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A C F G I L M O P Q R S

## A

AboutFrame - Class in org.expasy.bprg
  A simple Frame aimed at displaying varous informations about the software.
AboutFrame(String) - Constructor for class org.expasy.bprg.AboutFrame
  Constructor of the Frame.
addConstraints(GridBagConstraints, int, int, int, int, double, double, int, int, int, int) - Static method in class org.expasy.minitools.util.FileUtils
  Add contraints to the display of an element in a panel using GridBagLayout.
ALDENTE_PROJECT_EXTENSION - Static variable in class org.expasy.minitools.util.FileUtils
  Extension for aldente project files (*.prj)

## C

collectInfos(PhenyxSILACPeptide, SilacQuantiParam) - Method in class org.expasy.bprg.PeptideQuantiInfos

## F

FileUtils - Class in org.expasy.minitools.util
  Title: FileUtils
  Description:
  Copyright: Copyright (c) 2003
  Company: SIB
  Date: 24 avr. 2003
  Time: 13:53:32
findFileAsStream(String) - Static method in class org.expasy.minitools.util.FileUtils
  Similar to the `findImage` method, but dedicated to files.
findImage(String) - Static method in class org.expasy.minitools.util.FileUtils
  Finds an image using different methods to retrieve its location: first `java.net.URL url = UIManager.class.getResource("../..`
findImagePath(String) - Static method in class org.expasy.minitools.util.FileUtils
  Similar to the `findImage` method, but dedicated to files.

## G

getAACount(char[]) - Method in class org.expasy.bprg.PhenyxSILACPeptide
getAACounts(char[]) - Method in class org.expasy.bprg.PhenyxSILACPeptide
getAALabels() - Method in class org.expasy.bprg.SilacQuantiParam
getAAPresent(char[]) - Method in class org.expasy.bprg.PhenyxSILACPeptide
getC12Areas() - Method in class org.expasy.bprg.PeptideQuantiInfos
getC13Areas() - Method in class org.expasy.bprg.PeptideQuantiInfos
getDescription() - Method in class org.expasy.bprg.PhenyxSILACPeptide
getExtension(File) - Static method in class org.expasy.minitools.util.FileUtils
  Get the extension of a file.
getForm() - Method in class org.expasy.bprg.PeptideQuantiInfos
getHeavyMass() - Method in class org.expasy.bprg.PeptideQuantiInfos
getIntermAreas() - Method in class org.expasy.bprg.PeptideQuantiInfos
getIntermMasses() - Method in class org.expasy.bprg.PeptideQuantiInfos
getLabeledAANumber() - Method in class org.expasy.bprg.PeptideQuantiInfos
getLightMass() - Method in class org.expasy.bprg.PeptideQuantiInfos
getMasses() - Method in class org.expasy.bprg.PeptideQuantiInfos
getModifsExcept(String) - Method in class org.expasy.bprg.PhenyxSILACPeptide
getModifsExcept(String[]) - Method in class org.expasy.bprg.PhenyxSILACPeptide
getPeptideMass() - Method in class org.expasy.bprg.PhenyxSILACPeptide
getPeptideString() - Method in class org.expasy.bprg.PeptideQuantiInfos
getPeptideString() - Method in class org.expasy.bprg.PhenyxSILACPeptide
getProteinName() - Method in class org.expasy.bprg.PeptideQuantiInfos
getProteinName() - Method in class org.expasy.bprg.PhenyxSILACPeptide
getSpectrumId() - Method in class org.expasy.bprg.PhenyxSILACPeptide
getSpectrumLabel() - Method in class org.expasy.bprg.PhenyxSILACPeptide
getSumHeavyForms() - Method in class org.expasy.bprg.PeptideQuantiInfos
getSumLightForms() - Method in class org.expasy.bprg.PeptideQuantiInfos
  Return only C12 value (was also adding c12-1Da and c12-2Da)
getTagLabels() - Method in class org.expasy.bprg.SilacQuantiParam

## I

isFileFound() - Method in class org.expasy.bprg.PeptideQuantiInfos
isInJar() - Static method in class org.expasy.minitools.util.FileUtils
  Test is the executed application has been zipped in a jar.
isLabeledWith(String) - Method in class org.expasy.bprg.PhenyxSILACPeptide
isLabeledWith(String[]) - Method in class org.expasy.bprg.PhenyxSILACPeptide

## L

layout - package layout
log4j_properties_filepath - Static variable in class org.expasy.bprg.Resources

## M

main(String[]) - Static method in class org.expasy.bprg.AboutFrame
  Test this frame independently.
main(String[]) - Static method in class org.expasy.bprg.MainFrame
  Starting main function.
main(String[]) - Static method in class org.expasy.bprg.SilacQuanti
MainFrame - Class in org.expasy.bprg
MainFrame() - Constructor for class org.expasy.bprg.MainFrame
makeCompactGrid(Container, int, int, int, int, int, int) - Static method in class layout.SpringUtilities
  Aligns the first `rows` * `cols` components of `parent` in a grid.
makeGrid(Container, int, int, int, int, int, int) - Static method in class layout.SpringUtilities
  Aligns the first `rows` * `cols` components of `parent` in a grid.

## O

org.expasy.bprg - package org.expasy.bprg
org.expasy.minitools.util - package org.expasy.minitools.util

## P

PeptideQuantiInfos - Class in org.expasy.bprg
PeptideQuantiInfos() - Constructor for class org.expasy.bprg.PeptideQuantiInfos
PhenyxSILACPeptide - Class in org.expasy.bprg
PhenyxSILACPeptide(Cell[]) - Constructor for class org.expasy.bprg.PhenyxSILACPeptide
printSizes(Component) - Static method in class layout.SpringUtilities
  A debugging utility that prints to stdout the component's minimum, preferred, and maximum sizes.

## Q

quantifyAndWrite(File, SilacQuantiParam) - Method in class org.expasy.bprg.SilacQuanti

## R

Resources - Class in org.expasy.bprg
  Abstract class containing testing files paths.
runSilacQuanti() - Method in class org.expasy.bprg.MainFrame

## S

SilacQuanti - Class in org.expasy.bprg
  ne pas rechercher les peak ŕ -6Da, -12Da, ect ... si le pic 13C n'a pas été trouvé
SilacQuanti() - Constructor for class org.expasy.bprg.SilacQuanti
SilacQuantiParam - Class in org.expasy.bprg
SilacQuantiParam() - Constructor for class org.expasy.bprg.SilacQuantiParam
SpringUtilities - Class in layout
  A 1.4 file that provides utility methods for creating form- or grid-style layouts with SpringLayout.
SpringUtilities() - Constructor for class layout.SpringUtilities

A C F G I L M O P Q R S

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