Examples of EvaluationItem

Examples of org.lightforge.bioinformatics.alignment.dp.EvaluationItem

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  @SuppressWarnings({ "unchecked", "rawtypes" })
  private EvaluationItem[] buildEvalVectorSimpleGapPenalty(){
    EvaluationItem[] evalVector = new EvaluationItem[3];

    if (aboveAvailable()) evalVector[0] = new EvaluationItem(
        getAboveCell((Matrix2D)_context.get_matchMatrix()),
        getAboveScore(),
        CellPointerType.INS);
   
    if (leftAvailable()) evalVector[1] = new EvaluationItem(
        getLeftCell((Matrix2D)_context.get_matchMatrix()),
        getLeftScore(),
        CellPointerType.DEL);
   
    if (aboveLeftAvailable()) evalVector[2] = new EvaluationItem(
        getAboveLeftCell((Matrix2D)_context.get_matchMatrix()),
        getAboveLeftScore(),
        CellPointerType.MATCH);
   
    return evalVector;
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Examples of org.lightforge.bioinformatics.alignment.dp.EvaluationItem

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    SdpaCell matchCell = _context.get_matchMatrix().getCell(_row - 1, _column - 1);
    SdpaCell insCell = _context.get_insMatrix().getCell(_row - 1, _column - 1);
    SdpaCell delCell = _context.get_delMatrix().getCell(_row - 1, _column - 1);

    evalVector[0] = new EvaluationItem(
        matchCell,
        Numbers.boundedAddition(matchCell.get_score(), increment),
        CellPointerType.MATCH);
   
    evalVector[1] = new EvaluationItem(
        insCell,
        Numbers.boundedAddition(insCell.get_score(), increment),
        CellPointerType.MATCH);

    evalVector[2] = new EvaluationItem(
        delCell,
        Numbers.boundedAddition(delCell.get_score(), increment),
        CellPointerType.MATCH);

    return evalVector;
View Full Code Here

Examples of org.lightforge.bioinformatics.alignment.dp.EvaluationItem

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    EvaluationItem[] evalVector = new EvaluationItem[3];

    SdpaCell matchCell = _context.get_matchMatrix().getCell(_row - 1, _column);
    SdpaCell insCell = _context.get_insMatrix().getCell(_row - 1, _column);

    evalVector[0] = new EvaluationItem(
        matchCell,
        Numbers.boundedAddition(matchCell.get_score(), oValue),
        CellPointerType.INS);
   
    evalVector[1] = new EvaluationItem(
        insCell,
        Numbers.boundedAddition(insCell.get_score(), eValue),
        CellPointerType.INS);

    return evalVector;
View Full Code Here

Examples of org.lightforge.bioinformatics.alignment.dp.EvaluationItem

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    EvaluationItem[] evalVector = new EvaluationItem[3];

    SdpaCell matchCell = _context.get_matchMatrix().getCell(_row, _column - 1);
    SdpaCell delCell = _context.get_delMatrix().getCell(_row, _column - 1);

    evalVector[0] = new EvaluationItem(
        matchCell,
        Numbers.boundedAddition(matchCell.get_score(), oValue),
        CellPointerType.DEL);
   
    evalVector[1] = new EvaluationItem(
        delCell,
        Numbers.boundedAddition(delCell.get_score(), eValue),
        CellPointerType.DEL);

    return evalVector;
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