org.irisa.genouest.logol.utils
Class MySequenceIterator

java.lang.Object
  extended by org.irisa.genouest.logol.utils.MySequenceIterator
All Implemented Interfaces:
org.biojava.bio.seq.SequenceIterator, org.biojavax.bio.BioEntryIterator, org.biojavax.bio.seq.RichSequenceIterator

public class MySequenceIterator
extends java.lang.Object
implements org.biojavax.bio.seq.RichSequenceIterator

Simple Sequence implementation to fix memory issues with BioJava DNATools functions. Implements minimum number of functions for sequence data manipulation (no symbols and features) Fix : 1660

Author:
osallou

Constructor Summary
MySequenceIterator()
           
 
Method Summary
 boolean hasNext()
           
 org.biojavax.bio.BioEntry nextBioEntry()
           
 org.biojavax.bio.seq.RichSequence nextRichSequence()
           
 org.biojava.bio.seq.Sequence nextSequence()
           
static MySequenceIterator readFasta(java.io.BufferedReader br)
          Accessor to a Fasta reader
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

MySequenceIterator

public MySequenceIterator()
Method Detail

readFasta

public static MySequenceIterator readFasta(java.io.BufferedReader br)
Accessor to a Fasta reader

Parameters:
br - BufferedReader to a Fasta file
Returns:

nextRichSequence

public org.biojavax.bio.seq.RichSequence nextRichSequence()
                                                   throws java.util.NoSuchElementException,
                                                          org.biojava.bio.BioException
Specified by:
nextRichSequence in interface org.biojavax.bio.seq.RichSequenceIterator
Throws:
java.util.NoSuchElementException
org.biojava.bio.BioException

hasNext

public boolean hasNext()
Specified by:
hasNext in interface org.biojava.bio.seq.SequenceIterator
Specified by:
hasNext in interface org.biojavax.bio.BioEntryIterator

nextBioEntry

public org.biojavax.bio.BioEntry nextBioEntry()
                                       throws java.util.NoSuchElementException,
                                              org.biojava.bio.BioException
Specified by:
nextBioEntry in interface org.biojavax.bio.BioEntryIterator
Throws:
java.util.NoSuchElementException
org.biojava.bio.BioException

nextSequence

public org.biojava.bio.seq.Sequence nextSequence()
                                          throws java.util.NoSuchElementException,
                                                 org.biojava.bio.BioException
Specified by:
nextSequence in interface org.biojava.bio.seq.SequenceIterator
Throws:
java.util.NoSuchElementException
org.biojava.bio.BioException