index - index of the data point

getAllClasses

public java.util.List getAllClasses()

Get list of IntArrayLists with all class numbers.

setAllClasses

public void setAllClasses(java.util.List allClasses)

Set list of IntArrayLists with all class numbers.

getFileType

public static FileType getFileType()

Get the type of file.