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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3250 348d0f76-0448-11de-a6fe-93d51630548a

This commit is contained in:
weisburd 2010-04-23 15:50:09 +00:00
parent 10bcd72593
commit 9e28e4eb42
1 changed files with 35 additions and 70 deletions
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105
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/AminoAcidTable.java
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@ -8,35 +8,34 @@ import java.util.HashMap;
*/
public class AminoAcidTable {
protected static HashMap<String, String[]> aminoAcidTable = new HashMap<String, String[]>();
protected static HashMap<String, String[]> mtAminoAcidTable = new HashMap<String, String[]>(); //mitochondrial
protected static final String[] ISOLEUCINE = new String[] {"I" , "Isoleucine", "Ile"};
protected static final String[] LEUCINE = new String[] {"L" , "Leucine", "Leu"};
protected static final AminoAcid ISOLEUCINE = new AminoAcid("I" , "Isoleucine", "Ile");
protected static final AminoAcid LEUCINE = new AminoAcid("L" , "Leucine", "Leu");
protected static final AminoAcid VALINE = new AminoAcid("V" , "Valine", "Val");
protected static final AminoAcid PHENYLALANINE = new AminoAcid("F" , "Phenylalanine", "Phe");
protected static final AminoAcid METHIONINE = new AminoAcid("M" , "Methionine", "Met");
protected static final AminoAcid CYSTEINE = new AminoAcid("C" , "Cysteine", "Cys");
protected static final AminoAcid ALANINE = new AminoAcid("A" , "Alanine", "Ala");
protected static final AminoAcid STOP_CODON = new AminoAcid("*" , "Stop Codon", "Amb");
protected static final AminoAcid GLYCINE = new AminoAcid("G" , "Glycine", "Gly");
protected static final AminoAcid PROLINE = new AminoAcid("P" , "Proline", "Pro");
protected static final AminoAcid THEONINE = new AminoAcid("T" , "Threonine", "Thr");
protected static final AminoAcid SERINE = new AminoAcid("S" , "Serine", "Ser");
protected static final AminoAcid TYROSINE = new AminoAcid("Y" , "Tyrosine", "Tyr");
protected static final AminoAcid TRYPTOPHAN = new AminoAcid("W" , "Tryptophan", "Trp");
protected static final AminoAcid GLUTAMINE = new AminoAcid("Q" , "Glutamine", "Gln");
protected static final AminoAcid ASPARAGINE = new AminoAcid("N" , "Asparagine", "Asn");
protected static final AminoAcid HISTIDINE = new AminoAcid("H" , "Histidine", "His");
protected static final AminoAcid GLUTAMIC_ACID = new AminoAcid("E" , "Glutamic acid", "Glu");
protected static final AminoAcid ASPARTIC_ACID = new AminoAcid("D" , "Aspartic acid", "Asp");
protected static final AminoAcid LYSINE = new AminoAcid("K" , "Lysine", "Lys");
protected static final AminoAcid ARGININE = new AminoAcid("R" , "Arginine", "Arg");
protected static final String[] VALINE = new String[] {"V" , "Valine", "Val"};
protected static final String[] PHENYLALANINE = new String[] {"F" , "Phenylalanine", "Phe"};
protected static final String[] METHIONINE = new String[] {"M" , "Methionine", "Met"};
protected static final String[] CYSTEINE = new String[] {"C" , "Cysteine", "Cys"};
protected static final String[] ALANINE = new String[] {"A" , "Alanine", "Ala"};
protected static final String[] STOP_CODON = new String[] {"*" , "Stop Codon", "Amb"};
protected static final String[] GLYCINE = new String[] {"G" , "Glycine", "Gly"};
protected static final String[] PROLINE = new String[] {"P" , "Proline", "Pro"};
protected static final String[] THEONINE = new String[] {"T" , "Threonine", "Thr"};
protected static final String[] SERINE = new String[] {"S" , "Serine", "Ser"};
protected static final String[] TYROSINE = new String[] {"Y" , "Tyrosine", "Tyr"};
protected static final String[] TRYPTOPHAN = new String[] {"W" , "Tryptophan", "Trp"};
protected static final String[] GLUTAMINE = new String[] {"Q" , "Glutamine", "Gln"};
protected static final String[] ASPARAGINE = new String[] {"N" , "Asparagine", "Asn"};
protected static final String[] HISTIDINE = new String[] {"H" , "Histidine", "His"};
protected static final String[] GLUTAMIC_ACID = new String[] {"E" , "Glutamic acid", "Glu"};
protected static final String[] ASPARTIC_ACID = new String[] {"D" , "Aspartic acid", "Asp"};
protected static final String[] LYSINE = new String[] {"K" , "Lysine", "Lys"};
protected static final String[] ARGININE = new String[] {"R" , "Arginine", "Arg"};
protected static HashMap<String, AminoAcid> aminoAcidTable = new HashMap<String, AminoAcid>();
protected static HashMap<String, AminoAcid> mitochondrialAminoAcidTable = new HashMap<String, AminoAcid>();
static {
//code gotten from: http://algoart.com/aatable.htm
//populate the tables
aminoAcidTable.put("ATT", ISOLEUCINE);
aminoAcidTable.put("ATC", ISOLEUCINE);
aminoAcidTable.put("ATA", ISOLEUCINE);
@ -145,65 +144,31 @@ public class AminoAcidTable {
aminoAcidTable.put("TGA", STOP_CODON);
//populate the mitochondrial ammino-acid table:
mtAminoAcidTable.putAll(aminoAcidTable);
mtAminoAcidTable.put("AGA", STOP_CODON);
mtAminoAcidTable.put("AGG", STOP_CODON);
mtAminoAcidTable.put("ATA", METHIONINE);
mtAminoAcidTable.put("TGA", TRYPTOPHAN);
//populate the mitochondrial AA table
mitochondrialAminoAcidTable.putAll(aminoAcidTable);
mitochondrialAminoAcidTable.put("AGA", STOP_CODON);
mitochondrialAminoAcidTable.put("AGG", STOP_CODON);
mitochondrialAminoAcidTable.put("ATA", METHIONINE);
mitochondrialAminoAcidTable.put("TGA", TRYPTOPHAN);
}
/**
* Returns the 1-letter code for the matching amino acid.
* Returns the the matching amino acid.
*
* @param codon The 3-letter mRNA nucleotide codon 5' to 3'. Expects T's instead of U's. Not case sensitive.
* @param mitochondrial Whether this is from a mitochondrial gene (mitochondria have a slightly different codon table).
*
* @return The 1 letter code of the amino acid.
* @return The amino acid matching the given codon.
*/
public static String getAA1LetterCode(String codon, boolean mitochondrial) {
public static AminoAcid getAA(String codon, boolean mitochondrial) {
codon = codon.toUpperCase();
if(!aminoAcidTable.containsKey(codon)) {
throw new IllegalArgumentException("Invalid codon: " + codon);
}
return aminoAcidTable.get(codon)[0];
}
/**
* Returns the 3-letter code for the matching amino acid.
*
* @param codon The 3-letter mRNA nucleotide codon 5' to 3'. Expects T's instead of U's. Not case sensitive.
* @param mitochondrial Whether this is from a mitochondrial gene (mitochondria have a slightly different codon table).
*
* @return The 3 letter code of the amino acid.
*/
public static String getAA3LetterCode(String codon, boolean mitochondrial) {
codon = codon.toUpperCase();
if(!aminoAcidTable.containsKey(codon)) {
throw new IllegalArgumentException("Invalid codon: " + codon);
}
return aminoAcidTable.get(codon)[2];
}
/**
* Returns the full name of the matching amino acid.
*
* @param codon The 3-letter mRNA nucleotide codon 5' to 3'. Expects T's instead of U's. Not case sensitive.
* @param mitochondrial Whether this is from a mitochondrial gene (mitochondria have a slightly different codon table).
*
* @return The full name of the amino acid.
*/
public static String getAAName(String codon, boolean mitochondrial) {
codon = codon.toUpperCase();
if(!aminoAcidTable.containsKey(codon)) {
throw new IllegalArgumentException("Invalid codon: " + codon);
}
return aminoAcidTable.get(codon)[1];
return aminoAcidTable.get(codon);
}
}