public class DNA extends Object implements Serializable
java -ms1024m -mx1024m org.mathIT.genes.DNA
Constructor and Description |
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DNA(String name,
ArrayList<Character> sequence)
Constructor of this genome.
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DNA(String name,
char[] sequence)
Constructor of this genome.
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Modifier and Type | Method and Description |
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String |
asHTMLString()
Returns a string representing this genome, with line breaks encoded by
"
" instead of '\n'. |
static DNA |
encode(String name,
CharSequence string)
Factory method producing a genome from a specified DNA base sequence of
the letters A, C, G, T.
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double |
entropy()
Returns the entropy of the frequency distribution of this genome.
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TreeMap<Character,Integer> |
getFrequency()
Returns the frequency distribution of the 4 nucleobases.
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String |
getFrequencyAsHTMLGraph()
Returns the frequency distribution of the 64 codons as HTML graph.
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String |
getFrequencyAsHTMLTable()
Returns the frequency distribution of the 64 codons as HTML table.
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String |
getName()
Returns the name of this genome.
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StringBuilder |
getSequence()
Returns the nucleobase sequence of this genome.
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ArrayList<Character> |
getSequenceAsArrayList()
Returns the nucleobase sequence of this genome.
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static DNA |
loadDNA()
Returns a genome after opening a file in GNOM format, found by a file chooser dialog.
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static DNA |
loadFASTA()
Returns a genome after opening a file in FASTA format, determined by a file chooser dialog.
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double |
p(char b)
Returns the probability to obtain the specified nucleobase of this genome sequence.
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void |
save()
Saves this genome in gnom format.
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String |
toString()
Returns a string representing this genome.
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public DNA(String name, ArrayList<Character> sequence)
name
- the name of this genomesequence
- the sequence of nucleobasespublic DNA(String name, char[] sequence)
name
- the name of this genomesequence
- the sequence of nucleobasespublic String getName()
public StringBuilder getSequence()
public ArrayList<Character> getSequenceAsArrayList()
public TreeMap<Character,Integer> getFrequency()
public String getFrequencyAsHTMLTable()
public String getFrequencyAsHTMLGraph()
public double p(char b)
b
- the specified nucleobasepublic double entropy()
public String asHTMLString()
public String toString()
public static DNA encode(String name, CharSequence string)
name
- the name of the generated genomestring
- DNA base sequencepublic static DNA loadFASTA()
public void save()
public static DNA loadDNA()