*/
package jalview.util;
-import jalview.datamodel.SequenceI;
-
import java.util.ArrayList;
import java.util.List;
+import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.datamodel.SequenceI;
+
/**
* Assorted methods for analysing or comparing sequences.
*/
{
private static final int EIGHTY_FIVE = 85;
- private static final int TO_UPPER_CASE = 'a' - 'A';
+ private static final int NUCLEOTIDE_COUNT_PERCENT;
+
+ private static final int NUCLEOTIDE_COUNT_LONG_SEQUENCE_AMBIGUITY_PERCENT;
+
+ private static final int NUCLEOTIDE_COUNT_SHORT_SEQUENCE;
+
+ private static final int NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE;
- private static final char GAP_SPACE = ' ';
+ private static final boolean NUCLEOTIDE_AMBIGUITY_DETECTION;
- private static final char GAP_DOT = '.';
+ public static final char GAP_SPACE = ' ';
- private static final char GAP_DASH = '-';
+ public static final char GAP_DOT = '.';
- public static final String GapChars = new String(new char[] { GAP_SPACE,
- GAP_DOT, GAP_DASH });
+ public static final char GAP_DASH = '-';
+
+ public static final String GapChars = new String(
+ new char[]
+ { GAP_SPACE, GAP_DOT, GAP_DASH });
+
+ static
+ {
+ // these options read only at start of session
+ NUCLEOTIDE_COUNT_PERCENT = Cache.getDefault("NUCLEOTIDE_COUNT_PERCENT",
+ 55);
+ NUCLEOTIDE_COUNT_LONG_SEQUENCE_AMBIGUITY_PERCENT = Cache.getDefault(
+ "NUCLEOTIDE_COUNT_LONG_SEQUENCE_AMBIGUITY_PERCENT", 95);
+ NUCLEOTIDE_COUNT_SHORT_SEQUENCE = Cache
+ .getDefault("NUCLEOTIDE_COUNT_SHORT", 100);
+ NUCLEOTIDE_COUNT_VERY_SHORT_SEQUENCE = Cache
+ .getDefault("NUCLEOTIDE_COUNT_VERY_SHORT", 4);
+ NUCLEOTIDE_AMBIGUITY_DETECTION = Cache
+ .getDefault("NUCLEOTIDE_AMBIGUITY_DETECTION", true);
+ }
/**
* 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();
jlen--;
}
- int count = 0;
int match = 0;
float pid = -1;
{
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++;
}
-
- count++;
}
pid = (float) match / (float) ilen * 100;
{
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++;
}
-
- count++;
}
pid = (float) match / (float) jlen * 100;
* @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)
{
*/
public static final boolean isGap(char c)
{
- return (c == GAP_DASH || c == GAP_DOT || c == GAP_SPACE) ? true : false;
+ 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% 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 || seq.getLength() == 0)
{
return false;
}
- char[][] letters = new char[seqs.length][];
- for (int i = 0; i < seqs.length; i++)
+ 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++)
{
- if (seqs[i] != null)
+ char c = seq.getCharAt(i);
+ if (isNucleotide(c))
+ {
+ ntCount++;
+ }
+ else if (!isGap(c))
{
- char[] sequence = seqs[i].getSequence();
- if (sequence != null)
+ aaCount++;
+ if (isN(c))
{
- letters[i] = sequence;
+ 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;
+ }
- return areNucleotide(letters);
+ 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;
}
/**
* 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;
}
/**
*/
public static boolean isNucleotide(char c)
{
- if ('a' <= c && c <= 'z')
- {
- c -= TO_UPPER_CASE;
- }
+ return isNucleotide(c, false);
+ }
- switch (c)
+ /**
+ * includeAmbiguity = true also includes Nucleotide Ambiguity codes
+ */
+ public static boolean isNucleotide(char c, boolean includeAmbiguity)
+ {
+ char C = Character.toUpperCase(c);
+ switch (C)
{
case 'A':
case 'C':
case 'U':
return true;
}
+ if (includeAmbiguity)
+ {
+ boolean ambiguity = isNucleotideAmbiguity(C);
+ if (ambiguity)
+ return true;
+ }
return false;
}
/**
+ * Tests *only* nucleotide ambiguity codes (and not definite nucleotide codes)
+ */
+ public static boolean isNucleotideAmbiguity(char c)
+ {
+ switch (Character.toUpperCase(c))
+ {
+ case 'I':
+ case 'X':
+ case 'R':
+ case 'Y':
+ case 'W':
+ case 'S':
+ case 'M':
+ case 'K':
+ case 'B':
+ case 'H':
+ case 'D':
+ case 'V':
+ return true;
+ case 'N': // not counting N as nucleotide
+ }
+ return false;
+ }
+
+ public static boolean isN(char c)
+ {
+ return 'n' == Character.toLowerCase(c);
+ }
+
+ public static boolean isX(char c)
+ {
+ return 'x' == Character.toLowerCase(c);
+ }
+
+ /**
* Answers true if every character in the string is one of aAcCgGtTuU, or
* (optionally) a gap character (dot, dash, space), else false
*
*/
public static boolean isNucleotideSequence(String s, boolean allowGaps)
{
+ return isNucleotideSequence(s, allowGaps, false);
+ }
+
+ public static boolean isNucleotideSequence(String s, boolean allowGaps,
+ boolean includeAmbiguous)
+ {
if (s == null)
{
return false;
for (int i = 0; i < s.length(); i++)
{
char c = s.charAt(i);
- if (!isNucleotide(c))
+ if (!isNucleotide(c, includeAmbiguous))
{
if (!allowGaps || !isGap(c))
{
flattened.add(s);
}
}
- final SequenceI[] oneDArray = flattened.toArray(new SequenceI[flattened
- .size()]);
+ final SequenceI[] oneDArray = flattened
+ .toArray(new SequenceI[flattened.size()]);
return isNucleotide(oneDArray);
}
public static boolean isSameResidue(char c1, char c2,
boolean caseSensitive)
{
- if (caseSensitive)
- {
- return (c1 == c2);
- }
- else
- {
- return Character.toUpperCase(c1) == Character.toUpperCase(c2);
- }
+ return caseSensitive ? c1 == c2
+ : Character.toUpperCase(c1) == Character.toUpperCase(c2);
}
}
git://source.jalview.org / jalview.git / blobdiff