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

    java.lang.Object
      org.biojava.bio.program.phred.PhredTools

    public final class PhredTools

extends Object

PhredTools contains static methods for working with phred quality data.

Copyright (c) 2001

Company: AgResearch

Since:
  1.1 Note that Phred is a copyright of CodonCode Corporation.
Author:
  Mark Schreiber, Matthew Pocock

Constructor Summary
`PhredTools()`

Method Summary
`static SymbolList` | `createPhred(SymbolList dna, SymbolList quality)` Merges a Symbol List from the DNA alphabet with a SymbolList from the [0..99] subset of the IntegerAlphabet into a SymbolList from the PHRED alphabet.
`static Symbol` | `dnaSymbolFromPhred(Symbol phredSym)` Retrives the DNA symbol component of the Phred BasisSymbol from the PHRED alphabet.
`static FiniteAlphabet` | `getPhredAlphabet()` Retrieves the PHRED alphabet from the AlphabetManager.
`static Symbol` | `getPhredSymbol(Symbol dna, Symbol integer)` Creates a symbol from the PHRED alphabet by combining a Symbol from the DNA alphabet and a Symbol from the IntegerAlphabet (or one of its subsets).
`static IntegerAlphabet.IntegerSymbol` | `integerSymbolFromPhred(Symbol phredSym)` Retrives the IntegerSymbol component of the Phred BasisSymbol from the PHRED alphabet.
`static double` | `pFromQuality(double quality)` Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10)
`static double` | `pFromQuality(int quality)` Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10)
`static double` | `pFromQuality(IntegerAlphabet.IntegerSymbol quality)` Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10)
`static Distribution[]` | `phredAlignmentToDistArray(Alignment a)` converts an Alignment of PhredSequences to a Distribution[] where each position is the average distribution of the underlying column of the alignment.
`static Distribution[]` | `phredToDistArray(PhredSequence s)` Converts a Phred sequence to an array of distributions.
`static double` | `qualityFromP(double probOfError)` The quality value is related to the base call error probability by the formula QV = - 10 * log_10( P_e ) where P_e is the probability that the base call is an error.
`static StreamReader` | `readPhredQuality(BufferedReader br)` Constructs a StreamReader to read in Phred quality data in FASTA format.
`static StreamReader` | `readPhredSequence(BufferedReader br)` Calls SeqIOTools.readFastaDNA(br), added here for convinience.
`static void` | `writePhredQuality(OutputStream qual, OutputStream seq, SequenceDB db)` Writes Phred quality data in a Fasta type format.

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

Constructor Detail

### PhredTools

    public PhredTools()

Method Detail

### getPhredAlphabet

    public static final FiniteAlphabet getPhredAlphabet()

  Retrieves the PHRED alphabet from the AlphabetManager. The Phred alphabet is a cross product of a subset of the IntegerAlphabet from 0...99 and the DNA alphabet. The Phred alphabet is finite. The Phred Alphabet contains 400 BasisSymbols named, for example, (guanine 47). The BasisSymbols can be fragmented into their component AtomicSymbols using the `getSymbols()` method of BasisSymbol.

### dnaSymbolFromPhred

    public static final Symbol dnaSymbolFromPhred(Symbol phredSym)
                                           throws IllegalSymbolException

  Retrives the DNA symbol component of the Phred BasisSymbol from the PHRED alphabet.

  Throws:
    `IllegalSymbolException` - if the provided symbol is not from the PHRED alphabet.

### integerSymbolFromPhred

    public static final IntegerAlphabet.IntegerSymbol integerSymbolFromPhred(Symbol phredSym)
                                                                      throws IllegalSymbolException

  Retrives the IntegerSymbol component of the Phred BasisSymbol from the PHRED alphabet.

  Throws:
    `IllegalSymbolException` - if the provided symbol is not from the PHRED alphabet.

### createPhred

    public static SymbolList createPhred(SymbolList dna,
                                         SymbolList quality)
                                  throws IllegalArgumentException,
                                         IllegalAlphabetException,
                                         IllegalSymbolException

  Merges a Symbol List from the DNA alphabet with a SymbolList from the [0..99] subset of the IntegerAlphabet into a SymbolList from the PHRED alphabet.

  Throws:
    `IllegalAlphabetException` - if the alphabets are not of the required alphabets
    `IllegalArgumentException` - if the two SymbolLists are not of equal length.
    `IllegalSymbolException` - if a combination of Symbols cannot be represented by the PHRED alphabet.

### getPhredSymbol

    public static final Symbol getPhredSymbol(Symbol dna,
                                              Symbol integer)
                                       throws IllegalSymbolException

  Creates a symbol from the PHRED alphabet by combining a Symbol from the DNA alphabet and a Symbol from the IntegerAlphabet (or one of its subsets).

  Throws:
    `IllegalSymbolException` - if there is no Symbol in the PHRED alphabet that represents the two arguments.

### writePhredQuality

    public static void writePhredQuality(OutputStream qual,
                                         OutputStream seq,
                                         SequenceDB db)
                                  throws IOException,
                                         BioException

  Writes Phred quality data in a Fasta type format.

  Parameters:
    `db` - a bunch of PhredSequence objects
    `qual` - the OutputStream to write the quality data to.
    `seq` - the OutputStream to write the sequence data to.
  Throws:
    `IOException`
    `BioException`
  Since:
    1.2

### readPhredQuality

    public static StreamReader readPhredQuality(BufferedReader br)

  Constructs a StreamReader to read in Phred quality data in FASTA format. The data is converted into sequences consisting of Symbols from the IntegerAlphabet.

### readPhredSequence

    public static StreamReader readPhredSequence(BufferedReader br)

  Calls SeqIOTools.readFastaDNA(br), added here for convinience.

### qualityFromP

    public static double qualityFromP(double probOfError)

  The quality value is related to the base call error probability by the formula QV = - 10 * log_10( P_e ) where P_e is the probability that the base call is an error.

  Returns:
    a `double` value, note that for most Phred scores this will be rounded to the nearest `int`

### pFromQuality

    public static double pFromQuality(double quality)

  Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10)

### pFromQuality

    public static double pFromQuality(int quality)

  Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10)

### pFromQuality

    public static double pFromQuality(IntegerAlphabet.IntegerSymbol quality)

  Calculates the probability of an error from the quality score via the formula P_e = 10**(QV/-10)

### phredToDistArray

    public static Distribution[] phredToDistArray(PhredSequence s)

  Converts a Phred sequence to an array of distributions. Essentially a fuzzy sequence Assumes that all of the non called bases are equiprobable

### phredAlignmentToDistArray

    public static Distribution[] phredAlignmentToDistArray(Alignment a)

  converts an Alignment of PhredSequences to a Distribution[] where each position is the average distribution of the underlying column of the alignment.

  Throws:
    `ClassCastException` - if the sequences in the alignment are not instances of PhredSequence

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