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wiki/BioJava:Cookbook:Alphabets:Component.md

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[CrossProductAlphabets](Biojava:Cookbook:Alphabets:CrossProduct "wikilink")
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are used to represent groups of
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[Symbols](http://www.biojava.org/docs/api14/org/biojava/bio/symbol/Symbol.html)
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[Symbols](http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/Symbol.html)
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as a single Symbol. This is very useful for treating things like codons
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as single
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[Symbols](http://www.biojava.org/docs/api14/org/biojava/bio/symbol/Symbol.html).
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[Symbols](http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/Symbol.html).
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Sometimes however, you might want to covert the
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[Symbols](http://www.biojava.org/docs/api14/org/biojava/bio/symbol/Symbol.html)
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[Symbols](http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/Symbol.html)
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back into their component
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[Symbols](http://www.biojava.org/docs/api14/org/biojava/bio/symbol/Symbol.html).
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[Symbols](http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/Symbol.html).
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The following recipe demonstrates how this can be done.
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The
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[Symbols](http://www.biojava.org/docs/api14/org/biojava/bio/symbol/Symbol.html)
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[Symbols](http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/Symbol.html)
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from a
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[CrossProductAlphabet](Biojava:Cookbook:Alphabets:CrossProduct "wikilink")
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are implementations of the
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[AtomicSymbol](http://www.biojava.org/docs/api14/org/biojava/bio/symbol/AtomicSymbol.html)
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[AtomicSymbol](http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/AtomicSymbol.html)
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interface. The prefix 'Atomic' suggests that the
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[Symbols](http://www.biojava.org/docs/api14/org/biojava/bio/symbol/Symbol.html)
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[Symbols](http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/Symbol.html)
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cannot be divided so one might ask, 'how can an indivisible Symbol be
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divided into it's component parts?'. The full definition of the
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[AtomicSymbol](http://www.biojava.org/docs/api14/org/biojava/bio/symbol/AtomicSymbol.html)
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[AtomicSymbol](http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/AtomicSymbol.html)
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is that it cannot be divided into a simpler Symbol that is still part of
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the same
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[Alphabet](http://www.biojava.org/docs/api14/org/biojava/bio/symbol/Alphabet.html).
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[Alphabet](http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/Alphabet.html).
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The component parts of an
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[AtomicSymbol](http://www.biojava.org/docs/api14/org/biojava/bio/symbol/AtomicSymbol.html)
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[AtomicSymbol](http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/AtomicSymbol.html)
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from a
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[CrossProductAlphabet](Biojava:Cookbook:Alphabets:CrossProduct "wikilink")
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are not members of the same
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[Alphabet](http://www.biojava.org/docs/api14/org/biojava/bio/symbol/Alphabet.html)
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[Alphabet](http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/Alphabet.html)
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so the 'Atomic' definition still stands. A [codon](wp:codon "wikilink")
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would be from the (DNA x DNA x DNA) Alphabet whereas the components of
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the [codon](wp:codon "wikilink")
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[Symbol](http://www.biojava.org/docs/api14/org/biojava/bio/symbol/Symbol.html)
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[Symbol](http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/Symbol.html)
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are from the DNA alphabet.
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Contrast this with the definition of a
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[BasisSymbol](http://www.biojava.org/docs/api14/org/biojava/bio/symbol/BasisSymbol.html).
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[BasisSymbol](http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/BasisSymbol.html).
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A
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[BasisSymbol](http://www.biojava.org/docs/api14/org/biojava/bio/symbol/BasisSymbol.html)
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[BasisSymbol](http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/BasisSymbol.html)
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can be validly divided into components that are still part of the same
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[Alphabet](http://www.biojava.org/docs/api14/org/biojava/bio/symbol/Alphabet.html).
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[Alphabet](http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/Alphabet.html).
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In this way a
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[BasisSymbol](http://www.biojava.org/docs/api14/org/biojava/bio/symbol/BasisSymbol.html)
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[BasisSymbol](http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/BasisSymbol.html)
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can be ambiguous. For further discussion of
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[BasisSymbol](http://www.biojava.org/docs/api14/org/biojava/bio/symbol/BasisSymbol.html)
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[BasisSymbol](http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/BasisSymbol.html)
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follow this
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[link](http://www.biojava.org/docs/api14/org/biojava/bio/symbol/BasisSymbol.html).
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[link](http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/BasisSymbol.html).
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<java> package biojava\_in\_anger;
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wiki/BioJava:Cookbook:Alphabets:Component.mediawiki

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== How do I break Symbols from CrossProductAlphabets into their component Symbols? ==
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[[Biojava:Cookbook:Alphabets:CrossProduct|CrossProductAlphabets]] are used to represent groups of [http://www.biojava.org/docs/api14/org/biojava/bio/symbol/Symbol.html Symbols] as a single Symbol. This is very useful for treating things like codons as single [http://www.biojava.org/docs/api14/org/biojava/bio/symbol/Symbol.html Symbols]. Sometimes however, you might want to covert the [http://www.biojava.org/docs/api14/org/biojava/bio/symbol/Symbol.html Symbols] back into their component [http://www.biojava.org/docs/api14/org/biojava/bio/symbol/Symbol.html Symbols]. The following recipe demonstrates how this can be done.
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[[Biojava:Cookbook:Alphabets:CrossProduct|CrossProductAlphabets]] are used to represent groups of [http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/Symbol.html Symbols] as a single Symbol. This is very useful for treating things like codons as single [http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/Symbol.html Symbols]. Sometimes however, you might want to covert the [http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/Symbol.html Symbols] back into their component [http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/Symbol.html Symbols]. The following recipe demonstrates how this can be done.
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The [http://www.biojava.org/docs/api14/org/biojava/bio/symbol/Symbol.html Symbols] from a [[Biojava:Cookbook:Alphabets:CrossProduct|CrossProductAlphabet]] are implementations of the [http://www.biojava.org/docs/api14/org/biojava/bio/symbol/AtomicSymbol.html AtomicSymbol] interface. The prefix 'Atomic' suggests that the [http://www.biojava.org/docs/api14/org/biojava/bio/symbol/Symbol.html Symbols] cannot be divided so one might ask, 'how can an indivisible Symbol be divided into it's component parts?'. The full definition of the [http://www.biojava.org/docs/api14/org/biojava/bio/symbol/AtomicSymbol.html AtomicSymbol] is that it cannot be divided into a simpler Symbol that is still part of the same [http://www.biojava.org/docs/api14/org/biojava/bio/symbol/Alphabet.html Alphabet]. The component parts of an [http://www.biojava.org/docs/api14/org/biojava/bio/symbol/AtomicSymbol.html AtomicSymbol] from a [[Biojava:Cookbook:Alphabets:CrossProduct|CrossProductAlphabet]] are not members of the same [http://www.biojava.org/docs/api14/org/biojava/bio/symbol/Alphabet.html Alphabet] so the 'Atomic' definition still stands. A [[wp:codon|codon]] would be from the (DNA x DNA x DNA) Alphabet whereas the components of the [[wp:codon|codon]] [http://www.biojava.org/docs/api14/org/biojava/bio/symbol/Symbol.html Symbol] are from the DNA alphabet.
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The [http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/Symbol.html Symbols] from a [[Biojava:Cookbook:Alphabets:CrossProduct|CrossProductAlphabet]] are implementations of the [http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/AtomicSymbol.html AtomicSymbol] interface. The prefix 'Atomic' suggests that the [http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/Symbol.html Symbols] cannot be divided so one might ask, 'how can an indivisible Symbol be divided into it's component parts?'. The full definition of the [http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/AtomicSymbol.html AtomicSymbol] is that it cannot be divided into a simpler Symbol that is still part of the same [http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/Alphabet.html Alphabet]. The component parts of an [http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/AtomicSymbol.html AtomicSymbol] from a [[Biojava:Cookbook:Alphabets:CrossProduct|CrossProductAlphabet]] are not members of the same [http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/Alphabet.html Alphabet] so the 'Atomic' definition still stands. A [[wp:codon|codon]] would be from the (DNA x DNA x DNA) Alphabet whereas the components of the [[wp:codon|codon]] [http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/Symbol.html Symbol] are from the DNA alphabet.
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Contrast this with the definition of a [http://www.biojava.org/docs/api14/org/biojava/bio/symbol/BasisSymbol.html BasisSymbol]. A [http://www.biojava.org/docs/api14/org/biojava/bio/symbol/BasisSymbol.html BasisSymbol] can be validly divided into components that are still part of the same [http://www.biojava.org/docs/api14/org/biojava/bio/symbol/Alphabet.html Alphabet]. In this way a [http://www.biojava.org/docs/api14/org/biojava/bio/symbol/BasisSymbol.html BasisSymbol] can be ambiguous. For further discussion of [http://www.biojava.org/docs/api14/org/biojava/bio/symbol/BasisSymbol.html BasisSymbol] follow this [http://www.biojava.org/docs/api14/org/biojava/bio/symbol/BasisSymbol.html link].
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Contrast this with the definition of a [http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/BasisSymbol.html BasisSymbol]. A [http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/BasisSymbol.html BasisSymbol] can be validly divided into components that are still part of the same [http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/Alphabet.html Alphabet]. In this way a [http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/BasisSymbol.html BasisSymbol] can be ambiguous. For further discussion of [http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/BasisSymbol.html BasisSymbol] follow this [http://www.biojava.org/docs/api1.8/org/biojava/bio/symbol/BasisSymbol.html link].
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<java>
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package biojava_in_anger;

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