org.biojava.bio.seq
Class SequenceTools

java.lang.Object
  extended byorg.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
Throws:
java.lang.IndexOutOfBoundsException

subSequence

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

reverseComplement

public static Sequence reverseComplement(Sequence seq)
                                  throws IllegalAlphabetException
Throws:
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