AFLPcore
Class BinAnalysis

java.lang.Object
  |
  +--AFLPcore.Operation
        |
        +--AFLPcore.AnalysisOp
              |
              +--AFLPcore.BinAnalysis

All Implemented Interfaces:

java.lang.Cloneable

public class BinAnalysis

extends AnalysisOp

This class is an AnalysisOp which outputs information about all of the bins in the gel. For each bin in the gel, the name, if defined is printed out, as well as the location and range. Then all of the overall scoring information is displayed for the bin. Finally, the label assigned to each lane in the gel is printed out.

Sample output for a single bin (text enclosed in [] may not always be printed):

 [BinName at] 102.4 +/- 2.3 bp
 Mean: 101.9 StdDev: 0.02 #A: 10 #B 12 from 10/10 peaks.
 ABABBAABBABAABABBABBBA
 

or in general:

 [name at] location  +/- range
 overall score info line 1
 overall score info line 2
 .
 overall score info line n
 lane1Label|lane2Label|....|laneNLabel
 

Lines in the output string are seperated with '\n'

See Also:

Bin

Fields inherited from class AFLPcore.Operation

descript, helpFile, name, options

Constructor Summary

BinAnalysis()
Creates a new BinAnalysis object.

Method Summary

java.lang.String	analyze(Gel gel) Provides an anlysis for the the specified gel.
java.lang.String	getDescription() Gives a one sentence description of this analysis operation.
java.lang.String	getHelpFile() Gives a file that is the help file for this analysis operation
java.lang.String	getName() Gives the name of this bin analysis operation
Option[]	getOptions() No options for this operation, so null is returned.
void	setOptions(Option[] opts) Since there are no options for this operation, this method will do absolutely nothing.

Methods inherited from class AFLPcore.AnalysisOp

clone

Methods inherited from class java.lang.Object

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

Constructor Detail

BinAnalysis

public BinAnalysis()

Creates a new BinAnalysis object.

Method Detail

analyze

public java.lang.String analyze(Gel gel)

Provides an anlysis for the the specified gel. See the class description for the details of the analysis.

Overrides:

analyze in class AnalysisOp

Parameters:

gel - the gel to analyze

getOptions

public Option[] getOptions()

No options for this operation, so null is returned.

Overrides:

getOptions in class Operation

Returns:

null

setOptions

public void setOptions(Option[] opts)

Since there are no options for this operation, this method will do absolutely nothing.

Overrides:

setOptions in class Operation

Following copied from class: AFLPcore.Operation

Parameters:

opts - the values for the options that this operation understands.

getName

public java.lang.String getName()

Gives the name of this bin analysis operation

Overrides:

getName in class Operation

Returns:

the name, which is "Bin Display".

getDescription

public java.lang.String getDescription()

Gives a one sentence description of this analysis operation.

Overrides:

getDescription in class Operation

Returns:

the description

getHelpFile

public java.lang.String getHelpFile()

Gives a file that is the help file for this analysis operation

Overrides:

getHelpFile in class Operation

Returns:

a plaintext of html file containing help information