PhredSequence (BioJava-1.5-beta API)
Keywords: org.biojava.bio.program.phred.PhredSequence class

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## org.biojava.bio.program.phred
Class PhredSequence

    java.lang.Object
      org.biojava.utils.AbstractChangeable
          org.biojava.bio.seq.impl.SimpleSequence
              org.biojava.bio.program.phred.PhredSequence

All Implemented Interfaces:
  Serializable, Annotatable, Qualitative, FeatureHolder, RealizingFeatureHolder, Sequence, SymbolList, Changeable

    public class PhredSequence

extends SimpleSequence
implements Qualitative

PhredSequence is an extension of SimpleSequence that implements Qualitative to hold Phred quality scores.

Copyright: Copyright (c) 2001

Company: AgResearch

Since:
  1.1
Author:
  Mark Schreiber
See Also:
  Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder
`FeatureHolder.EmptyFeatureHolder`

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
`Annotatable.AnnotationForwarder`

Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder
`FeatureHolder.EmptyFeatureHolder`

Field Summary

Fields inherited from interface org.biojava.bio.symbol.SymbolList
`EDIT, EMPTY_LIST`

Fields inherited from interface org.biojava.bio.seq.FeatureHolder
`EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA`

Fields inherited from interface org.biojava.bio.Annotatable
`ANNOTATION`

Fields inherited from interface org.biojava.bio.seq.FeatureHolder
`EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA`

Constructor Summary
`PhredSequence(SymbolList phredSequence, String name, String urn, Annotation anno)` Constructs a new PhredSequence.

Method Summary
`SymbolList` | `getDNA()` Extracts the DNA part of the PhredAlpahbet SymbolList and returns it as a SymbolList
`Symbol` | `getDNAAt(int index)`
`SymbolList` | `getQuality()` Extracts the quality part if the Phred Alphabet and returns it as a SymbolList over the Integer SubAlphabet from 0..99.
`Symbol` | `getQualityAt(int index)` Retreives the quality symbol for the specified index.

Methods inherited from class org.biojava.bio.seq.impl.SimpleSequence
`containsFeature, countFeatures, createFeature, createFeature, edit, featureHolderAllocated, features, filter, filter, getAlphabet, getAnnotation, getChangeSupport, getFeatureHolder, getName, getSchema, getURN, iterator, length, realizeFeature, removeFeature, seqString, setName, setURN, subList, subStr, symbolAt, toList, toString`

Methods inherited from class org.biojava.utils.AbstractChangeable
`addChangeListener, addChangeListener, generateChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener`

Methods inherited from class java.lang.Object
`clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait`

Methods inherited from interface org.biojava.utils.Changeable
`addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener`

Methods inherited from interface org.biojava.utils.Changeable
`addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener`

Methods inherited from interface org.biojava.utils.Changeable
`addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener`

Methods inherited from interface org.biojava.utils.Changeable
`addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener`

Constructor Detail

### PhredSequence

    public PhredSequence(SymbolList phredSequence,
                         String name,
                         String urn,
                         Annotation anno)
                  throws IllegalAlphabetException

  Constructs a new PhredSequence.

  Parameters:
    `phredSequence` - - a SymbolList over the Phred Alphabet.
    `name` - - the name for the sequence.
    `urn` - - the URN for the sequence.
    `anno` - - the Annotation object for the sequence.
  Throws:
    `IllegalAlphabetException`

Method Detail

### getQuality

    public SymbolList getQuality()

  Extracts the quality part if the Phred Alphabet and returns it as a SymbolList over the Integer SubAlphabet from 0..99.

  Specified by:
    `getQuality` in interface `Qualitative`

### getDNA

    public SymbolList getDNA()

  Extracts the DNA part of the PhredAlpahbet SymbolList and returns it as a SymbolList

### getQualityAt

    public Symbol getQualityAt(int index)
                        throws IndexOutOfBoundsException

  Description copied from interface: `Qualitative`
  Retreives the quality symbol for the specified index.

  Specified by:
    `getQualityAt` in interface `Qualitative`
  Parameters:
    `index` - - Must be greater than zero.
  Throws:
    `IndexOutOfBoundsException` - if index is outside of the quality symbol list.

### getDNAAt

    public Symbol getDNAAt(int index)
                    throws IndexOutOfBoundsException

  Throws:
    `IndexOutOfBoundsException`

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