org.biojava.bio.seq
Class SequenceTools

java.lang.Object
  |
  +--org.biojava.bio.seq.SequenceTools

public final class SequenceTools

extends java.lang.Object

Methods for manipulating sequences.

Author:

Matthew Pocock

Constructor Summary

SequenceTools()

Method Summary

static void	addAllFeatures(Sequence seq, FeatureHolder fh) Add features to a sequence that contain the same information as all those in a feature holder.
static Sequence	createSequence(SymbolList syms, java.lang.String uri, java.lang.String name, Annotation ann)
static Sequence	reverseComplement(Sequence seq)
static Sequence	subSequence(Sequence seq, int start, int end)
static Sequence	subSequence(Sequence seq, int start, int end, java.lang.String name)
static Sequence	view(Sequence seq)
static Sequence	view(Sequence seq, java.lang.String name)

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceTools

public SequenceTools()

Method Detail

createSequence

public static Sequence createSequence(SymbolList syms,
                                      java.lang.String uri,
                                      java.lang.String name,
                                      Annotation ann)

subSequence

public static Sequence subSequence(Sequence seq,
                                   int start,
                                   int end)
                            throws java.lang.IndexOutOfBoundsException

java.lang.IndexOutOfBoundsException

subSequence

public static Sequence subSequence(Sequence seq,
                                   int start,
                                   int end,
                                   java.lang.String name)
                            throws java.lang.IndexOutOfBoundsException

java.lang.IndexOutOfBoundsException

reverseComplement

public static Sequence reverseComplement(Sequence seq)
                                  throws IllegalAlphabetException

IllegalAlphabetException

view

public static Sequence view(Sequence seq)

view

public static Sequence view(Sequence seq,
                            java.lang.String name)

addAllFeatures

public static void addAllFeatures(Sequence seq,
                                  FeatureHolder fh)
                           throws ChangeVetoException,
                                  BioException

Add features to a sequence that contain the same information as all those in a feature holder.

Parameters:

seq - the Sequence to add features to

fh - the features to add

Throws:

ChangeVetoException - if the sequence could not be modified

BioException - if there was an error creating the features