org.irisa.genouest.logol.utils
Class MySequenceIterator
java.lang.Object
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
Methods inherited from class java.lang.Object |
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
MySequenceIterator
public MySequenceIterator()
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