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
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 |
SequenceTools
public SequenceTools()
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 tofh
- the features to add
- Throws:
ChangeVetoException
- if the sequence could not be modified
BioException
- if there was an error creating the features