uk.ac.sanger.psu.gfmerge.util.io
Class GFMergeOutput

java.lang.Object
  |
  +--uk.ac.sanger.psu.gfmerge.util.io.GFMergeOutput

public class GFMergeOutput
extends java.lang.Object

class which writes EMBL files using BioJava SeqIOTools.writeEmbl().

Version:
1.0
Author:
Sebastian R. Spiegler

Constructor Summary
GFMergeOutput()
           
 
Method Summary
static void saveFeat2File(java.lang.String filename, java.util.ArrayList arrListOfFeatRegions, Prediction prediction)
          method which saves picked features to a file.
static void saveRemovedFeat2File(java.lang.String filename, java.util.ArrayList arrListOfFeatRegions_before, java.util.ArrayList arrListOfFeatRegions_after, Prediction prediction)
          method which saves removed features to a file.
private static void writeSeq2File(java.lang.String filename, org.biojava.bio.seq.Sequence seq)
          method which writes BioJava sequence to a file.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

GFMergeOutput

public GFMergeOutput()
Method Detail

saveFeat2File

public static void saveFeat2File(java.lang.String filename,
                                 java.util.ArrayList arrListOfFeatRegions,
                                 Prediction prediction)
method which saves picked features to a file.

Parameters:
filename - output filename
arrListOfFeatRegions - ArrayList of genemodel regions
prediction - Prediction object from which sequence is retrieved

saveRemovedFeat2File

public static void saveRemovedFeat2File(java.lang.String filename,
                                        java.util.ArrayList arrListOfFeatRegions_before,
                                        java.util.ArrayList arrListOfFeatRegions_after,
                                        Prediction prediction)
method which saves removed features to a file.

Parameters:
filename - output filename
arrListOfFeatRegions_before - ArrayList of genemodel regions before processing
arrListOfFeatRegions_after - ArrayList of genemodel regions after processing
prediction - Prediction object from which sequence is retrieved

writeSeq2File

private static void writeSeq2File(java.lang.String filename,
                                  org.biojava.bio.seq.Sequence seq)
method which writes BioJava sequence to a file.

Parameters:
filename - output filename
seq - BioJava sequence