protected override Object getTraceback()
{
StringBuilder align1Buf = new StringBuilder();
StringBuilder align2Buf = new StringBuilder();
Cell currentCell = getTracebackStartingCell();
while (traceBackIsNotDone(currentCell))
{
if (currentCell.getRow() - currentCell.getPrevCell().getRow() == 1)
{
align2Buf.Insert(0, sequence2[currentCell.getRow() - 1]);
}
else
{
align2Buf.Insert(0, '-');
}
if (currentCell.getCol() - currentCell.getPrevCell().getCol() == 1)
{
align1Buf.Insert(0, sequence1[currentCell.getCol() - 1]);
}
else
{
align1Buf.Insert(0, '-');
}
currentCell = currentCell.getPrevCell();
}
String[] alignments = new String[]
{
align1Buf.ToString(),
align2Buf.ToString()
};
return(alignments);
}
protected override void fillInCell(Cell currentCell, Cell cellAbove, Cell cellToLeft,
Cell cellAboveLeft)
{
int rowSpaceScore = cellAbove.getScore() + space;
int colSpaceScore = cellToLeft.getScore() + space;
int matchOrMismatchScore = cellAboveLeft.getScore();
if (sequence2[currentCell.getRow() - 1] == sequence1[currentCell.getCol() - 1])
{
matchOrMismatchScore += match;
}
else
{
matchOrMismatchScore += mismatch;
}
if (rowSpaceScore >= colSpaceScore)
{
if (matchOrMismatchScore >= rowSpaceScore)
{
currentCell.setScore(matchOrMismatchScore);
currentCell.setPrevCell(cellAboveLeft);
}
else
{
currentCell.setScore(rowSpaceScore);
currentCell.setPrevCell(cellAbove);
}
}
else
{
if (matchOrMismatchScore >= colSpaceScore)
{
currentCell.setScore(matchOrMismatchScore);
currentCell.setPrevCell(cellAboveLeft);
}
else
{
currentCell.setScore(colSpaceScore);
currentCell.setPrevCell(cellToLeft);
}
}
}
public void printScoreTable()
{
ensureTableIsFilledIn();
for (int i = 0; i < sequence2.Length + 2; i++)
{
for (int j = 0; j < sequence1.Length + 2; j++)
{
if (i == 0)
{
if (j == 0 || j == 1)
{
Console.Write(" ");
}
else
{
if (j == 2)
{
Console.Write(" ");
}
else
{
Console.Write(" ");
}
Console.Write(sequence1[j - 2]);
}
}
else if (j == 0)
{
if (i == 1)
{
Console.Write(" ");
}
else
{
Console.Write(" " + sequence2[i - 2]);
}
}
else
{
String toPrint;
Cell currentCell = scoreTable[i - 1, j - 1];
Cell prevCell = currentCell.getPrevCell();
if (prevCell != null)
{
if (currentCell.getCol() == prevCell.getCol() + 1 &&
currentCell.getRow() == prevCell.getRow() + 1)
{
toPrint = "\\";
}
else if (currentCell.getCol() == prevCell.getCol() + 1)
{
toPrint = "-";
}
else
{
toPrint = "|";
}
}
else
{
toPrint = " ";
}
int score = currentCell.getScore();
String s = score.ToString().PadLeft(3, '0');
toPrint += s;
Console.Write(toPrint);
}
Console.Write(' ');
}
Console.WriteLine();
}
}