NUCLEOTIDE_COUNT_PERCENT = Cache.getDefault("NUCLEOTIDE_COUNT_PERCENT",
55);
NUCLEOTIDE_COUNT_LONG_SEQUENCE_AMBIGUITY_PERCENT = Cache.getDefault(
NUCLEOTIDE_COUNT_PERCENT = Cache.getDefault("NUCLEOTIDE_COUNT_PERCENT",
55);
NUCLEOTIDE_COUNT_LONG_SEQUENCE_AMBIGUITY_PERCENT = Cache.getDefault(
.getDefault("NUCLEOTIDE_COUNT_SHORT", 100);
NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE = Cache
.getDefault("NUCLEOTIDE_COUNT_VERY_SHORT", 4);
.getDefault("NUCLEOTIDE_COUNT_SHORT", 100);
NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE = Cache
.getDefault("NUCLEOTIDE_COUNT_VERY_SHORT", 4);
if (allCount > NUCLEOTIDE_COUNT_SHORT_SEQUENCE)
{
// a long sequence.
// check for at least 55% nucleotide, and nucleotide and ambiguity codes
// (including N) must make up 95%
if (allCount > NUCLEOTIDE_COUNT_SHORT_SEQUENCE)
{
// a long sequence.
// check for at least 55% nucleotide, and nucleotide and ambiguity codes
// (including N) must make up 95%
// a short sequence.
// check if a short sequence is at least 55% nucleotide and the rest of
// the symbols are all X or all N
// a short sequence.
// check if a short sequence is at least 55% nucleotide and the rest of
// the symbols are all X or all N
/*
* Check for nucleotide count > 85% of total count (in a form that evades
* int / float conversion or divide by zero).
/*
* Check for nucleotide count > 85% of total count (in a form that evades
* int / float conversion or divide by zero).
// vs := NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE
// s := NUCLEOTIDE_COUNT_SHORT_SEQUENCE
// lp := NUCLEOTIDE_COUNT_LOWER_PERCENT
// vs := NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE
// s := NUCLEOTIDE_COUNT_SHORT_SEQUENCE
// lp := NUCLEOTIDE_COUNT_LOWER_PERCENT
- // vsp := 1 - (1/a) # this is the proportion of required nucleotides in
- // # a VERY_SHORT Sequence (4 bases).
- // # should be all but one base is nucleotide.
+ // vsp := 1 - (1/a) # this is the proportion of required definite
+ // nucleotides
+ // # in a VERY_SHORT Sequence (4 bases).
+ // # This should be equivalent to all but one base in the sequence.
// # required for this length of sequence.
// minNt := tp * a # the minimum number of definite nucleotide bases
// # required for this length of sequence.
// minNt := tp * a # the minimum number of definite nucleotide bases
// ntCount >= tp * allCount && nCount + ntaCount == aaCount
// but without going into float/double land
long LHS = 100 * allCount
// ntCount >= tp * allCount && nCount + ntaCount == aaCount
// but without going into float/double land
long LHS = 100 * allCount