+
+ public void setBackgroundFrequencies(Map<Character, Float> bkgdFreqs)
+ {
+ backgroundFrequencies = bkgdFreqs;
+ }
+
+ public void setBackgroundFrequencies(ResidueCount bkgdFreqs)
+ {
+ backgroundFrequencies = new HashMap<>();
+
+ int total = bkgdFreqs.getTotalResidueCount();
+
+ for (char c : bkgdFreqs.getSymbolCounts().symbols)
+ {
+ backgroundFrequencies.put(c, bkgdFreqs.getCount(c) * 1f / total);
+ }
+
+ }
+
+ public Map<Character, Float> getBackgroundFrequencies()
+ {
+ return backgroundFrequencies;
+ }