public AminoAcidCompoundSet() { aminoAcidCompoundCache.put("A", new AminoAcidCompound(this, "A", "Ala", "Alanine", 71.0788f)); aminoAcidCompoundCache.put("R", new AminoAcidCompound(this, "R", "Arg", "Arginine", 156.1875f)); aminoAcidCompoundCache.put("N", new AminoAcidCompound(this, "N", "Asn", "Asparagine", 114.1039f)); aminoAcidCompoundCache.put("D", new AminoAcidCompound(this, "D", "Asp", "Aspartic acid", 115.0886f)); aminoAcidCompoundCache.put("C", new AminoAcidCompound(this, "C", "Cys", "Cysteine", 103.1388f)); aminoAcidCompoundCache.put("E", new AminoAcidCompound(this, "E", "Glu", "Glutamic acid", 129.1155f)); aminoAcidCompoundCache.put("Q", new AminoAcidCompound(this, "Q", "Gln", "Glutamine", 128.1307f)); aminoAcidCompoundCache.put("G", new AminoAcidCompound(this, "G", "Gly", "Glycine", 57.0519f)); aminoAcidCompoundCache.put("H", new AminoAcidCompound(this, "H", "His", "Histidine", 137.1411f)); aminoAcidCompoundCache.put("I", new AminoAcidCompound(this, "I", "Ile", "Isoleucine", 113.1594f)); aminoAcidCompoundCache.put("L", new AminoAcidCompound(this, "L", "Leu", "Leucine", 113.1594f)); aminoAcidCompoundCache.put("K", new AminoAcidCompound(this, "K", "Lys", "Lysine", 128.1741f)); aminoAcidCompoundCache.put("M", new AminoAcidCompound(this, "M", "Met", "Methionine", 131.1986f)); aminoAcidCompoundCache.put("F", new AminoAcidCompound(this, "F", "Phe", "Phenylalanine", 147.1766f)); aminoAcidCompoundCache.put("P", new AminoAcidCompound(this, "P", "Pro", "Proline", 97.1167f)); aminoAcidCompoundCache.put("S", new AminoAcidCompound(this, "S", "Ser", "Serine", 87.0782f)); aminoAcidCompoundCache.put("T", new AminoAcidCompound(this, "T", "Thr", "Threonine", 101.1051f)); aminoAcidCompoundCache.put("W", new AminoAcidCompound(this, "W", "Trp", "Tryptophan", 186.2132f)); aminoAcidCompoundCache.put("Y", new AminoAcidCompound(this, "Y", "Tyr", "Tyrosine", 163.1760f)); aminoAcidCompoundCache.put("V", new AminoAcidCompound(this, "V", "Val", "Valine", 99.1326f)); aminoAcidCompoundCache.put("B", new AminoAcidCompound(this, "B", "Asx", "Asparagine or Aspartic acid", null)); aminoAcidCompoundCache.put("Z", new AminoAcidCompound(this, "Z", "Glx", "Glutamine or Glutamic acid", null)); aminoAcidCompoundCache.put("J", new AminoAcidCompound(this, "J", "Xle", "Leucine or Isoleucine", null)); aminoAcidCompoundCache.put("X", new AminoAcidCompound(this, "X", "Xaa", "Unspecified", null)); aminoAcidCompoundCache.put("-", new AminoAcidCompound(this, "-", "---", "Unspecified", null)); aminoAcidCompoundCache.put(".", new AminoAcidCompound(this, ".", "...", "Unspecified", null)); aminoAcidCompoundCache.put("_", new AminoAcidCompound(this, "_", "___", "Unspecified", null)); aminoAcidCompoundCache.put("*", new AminoAcidCompound(this, "*", "***", "Stop", null));
public CaseFreeAminoAcidCompoundSet() { aminoAcidCompoundCache.put("A", new AminoAcidCompound(null, "A", "Ala", "Alanine", 71.0788f)); aminoAcidCompoundCache.put("R", new AminoAcidCompound(null, "R", "Arg", "Arginine", 156.1875f)); aminoAcidCompoundCache.put("N", new AminoAcidCompound(null, "N", "Asn", "Asparagine", 114.1039f)); aminoAcidCompoundCache.put("D", new AminoAcidCompound(null, "D", "Asp", "Aspartic acid", 115.0886f)); aminoAcidCompoundCache.put("C", new AminoAcidCompound(null, "C", "Cys", "Cysteine", 103.1388f)); aminoAcidCompoundCache.put("E", new AminoAcidCompound(null, "E", "Glu", "Glutamic acid", 129.1155f)); aminoAcidCompoundCache.put("Q", new AminoAcidCompound(null, "Q", "Gln", "Glutamine", 128.1307f)); aminoAcidCompoundCache.put("G", new AminoAcidCompound(null, "G", "Gly", "Glycine", 57.0519f)); aminoAcidCompoundCache.put("H", new AminoAcidCompound(null, "H", "His", "Histidine", 137.1411f)); aminoAcidCompoundCache.put("I", new AminoAcidCompound(null, "I", "Ile", "Isoleucine", 113.1594f)); aminoAcidCompoundCache.put("L", new AminoAcidCompound(null, "L", "Leu", "Leucine", 113.1594f)); aminoAcidCompoundCache.put("K", new AminoAcidCompound(null, "K", "Lys", "Lysine", 128.1741f)); aminoAcidCompoundCache.put("M", new AminoAcidCompound(null, "M", "Met", "Methionine", 131.1986f)); aminoAcidCompoundCache.put("F", new AminoAcidCompound(null, "F", "Phe", "Phenylalanine", 147.1766f)); aminoAcidCompoundCache.put("P", new AminoAcidCompound(null, "P", "Pro", "Proline", 97.1167f)); aminoAcidCompoundCache.put("S", new AminoAcidCompound(null, "S", "Ser", "Serine", 87.0782f)); aminoAcidCompoundCache.put("T", new AminoAcidCompound(null, "T", "Thr", "Threonine", 101.1051f)); aminoAcidCompoundCache.put("W", new AminoAcidCompound(null, "W", "Trp", "Tryptophan", 186.2132f)); aminoAcidCompoundCache.put("Y", new AminoAcidCompound(null, "Y", "Tyr", "Tyrosine", 163.1760f)); aminoAcidCompoundCache.put("V", new AminoAcidCompound(null, "V", "Val", "Valine", 99.1326f)); aminoAcidCompoundCache.put("B", new AminoAcidCompound(null, "B", "Asx", "Asparagine or Aspartic acid", null)); aminoAcidCompoundCache.put("Z", new AminoAcidCompound(null, "Z", "Glx", "Glutamine or Glutamic acid", null)); aminoAcidCompoundCache.put("J", new AminoAcidCompound(null, "J", "Xle", "Leucine or Isoleucine", null)); aminoAcidCompoundCache.put("X", new AminoAcidCompound(null, "X", "Xaa", "Unspecified", null)); aminoAcidCompoundCache.put("-", new AminoAcidCompound(null, "-", "---", "Unspecified", null)); aminoAcidCompoundCache.put(".", new AminoAcidCompound(null, ".", "...", "Unspecified", null)); aminoAcidCompoundCache.put("_", new AminoAcidCompound(null, "_", "___", "Unspecified", null)); aminoAcidCompoundCache.put("*", new AminoAcidCompound(null, "*", "***", "Stop", null));
public AminoAcidCompoundSet() { aminoAcidCompoundCache.put("A", new AminoAcidCompound(this, "A", "Ala", "Alanine", 71.0788f)); aminoAcidCompoundCache.put("R", new AminoAcidCompound(this, "R", "Arg", "Arginine", 156.1875f)); aminoAcidCompoundCache.put("N", new AminoAcidCompound(this, "N", "Asn", "Asparagine", 114.1039f)); aminoAcidCompoundCache.put("D", new AminoAcidCompound(this, "D", "Asp", "Aspartic acid", 115.0886f)); aminoAcidCompoundCache.put("C", new AminoAcidCompound(this, "C", "Cys", "Cysteine", 103.1388f)); aminoAcidCompoundCache.put("E", new AminoAcidCompound(this, "E", "Glu", "Glutamic acid", 129.1155f)); aminoAcidCompoundCache.put("Q", new AminoAcidCompound(this, "Q", "Gln", "Glutamine", 128.1307f)); aminoAcidCompoundCache.put("G", new AminoAcidCompound(this, "G", "Gly", "Glycine", 57.0519f)); aminoAcidCompoundCache.put("H", new AminoAcidCompound(this, "H", "His", "Histidine", 137.1411f)); aminoAcidCompoundCache.put("I", new AminoAcidCompound(this, "I", "Ile", "Isoleucine", 113.1594f)); aminoAcidCompoundCache.put("L", new AminoAcidCompound(this, "L", "Leu", "Leucine", 113.1594f)); aminoAcidCompoundCache.put("K", new AminoAcidCompound(this, "K", "Lys", "Lysine", 128.1741f)); aminoAcidCompoundCache.put("M", new AminoAcidCompound(this, "M", "Met", "Methionine", 131.1986f)); aminoAcidCompoundCache.put("F", new AminoAcidCompound(this, "F", "Phe", "Phenylalanine", 147.1766f)); aminoAcidCompoundCache.put("P", new AminoAcidCompound(this, "P", "Pro", "Proline", 97.1167f)); aminoAcidCompoundCache.put("S", new AminoAcidCompound(this, "S", "Ser", "Serine", 87.0782f)); aminoAcidCompoundCache.put("T", new AminoAcidCompound(this, "T", "Thr", "Threonine", 101.1051f)); aminoAcidCompoundCache.put("W", new AminoAcidCompound(this, "W", "Trp", "Tryptophan", 186.2132f)); aminoAcidCompoundCache.put("Y", new AminoAcidCompound(this, "Y", "Tyr", "Tyrosine", 163.1760f)); aminoAcidCompoundCache.put("V", new AminoAcidCompound(this, "V", "Val", "Valine", 99.1326f)); aminoAcidCompoundCache.put("B", new AminoAcidCompound(this, "B", "Asx", "Asparagine or Aspartic acid", null)); aminoAcidCompoundCache.put("Z", new AminoAcidCompound(this, "Z", "Glx", "Glutamine or Glutamic acid", null)); aminoAcidCompoundCache.put("J", new AminoAcidCompound(this, "J", "Xle", "Leucine or Isoleucine", null)); aminoAcidCompoundCache.put("X", new AminoAcidCompound(this, "X", "Xaa", "Unspecified", null)); aminoAcidCompoundCache.put("-", new AminoAcidCompound(this, "-", "---", "Unspecified", null)); aminoAcidCompoundCache.put(".", new AminoAcidCompound(this, ".", "...", "Unspecified", null)); aminoAcidCompoundCache.put("_", new AminoAcidCompound(this, "_", "___", "Unspecified", null)); aminoAcidCompoundCache.put("*", new AminoAcidCompound(this, "*", "***", "Stop", null));
public ModifiedAminoAcidCompoundSet(List<AminoAcidComposition> aaList, Map<Character, Double> aaSymbol2MolecularWeight) { this.aminoAcidCompoundCache.put("-", new AminoAcidCompound(null, "-", "", "", 0.0f)); for (AminoAcidComposition aa : aaList) { this.aminoAcidCompoundCache.put(aa.getSymbol(), new AminoAcidCompound(null, aa.getSymbol(), aa.getShorName(), aa.getName(), aaSymbol2MolecularWeight.get(aa.getSymbol().charAt(0)).floatValue())); } }