final private int dnaWidth;
- final private Alignment dataset;
+ final private AlignmentI dataset;
/*
* Working variables for the translation.
char[] originalSequence = sequence.toCharArray();
int length = originalSequence.length;
char[] reversedSequence = new char[length];
-
+ int bases = 0;
for (int i = 0; i < length; i++)
{
- reversedSequence[length - i - 1] = complement ? getComplement(originalSequence[i])
+ char c = complement ? getComplement(originalSequence[i])
: originalSequence[i];
+ reversedSequence[length - i - 1] = c;
+ if (!Comparison.isGap(c))
+ {
+ bases++;
+ }
}
- SequenceI reversed = new Sequence(newName, reversedSequence, 1, length);
+ SequenceI reversed = new Sequence(newName, reversedSequence, 1, bases);
return reversed;
}
public static char getComplement(char c)
{
char result = c;
- switch (c) {
+ switch (c)
+ {
+ case '-':
+ case '.':
+ case ' ':
+ break;
case 'a':
result = 't';
break;