JMotifXBlockSequenceExtractor jmxBSXr = new JMotifXBlockSequenceExtractor();
String backgroundType = configMap.get("backgroundType");
if(backgroundType.equalsIgnoreCase("input")){
inputBackgroundFile = configMap.get("backgroudSequenceFile");
JMotifXSequenceFileReader jmotifxR = new JMotifXSequenceFileReader();
ArrayList<String> inputBGSeqs = jmotifxR.extractSequences(inputBackgroundFile);
// preprocess input background sequence if not already done...
// preprocessing at this stage involves, extracting a block sequence of the inputted sequence,
// presupposing the inputed peptide sequences are of variable lengths.
blockInputBGSeqs = jmxBSXr.extractBlockSequence(inputBGSeqs, configMap, db);
} else if(backgroundType.equalsIgnoreCase("database")){