Package org.lightforge.bioinformatics.alignment

Examples of org.lightforge.bioinformatics.alignment.Alignment

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  @Override
  protected void traceBackGlobal() {
    for (SdpaCell finalCell : getFinalCells()) {
      traceBackGlobal(finalCell,
          new Alignment(finalCell.get_score(), _alignmentType));
    }
  }
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    TreeMap<Long, Vector<SdpaCell>> treeMap = new TreeMap<Long, Vector<SdpaCell>>(_context.get_lookupTable());

    for (Long score : treeMap.descendingKeySet()) {
      for (Cell2D cell : treeMap.get(score)) {
        if (!((SdpaCell)cell).is_alreadyUsedInTraceBack()) {
          traceBackLocal(cell, new Alignment(cell.get_score(), _alignmentType));
        }
      }
    }
  }
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    }
  }

  @Override
  protected void traceBackGlobal(Cell2D originCell, Alignment parentAlignment) {
    Alignment alignment;

    if (((SdpaCell)originCell).initialCell()) {
      _alignments.add(parentAlignment);
    } else {

      for (CellPointer cp : originCell.get_pointers()){
        if (cp != null){
          alignment = parentAlignment.clone();

          switch (cp.get_type()) {
          case INS:
            alignment.addPrefix(_querySequence.charAt(originCell.get_row() -1), '-');
            alignment.set_startQueryPosition(originCell.get_row());   
            alignment.set_finalQueryPosition(originCell.get_row());   
            traceBack((SdpaCell)cp.get_cell(), alignment);
            break;
          case DEL:
            alignment.addPrefix('-', _targetSequence.charAt(originCell.get_column() -1));
            alignment.set_startTargetPosition(originCell.get_column());   
            alignment.set_finalTargetPosition(originCell.get_column());   
            traceBack((SdpaCell)cp.get_cell(), alignment);
            break;
          case MATCH:
            alignment.addPrefix(_querySequence.charAt(originCell.get_row() -1),
                _targetSequence.charAt(originCell.get_column() -1));
            alignment.set_startQueryPosition(originCell.get_row());   
            alignment.set_finalQueryPosition(originCell.get_row());   
            alignment.set_startTargetPosition(originCell.get_column());   
            alignment.set_finalTargetPosition(originCell.get_column());   
            traceBack((SdpaCell)cp.get_cell(), alignment);
            break;
          default:
            throw new CellPointerUnrecognizedTypeException(cp.get_type().toString());
          }
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    }
  }

  @Override
  protected void traceBackLocal(Cell2D originCell, Alignment parentAlignment) {
    Alignment alignment;
    boolean alreadyUsedInTraceBack = ((SdpaCell) originCell).is_alreadyUsedInTraceBack();
    ((SdpaCell) originCell).set_alreadyUsedInTraceBack(true);

    if ((((SdpaCell)originCell).initialCell() || alreadyUsedInTraceBack) && parentAlignment.is_open()) {
      parentAlignment.refine();
     
      if (_eValueParameters) parentAlignment.set_eValue(_lambda, _k, _querySequence.length(), _targetSequence.length());
     
      if ((parentAlignment.get_size() > _sizeThreshold) &&
          ((!parentAlignment.has_EValue())||
              ((parentAlignment.has_EValue()) && (parentAlignment.get_eValue() < _eValueThreshold)))) {

        _alignments.add(parentAlignment);
      }
     
      parentAlignment.set_open(false);
    } else {

      for (CellPointer cp : originCell.get_pointers()){
        if (cp != null) {
          alignment = parentAlignment.clone();

          switch (cp.get_type()) {
          case INS:
            alignment.addPrefix(_querySequence.charAt(originCell.get_row() -1), '-');
            alignment.set_startQueryPosition(originCell.get_row());   
            alignment.set_finalQueryPosition(originCell.get_row());   
            traceBack((SdpaCell)cp.get_cell(), alignment);
            break;
          case DEL:
            alignment.addPrefix('-', _targetSequence.charAt(originCell.get_column() -1));
            alignment.set_startTargetPosition(originCell.get_column());   
            alignment.set_finalTargetPosition(originCell.get_column());   
            traceBack((SdpaCell)cp.get_cell(), alignment);
            break;
          case MATCH:
            alignment.addPrefix(_querySequence.charAt(originCell.get_row() -1),
                _targetSequence.charAt(originCell.get_column() -1));
            alignment.set_startQueryPosition(originCell.get_row());   
            alignment.set_finalQueryPosition(originCell.get_row());   
            alignment.set_startTargetPosition(originCell.get_column());   
            alignment.set_finalTargetPosition(originCell.get_column());   
            traceBack((SdpaCell)cp.get_cell(), alignment);
            break;
          default:
            throw new CellPointerUnrecognizedTypeException(cp.get_type().toString());
          }

          parentAlignment.set_open(alignment.is_open());
        }     
      }
    }
  }
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Related Classes of org.lightforge.bioinformatics.alignment.Alignment

  • org.lightforge.bioinformatics.alignment.dp.sdpa.Sdpa
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