IMPACT_S

Class SequenceTranslator

java.lang.Object

IMPACT_S.SequenceTranslator

public class SequenceTranslator
extends java.lang.Object

Translate sequences from DNA or RNA into Protein, allowing choice of a specific translation table and start site. Translation Tables information from NCBI (as is in Oct 2011):
http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG23

Author:

Emanuel Maldonado

See Also:

GUIProtToSwissModel, FileFormat, FileFormatConverter

Constructor Summary

Constructors

Constructor and Description
SequenceTranslator(FileFormatConverter ffc, boolean dna) Initialize sequence translator.

Method Summary

Modifier and Type	Method and Description
java.lang.String	getAA(java.lang.String codon) Get matching AA for given codon.
java.lang.String[]	getAAList(boolean longn) Get list of all AminoAcids names, by the standard table.
java.util.HashMap<java.lang.String,java.lang.String>	getAANamesMap(boolean shlong) Get Amino-Acid names table.
java.lang.String	getSequence(int selectedindex) Get sequence from list of sequences.
void	setUseTranslationTable(int table, boolean fordna) Choose translation table to use. Standard table is initialized by default.
java.lang.String	translateSequence(int startsite, int selsequence, boolean keepGaps) Translate a DNA/RNA sequence into Protein.
java.lang.String	translateSequence(int startsite, java.lang.String sequence, boolean keepGaps) Translate a DNA/RNA sequence into Protein.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SequenceTranslator

public SequenceTranslator(FileFormatConverter ffc,
                          boolean dna)

Initialize sequence translator.

Parameters:

ffc - file format converter containing MSA data.

dna - tell to use table for dna (if true), or rna (if false).

Method Detail

getAANamesMap

public java.util.HashMap<java.lang.String,java.lang.String> getAANamesMap(boolean shlong)

Get Amino-Acid names table. Either with long names (3-letter code) or short names (1-letter code), mapped conversely.

Parameters:

shlong - choose either from short or long names.

Returns:

table of AA names.

getAAList

public java.lang.String[] getAAList(boolean longn)

Get list of all AminoAcids names, by the standard table.

Parameters:

longn - if true return the longs names(3 letters); otherwise, only the symbol letter.

Returns:

list of names either long or short.

getAA

public java.lang.String getAA(java.lang.String codon)

Get matching AA for given codon. The codon can be rna or dna, depending on whether how the constructor was initialized.

Parameters:

codon - the codon having a corresponding AA.

Returns:

the AA for the given codon; or null if does not exist.

setUseTranslationTable

public void setUseTranslationTable(int table,
                                   boolean fordna)

Choose translation table to use.
Standard table is initialized by default.

 Existing tables: 1(standard),2,3,4,5,6,9,10,11,12,13,14,15,16,21,22,23
    Table choice: 0          ,1,2,3,4,5,6,7 ,8 ,9 ,10,11,12,13,14,15,16
 

Table information was taken from NCBI, in http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes#SG23

Parameters:

table - which table. See Table choice.

fordna - tell to use table for dna (if true), or rna (if false).

getSequence

public java.lang.String getSequence(int selectedindex)

Get sequence from list of sequences.

Parameters:

selectedindex - the index matching the sequence.

Returns:

sequence.

translateSequence

public java.lang.String translateSequence(int startsite,
                                          int selsequence,
                                          boolean keepGaps)

Translate a DNA/RNA sequence into Protein.

Parameters:

startsite - select where to start translating.

selsequence - select sequence to translate.

keepGaps - whether or not to keeps gaps if they exist.

Returns:

the translated sequence.

translateSequence

public java.lang.String translateSequence(int startsite,
                                          java.lang.String sequence,
                                          boolean keepGaps)

Translate a DNA/RNA sequence into Protein.

Parameters:

startsite - select where to start translating.

sequence - the sequence to translate in one line.

keepGaps - whether or not to keeps gaps if they exist.

Returns:

the translated sequence.