public static final int[] purinepyrimidineIndex;
- public static final Map<String, Integer> aa3Hash = new HashMap<String, Integer>();
+ public static final Map<String, Integer> aa3Hash = new HashMap<>();
- public static final Map<String, String> aa2Triplet = new HashMap<String, String>();
+ public static final Map<String, String> aa2Triplet = new HashMap<>();
- public static final Map<String, String> nucleotideName = new HashMap<String, String>();
+ public static final Map<String, String> nucleotideName = new HashMap<>();
// lookup from modified amino acid (e.g. MSE) to canonical form (e.g. MET)
- public static final Map<String, String> modifications = new HashMap<String, String>();
+ public static final Map<String, String> modifications = new HashMap<>();
+
+ // amino acid background Frequencies
+ public static final Map<Character, Float> aminoBackgroundFrequencies = new HashMap<>();
+
+ // nucleotide background Frequencies
+ public static final Map<Character, Float> nucleotideBackgroundFrequencies = new HashMap<>();
static
{
/**
* Nucleotide Ambiguity Codes
*/
- public static final Map<String, String[]> ambiguityCodes = new Hashtable<String, String[]>();
+ public static final Map<String, String[]> ambiguityCodes = new Hashtable<>();
/**
* Codon triplets with additional symbols for unambiguous codons that include
* ambiguity codes
*/
- public static final Hashtable<String, String> codonHash2 = new Hashtable<String, String>();
+ public static final Hashtable<String, String> codonHash2 = new Hashtable<>();
/**
* all ambiguity codes for a given base
*/
- public final static Hashtable<String, List<String>> _ambiguityCodes = new Hashtable<String, List<String>>();
+ public final static Hashtable<String, List<String>> _ambiguityCodes = new Hashtable<>();
static
{
List<String> codesfor = _ambiguityCodes.get(r);
if (codesfor == null)
{
- _ambiguityCodes.put(r, codesfor = new ArrayList<String>());
+ _ambiguityCodes.put(r, codesfor = new ArrayList<>());
}
if (!codesfor.contains(acode.getKey()))
{
}
// Stores residue codes/names and colours and other things
- public static Map<String, Map<String, Integer>> propHash = new Hashtable<String, Map<String, Integer>>();
+ public static Map<String, Map<String, Integer>> propHash = new Hashtable<>();
- public static Map<String, Integer> hydrophobic = new Hashtable<String, Integer>();
+ public static Map<String, Integer> hydrophobic = new Hashtable<>();
- public static Map<String, Integer> polar = new Hashtable<String, Integer>();
+ public static Map<String, Integer> polar = new Hashtable<>();
- public static Map<String, Integer> small = new Hashtable<String, Integer>();
+ public static Map<String, Integer> small = new Hashtable<>();
- public static Map<String, Integer> positive = new Hashtable<String, Integer>();
+ public static Map<String, Integer> positive = new Hashtable<>();
- public static Map<String, Integer> negative = new Hashtable<String, Integer>();
+ public static Map<String, Integer> negative = new Hashtable<>();
- public static Map<String, Integer> charged = new Hashtable<String, Integer>();
+ public static Map<String, Integer> charged = new Hashtable<>();
- public static Map<String, Integer> aromatic = new Hashtable<String, Integer>();
+ public static Map<String, Integer> aromatic = new Hashtable<>();
- public static Map<String, Integer> aliphatic = new Hashtable<String, Integer>();
+ public static Map<String, Integer> aliphatic = new Hashtable<>();
- public static Map<String, Integer> tiny = new Hashtable<String, Integer>();
+ public static Map<String, Integer> tiny = new Hashtable<>();
- public static Map<String, Integer> proline = new Hashtable<String, Integer>();
+ public static Map<String, Integer> proline = new Hashtable<>();
static
{
public static Hashtable<String, String> toDssp3State;
static
{
- toDssp3State = new Hashtable<String, String>();
+ toDssp3State = new Hashtable<>();
toDssp3State.put("H", "H");
toDssp3State.put("E", "E");
toDssp3State.put("C", " ");
}
+ static
+ {
+ aminoBackgroundFrequencies.put('A', 0.0826f);
+ aminoBackgroundFrequencies.put('Q', 0.0393f);
+ aminoBackgroundFrequencies.put('L', 0.0965f);
+ aminoBackgroundFrequencies.put('S', 0.0661f);
+ aminoBackgroundFrequencies.put('R', 0.0553f);
+ aminoBackgroundFrequencies.put('E', 0.0674f);
+ aminoBackgroundFrequencies.put('K', 0.0582f);
+ aminoBackgroundFrequencies.put('T', 0.0535f);
+ aminoBackgroundFrequencies.put('N', 0.0406f);
+ aminoBackgroundFrequencies.put('G', 0.0708f);
+ aminoBackgroundFrequencies.put('M', 0.0241f);
+ aminoBackgroundFrequencies.put('W', 0.0109f);
+ aminoBackgroundFrequencies.put('D', 0.0546f);
+ aminoBackgroundFrequencies.put('H', 0.0227f);
+ aminoBackgroundFrequencies.put('F', 0.0386f);
+ aminoBackgroundFrequencies.put('Y', 0.0292f);
+ aminoBackgroundFrequencies.put('C', 0.0137f);
+ aminoBackgroundFrequencies.put('I', 0.0593f);
+ aminoBackgroundFrequencies.put('P', 0.0472f);
+ aminoBackgroundFrequencies.put('V', 0.0686f);
+
+ }
+
+ static
+ {
+ nucleotideBackgroundFrequencies.put('A', 0.25f);
+ nucleotideBackgroundFrequencies.put('C', 0.25f);
+ nucleotideBackgroundFrequencies.put('T', 0.25f);
+ nucleotideBackgroundFrequencies.put('G', 0.25f);
+
+ }
+
public static String getCanonicalAminoAcid(String aA)
{
String canonical = modifications.get(aA);
// / cut here
public static void main(String[] args)
{
- Hashtable<String, Vector<String>> aaProps = new Hashtable<String, Vector<String>>();
+ Hashtable<String, Vector<String>> aaProps = new Hashtable<>();
System.out.println("my %aa = {");
// invert property hashes
for (String pname : propHash.keySet())
Vector<String> aprops = aaProps.get(rname);
if (aprops == null)
{
- aprops = new Vector<String>();
+ aprops = new Vector<>();
aaProps.put(rname, aprops);
}
Integer hasprop = phash.get(rname);
public static List<String> getResidues(boolean forNucleotide,
boolean includeAmbiguous)
{
- List<String> result = new ArrayList<String>();
+ List<String> result = new ArrayList<>();
if (forNucleotide)
{
for (String nuc : nucleotideName.keySet())