+ return c == GAP_DASH || c == GAP_DOT || c == GAP_SPACE;
+ }
+
+ /**
+ * Overloaded method signature to test whether a single sequence is nucleotide
+ * (that is, more than 85% CGTAUNX)
+ *
+ * @param seq
+ * @return
+ */
+ public static final boolean isNucleotide(SequenceI seq)
+ {
+ if (seq == null || seq.getLength() == 0)
+ {
+ return false;
+ }
+ long ntCount = 0; // nucleotide symbol count (does not include ntaCount)
+ long aaCount = 0; // non-nucleotide, non-gap symbol count (includes nCount
+ // and ntaCount)
+ long nCount = 0; // "Unknown" (N) symbol count
+ long xCount = 0; // Also used as "Unknown" (X) symbol count
+ long ntaCount = 0; // nucleotide ambiguity symbol count
+
+ int len = seq.getLength();
+ for (int i = 0; i < len; i++)
+ {
+ char c = seq.getCharAt(i);
+ if (isNucleotide(c))
+ {
+ ntCount++;
+ }
+ else if (!isGap(c))
+ {
+ aaCount++;
+ if (isN(c))
+ {
+ nCount++;
+ }
+ else
+ {
+ if (isX(c))
+ {
+ xCount++;
+ }
+ if (isNucleotideAmbiguity(c))
+ {
+ ntaCount++;
+ }
+ }
+ }
+ }
+ long allCount = ntCount + aaCount;
+
+ if (NUCLEOTIDE_AMBIGUITY_DETECTION)
+ {
+ Console.debug("Performing new nucleotide detection routine");
+ 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%
+ return ntCount * 100 >= NUCLEOTIDE_COUNT_PERCENT * allCount
+ && 100 * (ntCount + nCount
+ + ntaCount) >= NUCLEOTIDE_COUNT_LONG_SEQUENCE_AMBIGUITY_PERCENT
+ * allCount;
+ }
+ else if (allCount > NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE)
+ {
+ // 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
+ if (ntCount * 100 >= NUCLEOTIDE_COUNT_PERCENT * allCount
+ && (nCount == aaCount || xCount == aaCount))
+ {
+ return true;
+ }
+
+ // a short sequence.
+ // check for at least x% nucleotide and all the rest nucleotide
+ // ambiguity codes (including N), where x slides from 75% for sequences
+ // of length 4 (i.e. only one non-nucleotide) to 55% for sequences of
+ // length 100
+ return myShortSequenceNucleotideProportionCount(ntCount, allCount)
+ && nCount + ntaCount == aaCount;
+ }
+ else
+ {
+ // a very short sequence. (<4)
+ // all bases must be nucleotide
+ return ntCount > 0 && ntCount == allCount;
+ }
+ }
+ else
+ {
+ Console.debug("Performing old nucleotide detection routine");
+ /*
+ * Check for nucleotide count > 85% of total count (in a form that evades
+ * int / float conversion or divide by zero).
+ */
+ if ((ntCount + nCount) * 100 > EIGHTY_FIVE * allCount)
+ {
+ return ntCount > 0; // all N is considered protein. Could use a
+ // threshold here too
+ }
+ }
+ return false;
+ }
+
+ protected static boolean myShortSequenceNucleotideProportionCount(
+ long ntCount, long allCount)
+ {
+ /**
+ * this method is valid only for NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE <=
+ * allCount <= NUCLEOTIDE_COUNT_SHORT_SEQUENCE
+ */
+ // the following is a simplified integer version of:
+ //
+ // a := allCount # the number of bases in the sequence
+ // n : = ntCount # the number of definite nucleotide bases
+ // 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 definite
+ // nucleotides
+ // # in a VERY_SHORT Sequence (4 bases).
+ // # This should be equivalent to all but one base in the sequence.
+ // p := (a - vs)/(s - vs) # proportion of the way between
+ // # VERY_SHORT and SHORT thresholds.
+ // tp := vsp + p * (lp/100 - vsp) # the proportion of definite nucleotides
+ // # required for this length of sequence.
+ // minNt := tp * a # the minimum number of definite nucleotide bases
+ // # required for this length of sequence.
+ //
+ // We are then essentially returning:
+ // # ntCount >= 55% of allCount and the rest are all nucleotide ambiguity:
+ // ntCount >= tp * allCount && nCount + ntaCount == aaCount
+ // but without going into float/double land
+ long LHS = 100 * allCount
+ * (NUCLEOTIDE_COUNT_SHORT_SEQUENCE
+ - NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE)
+ * (ntCount - allCount + 1);
+ long RHS = allCount * (allCount - NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE)
+ * (allCount * NUCLEOTIDE_COUNT_PERCENT - 100 * allCount + 100);
+ return LHS >= RHS;