javagene.io
Class Gff

java.lang.Object
  javagene.io.Gff

public class Gff
extends java.lang.Object

Read and write FeatureLists as GFF/GTF formatted files.

The GFF moniker is applied to a variety of tab-delimited formats that mock the notion of a standard. This class should parse most files bearing at least a passing resemblance to any of the formats. You will, however, need to research the semantics of the files you encounter. Generally, the format consists of 9 tab-delimited fields:

 seqname   source   featureType   start   end   score   strand   frame   attributes
 

The 9th field consists of key-value pairs separated by semicolons, the first of which JavaGene interprets as the group id (as used in GFF1). It is the precise meaning of this 9th field that varies from week to week. The Feature and FeatureList objects provide various utility methods to ease the task of accessing and using the attributes. The proper interpretation of any particular attribute, however, is left to you.

Method Summary

static FeatureList	read(java.lang.String filename) Read a file into a FeatureList.
static void	write(FeatureList features, java.lang.String filename) Write features in FeatureList to file.

Methods inherited from class java.lang.Object

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

Method Detail

read

public static FeatureList read(java.lang.String filename)
                        throws java.io.IOException

Read a file into a FeatureList. Each line of the file becomes one Feature object.

Parameters:

filename - The path to the GFF file.

Returns:

A FeatureList.

Throws:

java.io.IOException - Something went wrong -- check exception detail message.

write

public static void write(FeatureList features,
                         java.lang.String filename)
                  throws java.io.IOException

Write features in FeatureList to file. Each Feature becomes one line in the file.

Parameters:

features - The list of features to write.

filename - The path to the file.

Throws:

java.io.IOException - Something went wrong -- check exception detail message.