private static final int TO_UPPER_CASE = 'a' - 'A';
- private static final char GAP_SPACE = ' ';
+ public static final char GAP_SPACE = ' ';
- private static final char GAP_DOT = '.';
+ public static final char GAP_DOT = '.';
- private static final char GAP_DASH = '-';
+ public static final char GAP_DASH = '-';
- public static final String GapChars = new String(new char[] { GAP_SPACE,
- GAP_DOT, GAP_DASH });
+ public static final String GapChars = new String(
+ new char[]
+ { GAP_SPACE, GAP_DOT, GAP_DASH });
/**
* DOCUMENT ME!
* int
* @return float
*/
- public static float compare(SequenceI ii, SequenceI jj, int start, int end)
+ public static float compare(SequenceI ii, SequenceI jj, int start,
+ int end)
{
String si = ii.getSequenceAsString();
String sj = jj.getSequenceAsString();
{
for (int j = 0; j < jlen; j++)
{
- if (si.substring(start + j, start + j + 1).equals(
- sj.substring(start + j, start + j + 1)))
+ if (si.substring(start + j, start + j + 1)
+ .equals(sj.substring(start + j, start + j + 1)))
{
match++;
}
{
for (int j = 0; j < jlen; j++)
{
- if (si.substring(start + j, start + j + 1).equals(
- sj.substring(start + j, start + j + 1)))
+ if (si.substring(start + j, start + j + 1)
+ .equals(sj.substring(start + j, start + j + 1)))
{
match++;
}
* @param s2
* SequenceI
* @return float
+ * @deprecated use PIDModel.computePID()
*/
+ @Deprecated
public final static float PID(String seq1, String seq2)
{
return PID(seq1, seq2, 0, seq1.length());
static final int caseShift = 'a' - 'A';
// Another pid with region specification
- public final static float PID(String seq1, String seq2, int start, int end)
+ /**
+ * @deprecated use PIDModel.computePID()
+ */
+ @Deprecated
+ public final static float PID(String seq1, String seq2, int start,
+ int end)
{
return PID(seq1, seq2, start, end, true, false);
}
* @param ungappedOnly
* - if true - only count PID over ungapped columns
* @return
+ * @deprecated use PIDModel.computePID()
*/
+ @Deprecated
public final static float PID(String seq1, String seq2, int start,
int end, boolean wcGaps, boolean ungappedOnly)
{
/**
* Overloaded method signature to test whether a single sequence is nucleotide
- * (that is, more than 85% CGTA)
+ * (that is, more than 85% CGTAUNX)
*
* @param seq
* @return
*/
public static final boolean isNucleotide(SequenceI seq)
{
- return isNucleotide(new SequenceI[] { seq });
- }
-
- /**
- * Answers true if more than 85% of the sequence residues (ignoring gaps) are
- * A, G, C, T or U, else false. This is just a heuristic guess and may give a
- * wrong answer (as AGCT are also amino acid codes).
- *
- * @param seqs
- * @return
- */
- public static final boolean isNucleotide(SequenceI[] seqs)
- {
- if (seqs == null)
+ if (seq == null)
{
return false;
}
- char[][] letters = new char[seqs.length][];
- for (int i = 0; i < seqs.length; i++)
+ long ntCount = 0;
+ long aaCount = 0;
+ long nCount = 0;
+
+ int len = seq.getLength();
+ for (int i = 0; i < len; i++)
{
- if (seqs[i] != null)
+ char c = seq.getCharAt(i);
+ if (isNucleotide(c) || isX(c))
{
- char[] sequence = seqs[i].getSequence();
- if (sequence != null)
+ ntCount++;
+ }
+ else if (!isGap(c))
+ {
+ aaCount++;
+ if (isN(c))
{
- letters[i] = sequence;
+ nCount++;
}
}
}
-
- return areNucleotide(letters);
+ /*
+ * 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 * (ntCount + aaCount))
+ {
+ return ntCount > 0; // all N is considered protein. Could use a threshold
+ // here too
+ }
+ else
+ {
+ return false;
+ }
}
/**
* A, G, C, T or U, else false. This is just a heuristic guess and may give a
* wrong answer (as AGCT are also amino acid codes).
*
- * @param letters
+ * @param seqs
* @return
*/
- static final boolean areNucleotide(char[][] letters)
+ public static final boolean isNucleotide(SequenceI[] seqs)
{
- int ntCount = 0;
- int aaCount = 0;
- for (char[] seq : letters)
+ if (seqs == null)
+ {
+ return false;
+ }
+ // true if we have seen a nucleotide sequence
+ boolean na = false;
+ for (SequenceI seq : seqs)
{
if (seq == null)
{
continue;
}
+ na = true;
// TODO could possibly make an informed guess just from the first sequence
// to save a lengthy calculation
- for (char c : seq)
+ if (seq.isProtein())
{
- if (isNucleotide(c))
- {
- ntCount++;
- }
- else if (!isGap(c))
- {
- aaCount++;
- }
+ // if even one looks like protein, the alignment is protein
+ return false;
}
}
-
- /*
- * Check for nucleotide count > 85% of total count (in a form that evades
- * int / float conversion or divide by zero).
- */
- if (ntCount * 100 > EIGHTY_FIVE * (ntCount + aaCount))
- {
- return true;
- }
- else
- {
- return false;
- }
-
+ return na;
}
/**
{
c -= TO_UPPER_CASE;
}
-
switch (c)
{
case 'A':
return false;
}
+ public static boolean isN(char c)
+ {
+ switch (c)
+ {
+ case 'N':
+ case 'n':
+ return true;
+ }
+ return false;
+ }
+
+ public static boolean isX(char c)
+ {
+ switch (c)
+ {
+ case 'X':
+ case 'x':
+ return true;
+ }
+ return false;
+ }
+
/**
* Answers true if every character in the string is one of aAcCgGtTuU, or
* (optionally) a gap character (dot, dash, space), else false
flattened.add(s);
}
}
- final SequenceI[] oneDArray = flattened.toArray(new SequenceI[flattened
- .size()]);
+ final SequenceI[] oneDArray = flattened
+ .toArray(new SequenceI[flattened.size()]);
return isNucleotide(oneDArray);
}
git://source.jalview.org / jalview.git / blobdiff