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java.lang.Objectorg.biojava.bio.seq.ProteinTools
The central port-of-call for all information and functionality specific to SymbolLists over the protein alphabet.
Constructor Summary | |
ProteinTools()
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Method Summary | |
static GappedSequence |
createGappedProteinSequence(java.lang.String theProtein,
java.lang.String name)
Get a new protein as a GappedSequence |
static SymbolList |
createProtein(java.lang.String theProtein)
Return a new Protein SymbolList for protein. |
static Sequence |
createProteinSequence(java.lang.String protein,
java.lang.String name)
Return a new PROTEIN Sequence for protein. |
static FiniteAlphabet |
getAlphabet()
Gets the protein alphabet |
static SymbolPropertyTable |
getSymbolPropertyTable(java.lang.String name)
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static FiniteAlphabet |
getTAlphabet()
Gets the protein alphabet including the translation termination symbols |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
public ProteinTools()
Method Detail |
public static final FiniteAlphabet getAlphabet()
public static final FiniteAlphabet getTAlphabet()
public static final SymbolPropertyTable getSymbolPropertyTable(java.lang.String name)
public static SymbolList createProtein(java.lang.String theProtein) throws IllegalSymbolException
theProtein
- a String to parse into Protein
IllegalSymbolException
- if dna contains
any non-Amino Acid characters.public static GappedSequence createGappedProteinSequence(java.lang.String theProtein, java.lang.String name) throws IllegalSymbolException
IllegalSymbolException
public static Sequence createProteinSequence(java.lang.String protein, java.lang.String name) throws IllegalSymbolException
protein
- a String to parse into PROTEINname
- a String to use as the name
IllegalSymbolException
- if protein contains
any non-PROTEIN characters
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