public class ORF extends Object implements Serializable
Constructor and Description |
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ORF(ArrayList<Codon> sequence)
Constructor of this gene.
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ORF(Codon[] sequence)
Constructor of this gene.
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ORF(String info,
ArrayList<Codon> sequence)
Constructor of this gene.
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ORF(String info,
CharSequence string)
Constructor of this gene where sequence is a DNA sequence without start and stop codons.
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ORF(TreeMap<Codon,Double> frequency)
Constructor of this gene.
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Modifier and Type | Method and Description |
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static ArrayList<ORF> |
decode(CharSequence string)
Factory method producing a list of genes from a specified DNA base sequence
of the letters A, C, G, T.
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static double |
entropy(ArrayList<ORF> orfs)
Returns the entropy of the frequency distribution of this gene.
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static String |
getFrequencyAsHTMLGraph(ArrayList<ORF> orfs)
Returns the frequency distribution of the codons in the specified list of ORF's as HTML graph.
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static String |
getFrequencyAsHTMLTable(ArrayList<ORF> genes)
Returns the frequency distribution of the codons in the specified list of genes as HTML table.
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String |
getInfo()
Returns the info of this ORF.
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ArrayList<Codon> |
getSequence()
Returns the codon sequence of this gene.
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static ArrayList<ORF> |
loadFASTA(boolean completeGenome)
Returns a genome after opening a file in FASTA format, determined by a file chooser dialog.
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static ArrayList<ORF> |
loadORFs()
Returns a genome after opening a file in GNOM format, found by a file chooser dialog.
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static void |
save(ArrayList<ORF> orfs)
Saves this genome in GENE format.
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String |
toString()
Returns a string representing this gene.
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public ORF(String info, CharSequence string)
info
- information about this ORFstring
- a DNA sequencepublic ORF(String info, ArrayList<Codon> sequence)
info
- information about this ORFsequence
- a sequence of codonspublic ORF(ArrayList<Codon> sequence)
sequence
- a sequence of codonspublic ORF(Codon[] sequence)
sequence
- a sequence of codonspublic String getInfo()
public ArrayList<Codon> getSequence()
public static String getFrequencyAsHTMLTable(ArrayList<ORF> genes)
genes
- a list of genespublic static String getFrequencyAsHTMLGraph(ArrayList<ORF> orfs)
orfs
- a list of ORF'spublic static double entropy(ArrayList<ORF> orfs)
orfs
- a list of ORF'spublic String toString()
public static ArrayList<ORF> decode(CharSequence string)
string
- DNA base sequencepublic static ArrayList<ORF> loadFASTA(boolean completeGenome)
completeGenome
- flag specifying whether the file represents a complete genomepublic static void save(ArrayList<ORF> orfs)
orfs
- a list of ORF's