Examples of bgu.bio.algorithms.alignment.EditDistance.printAlignments()

Class bgu.bio.algorithms.alignment.EditDistance

Examples of bgu.bio.algorithms.alignment.EditDistance.printAlignments()

bgu.bio.algorithms.alignment.EditDistance.printAlignments()
Output the local alignments ending in the (i, j) cell. aligned1 and aligned2 are suffixes of final aligned strings found in backtracking before calling this function. Note: the strings are replicated at each recursive call. Use buffers or stacks to improve efficiency.

        if (str1 == null || str2 == null)
          return error("got no strings");


        ed.buildMatrix();
        int score = (int) ed.getAlignmentScore();
        String[] res = ed.printAlignments();


        result.put("command", "OK");
        result.put("score", score);
        result.put("line1", res[0]);
        result.put("middle", res[1]);

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    string2 = string2 == null ? "" : string2;
    EditDistance ed = new EditDistance(string1, string2,
        new IdentityEditDistanceScoringMatrix());


    int score = (int) ed.getAlignmentScore();
    String[] res = ed.printAlignments();
    response.setResponse(Arrays.toString(res));
    return response;
  }
}

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