Package jmotifx

Examples of jmotifx.JMotifXSequenceFileReader

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        //  else,
        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")){
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        String centerResidue = configMap.get("centerResidue");
        AminoAcid[] aa = db.getAminoAcids();
        // to determine the number of random sequences to generate,
        // extract the number of input peptide sequences, and multiply by a factor of 10 [default];
        String inputPeptideSequenceFile = configMap.get("peptideSequenceFile");
        JMotifXSequenceFileReader fR = new JMotifXSequenceFileReader();
        int inputPeptides = fR.extractSequences(inputPeptideSequenceFile).size();
        int randoms = inputPeptides * 10;
        int preNPostCenterLength = peptideWindow/2;
        for(int i = 0 ; i < randoms; i++){
            String randomBlockSequence;
            //generate random
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    public ArrayList<String> extractInputPeptideSeqeunces(HashMap<String, String> configMap, Database db)
            throws FileNotFoundException, IOException {
        //throw new UnsupportedOperationException("Not yet implemented");
        ArrayList<String> inputPeptideSequences;
        String inputSequenceFile = configMap.get("peptideSequenceFile");
        JMotifXSequenceFileReader jmotifxR = new JMotifXSequenceFileReader();
        System.out.println(" MotifXPeptideSequenceExtractor: Reading sequences from file..." + new File(inputSequenceFile).getName());
        ArrayList<String> inseqs = jmotifxR.extractSequences(inputSequenceFile);
       
        //Extract block sequences....
        JMotifXBlockSequenceExtractor bseqExt = new JMotifXBlockSequenceExtractor();
        int peptideWindow = Integer.parseInt(configMap.get("peptideWindow"));
        String centerResidue = configMap.get("centerResidue");
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Related Classes of jmotifx.JMotifXSequenceFileReader

  • jmotifx.motifx.MotifXBackgroundExtractor
  • jmotifx.motifx.MotifXPeptideSequenceExtractor
  • jmotifx.preprocess.JMotifXBlockSequenceExtractor
  • java.io.FileReader
  • java.io.BufferedReader
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