uk.ac.sanger.psu.gfmerge.util.getopt
Class SimpleArg

java.lang.Object
  |
  +--uk.ac.sanger.psu.gfmerge.util.getopt.SimpleArg

public class SimpleArg
extends java.lang.Object

class for objects containing the command line arguments. Input files used have to be in EMBL format.

Version:
1.0
Author:
Sebastian R. Spiegler

Field Summary
private  java.lang.String annotatedTrainSet
          annotation of training set (for acp calculation)
private  java.lang.String blastFile
          blast file which is used for evidence of correct predictions (EMBL format).
private  java.lang.String cDNAFile
          cDNA file which is used for evidence of correct predictions (EMBL format).
private  boolean considerCDnaStrand
          switch for strand consideration of cDNA.
private  int debug
          debugging mode.
private  java.lang.String filename
          filename of output file.
private  boolean fileOfRemovedGms
          switch for output of a file containt all removed genemodels as well as a file of each analysis level with the removed genemodels.
private  int fuzzyBoundaries
          allowed difference between genemodel and cDNA splice site to be assigned as correct splice site.
private  java.util.ArrayList predictedTrainSet
          predictions of training set (for acp calculation).
private  java.util.ArrayList predictions
          predictions which will be collapsed into one (EMBL format).
 
Constructor Summary
SimpleArg(java.lang.String[] args)
          constructor of SimpleArg objects.
 
Method Summary
private  void checkArguments()
          method which checks arguments (briefly)
 boolean doConsiderCDnaStrand()
          accessor method which returns switch for cDNA strand consideration.
 boolean doFileOfRemovedGms()
          accessor method returns switch whether removed genemodels should be saved to file or not.
private  void doHelp(int returnValue)
          Stub for providing help on usage
 org.biojava.bio.seq.Sequence getAnnotatedTrainSet_Sequence()
          accessor method which returns a sequence object of the annotated training set, used filename is stored in attribute 'annotatedTrainSet' , retrieved from command-line argument (-a)
 java.lang.String getAnnotatedTrainSet()
          accessor method which returns the filename of the annotated training set file stored in attribute 'annotatedTrainSet', retrieved from command-line argument (-a)
 java.lang.String getBlastFile()
          accessor method which returns an blast filename, retrieved from command-line argument (-b)
 java.lang.String getCDNAFile()
          accessor method which returns an cDNA filename, retrieved from command-line argument (-c)
 int getDebug()
          accessor method which returns debug mode (int variable).
 int getFuzzyBoundariesValue()
          accessor method which returns the value of tolerance inbetween cDNA and genemodel splice sites.
 java.lang.String getOutputFilename()
          accessor method which returns an output filename, retrieved from command-line argument (-f)
 java.util.ArrayList getPredictedTrainSet_Sequences()
          accessor method which returns an array list of sequence objects containing predictions on the training set of different gene predicters, used filename are stored in attribute 'predictedTrainSet' , retrieved from command-line argument (-t)
 java.util.ArrayList getPredictedTrainSet()
          accessor method which returns an array list of filenames of predictions from different gene prediction programs on the training set, retrieved from command-line argument (-t)
 java.util.ArrayList getPredictions_Sequences()
          accessor method which returns an array list of sequence objects containing predictions of different gene predicters, used filename are stored in attribute 'predictions' , retrieved from command-line argument (-p)
 java.util.ArrayList getPredictions()
          accessor method which returns an array list of filenames of predictions, stored in attribute 'predictions', retrieved from command-line argument (-p)
private  void setArguments(java.lang.String[] _args)
          method which retrieves command line arguments and saves them.
private  java.util.ArrayList strArrToArrList(java.lang.String[] strArr)
          method which converts String[] into an ArrayList
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

annotatedTrainSet

private java.lang.String annotatedTrainSet
annotation of training set (for acp calculation)


predictedTrainSet

private java.util.ArrayList predictedTrainSet
predictions of training set (for acp calculation).


predictions

private java.util.ArrayList predictions
predictions which will be collapsed into one (EMBL format).


blastFile

private java.lang.String blastFile
blast file which is used for evidence of correct predictions (EMBL format).


cDNAFile

private java.lang.String cDNAFile
cDNA file which is used for evidence of correct predictions (EMBL format).


debug

private int debug
debugging mode.


filename

private java.lang.String filename
filename of output file.


fileOfRemovedGms

private boolean fileOfRemovedGms
switch for output of a file containt all removed genemodels as well as a file of each analysis level with the removed genemodels.


considerCDnaStrand

private boolean considerCDnaStrand
switch for strand consideration of cDNA. Default is false.


fuzzyBoundaries

private int fuzzyBoundaries
allowed difference between genemodel and cDNA splice site to be assigned as correct splice site.

Constructor Detail

SimpleArg

public SimpleArg(java.lang.String[] args)
constructor of SimpleArg objects.

Parameters:
args - command line arguments from main method
Method Detail

setArguments

private void setArguments(java.lang.String[] _args)
method which retrieves command line arguments and saves them.

Parameters:
_args -

doHelp

private void doHelp(int returnValue)
Stub for providing help on usage

Parameters:
returnValue -

strArrToArrList

private java.util.ArrayList strArrToArrList(java.lang.String[] strArr)
method which converts String[] into an ArrayList

Parameters:
strArr - String[]
Returns:
ArrayList

checkArguments

private void checkArguments()
method which checks arguments (briefly)


getAnnotatedTrainSet

public java.lang.String getAnnotatedTrainSet()
accessor method which returns the filename of the annotated training set file stored in attribute 'annotatedTrainSet', retrieved from command-line argument (-a)

Returns:
String

getAnnotatedTrainSet_Sequence

public org.biojava.bio.seq.Sequence getAnnotatedTrainSet_Sequence()
accessor method which returns a sequence object of the annotated training set, used filename is stored in attribute 'annotatedTrainSet' , retrieved from command-line argument (-a)

Returns:
Sequence

getPredictedTrainSet

public java.util.ArrayList getPredictedTrainSet()
accessor method which returns an array list of filenames of predictions from different gene prediction programs on the training set, retrieved from command-line argument (-t)

Returns:
ArrayList

getPredictedTrainSet_Sequences

public java.util.ArrayList getPredictedTrainSet_Sequences()
accessor method which returns an array list of sequence objects containing predictions on the training set of different gene predicters, used filename are stored in attribute 'predictedTrainSet' , retrieved from command-line argument (-t)

Returns:
ArrayList of Sequences

getPredictions

public java.util.ArrayList getPredictions()
accessor method which returns an array list of filenames of predictions, stored in attribute 'predictions', retrieved from command-line argument (-p)

Returns:
ArrayList of Strings

getPredictions_Sequences

public java.util.ArrayList getPredictions_Sequences()
accessor method which returns an array list of sequence objects containing predictions of different gene predicters, used filename are stored in attribute 'predictions' , retrieved from command-line argument (-p)

Returns:
ArrayList of Sequences

getDebug

public int getDebug()
accessor method which returns debug mode (int variable).

Returns:
int
See Also:
Debug

getBlastFile

public java.lang.String getBlastFile()
accessor method which returns an blast filename, retrieved from command-line argument (-b)

Returns:
blast filename

getCDNAFile

public java.lang.String getCDNAFile()
accessor method which returns an cDNA filename, retrieved from command-line argument (-c)

Returns:
cDNA filename

getOutputFilename

public java.lang.String getOutputFilename()
accessor method which returns an output filename, retrieved from command-line argument (-f)

Returns:
output filename

doFileOfRemovedGms

public boolean doFileOfRemovedGms()
accessor method returns switch whether removed genemodels should be saved to file or not. retrieved from command-line argument (-b). Default is no output.

Returns:
boolean switch for ouput of removed files

getFuzzyBoundariesValue

public int getFuzzyBoundariesValue()
accessor method which returns the value of tolerance inbetween cDNA and genemodel splice sites.

Returns:
tolerance inbetween cDNA and genemodel splice sites

doConsiderCDnaStrand

public boolean doConsiderCDnaStrand()
accessor method which returns switch for cDNA strand consideration. Default is false/no strand consideration.

Returns:
switch for cDNA strand consideration