AFLPcore
Class FeatureList

java.lang.Object
  |
  +--AFLPcore.FeatureList

public class FeatureList

extends java.lang.Object

This is a static class that provides a list of all of the features in the program. This is done so that features can be added to the program without much effort. For example, a dialog that wants to display a list of scoring functions for bins should query this class to get the list. This way, a new scoring function can be added to the program by simply modifying this class. The class contains several different types of managers for different operations, see the manager descriptions for details on the types of operation supported by each. Features can be added by either directly modifying the class, or by extending it, overriding the createManagerType calling the super and then adding the new feature. One should make sure that the default is set.

New managers could be added, but the program will not have support for these managers, so the program would have to be modified too.

One possible enhancement to this class would be adding methods to scan directories for class files and adding them to the manager. This would mean that new features could be added without recompiling the program. However, this may be difficult if not impossible. Note: many other classes rely on this class to retrieve various components. For example, an import filter may query this class to see which sizing functions are available.

See Also:

ImportMgr, ScoreManager, PeakMgr, CutoffMgr, StandardMgr, AnalysisMgr, Mgr

Constructor Summary

FeatureList()

Method Summary

static void	createManagerList(Manager mgr, java.io.PrintWriter out)
static void	generateFileList()
static AnalysisMgr	getAnalysisMgr() Gives a manager that contains all of the functions used to analyize a gel known to the program.
static BinOpMgr	getBinOpMgr() Gives a manager that contains all of the operations on bins known to the program.
static CutoffMgr	getCutoffMgr() Gives a manager that contains all of the cutoff functions known to the program.
static GelOpMgr	getGelOpMgr() Gives a manager that contains all of the operations on a gel known to the program.
static ImportMgr	getImportMgr() Gives a manager that contains all of the import filters known to the program.
static LaneOpMgr	getLaneOpMgr() Gives a manager that contains all of the operations on lanes known to the program.
static PeakMgr	getPeakMgr() Gives a manager that contains all of the peak locating algorithms known to the program.
static ScoreManager	getScoreMgr() Gives a manager that contains all of the scoring methods known to the program.
static SizeMgr	getSizeMgr() Gives a manager that contains all of the functions used to size a lane known to the program.
static StandardMgr	getStandardMgr() Gives a manager that contains all of the size standard definitions known to the program.
static java.lang.String	nextLine(java.io.BufferedReader inStream) Gets a line from the specified input stream.

Methods inherited from class java.lang.Object

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

Constructor Detail

FeatureList

public FeatureList()

Method Detail

getImportMgr

public static ImportMgr getImportMgr()

Gives a manager that contains all of the import filters known to the program.

See Also:

ImportMgr, ImportFilter

getScoreMgr

public static ScoreManager getScoreMgr()

Gives a manager that contains all of the scoring methods known to the program.

See Also:

ScoreManager, ScoreFunction

getPeakMgr

public static PeakMgr getPeakMgr()

Gives a manager that contains all of the peak locating algorithms known to the program.

See Also:

PeakMgr, PeakLocate

getCutoffMgr

public static CutoffMgr getCutoffMgr()

Gives a manager that contains all of the cutoff functions known to the program.

See Also:

CutoffMgr, CutoffFunction

getSizeMgr

public static SizeMgr getSizeMgr()

Gives a manager that contains all of the functions used to size a lane known to the program.

See Also:

SizeMgr, SizeFunction

getAnalysisMgr

public static AnalysisMgr getAnalysisMgr()

Gives a manager that contains all of the functions used to analyize a gel known to the program.

See Also:

AnalysisMgr, AnalysisOp

getGelOpMgr

public static GelOpMgr getGelOpMgr()

Gives a manager that contains all of the operations on a gel known to the program.

See Also:

GelOpMgr, GelOperation

getLaneOpMgr

public static LaneOpMgr getLaneOpMgr()

Gives a manager that contains all of the operations on lanes known to the program.

See Also:

LaneOpMgr, LaneOperation

getBinOpMgr

public static BinOpMgr getBinOpMgr()

Gives a manager that contains all of the operations on bins known to the program.

See Also:

BinOpMgr, BinOperation

getStandardMgr

public static StandardMgr getStandardMgr()
                                  throws java.io.IOException

Gives a manager that contains all of the size standard definitions known to the program.

Throws:

java.io.IOException - occurs if a problem is encountered when reading from the file that contains the definitions.

See Also:

StandardMgr, SizeStandard

nextLine

public static java.lang.String nextLine(java.io.BufferedReader inStream)
                                 throws java.io.IOException

Gets a line from the specified input stream. It will skip over blank lines and lines beginning with a '#'. Additionally, white space will be trimmed from both ends of the string.

Parameters:

inStream - the stream to read from

Returns:

the line that isn't blank or a comment. null will be returned if the end of the stream is reached.

Throws:

java.io.IOException - if an I/O problem occurs.

generateFileList

public static void generateFileList()
                             throws java.io.IOException

createManagerList

public static void createManagerList(Manager mgr,
                                     java.io.PrintWriter out)