/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
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)
+ *
+ * @param seq
+ * @return
+ */
+ public static final boolean isNucleotide(SequenceI seq)
+ {
+ if (seq==null)
+ {
+ return false;
+ }
+ long ntCount = 0;
+ long aaCount = 0;
+
+ 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++;
+ }
+ }
+ /*
+ * 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;
+ }
+ }
+
+ /**
* 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).
{
return false;
}
- int ntCount = 0;
- int aaCount = 0;
+ // 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.getSequence())
- {
- if ('a' <= c && c <= 'z')
- {
- c -= TO_UPPER_CASE;
- }
-
- if (c == 'A' || c == 'G' || c == 'C' || c == 'T' || c == 'U')
- {
- ntCount++;
- }
- else if (!Comparison.isGap(c))
- {
- aaCount++;
- }
+ if (seq.isProtein()) {
+ // if even one looks like protein, the alignment is protein
+ return false;
}
}
+ return na;
+ }
+
+ /**
+ * Answers true if the character is one of aAcCgGtTuU
+ *
+ * @param c
+ * @return
+ */
+ public static boolean isNucleotide(char c)
+ {
+ if ('a' <= c && c <= 'z')
+ {
+ c -= TO_UPPER_CASE;
+ }
- /*
- * 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))
+ switch (c)
{
+ case 'A':
+ case 'C':
+ case 'G':
+ case 'T':
+ case 'U':
return true;
}
- else
+ return false;
+ }
+
+ /**
+ * Answers true if every character in the string is one of aAcCgGtTuU, or
+ * (optionally) a gap character (dot, dash, space), else false
+ *
+ * @param s
+ * @param allowGaps
+ * @return
+ */
+ public static boolean isNucleotideSequence(String s, boolean allowGaps)
+ {
+ if (s == null)
{
return false;
}
-
+ for (int i = 0; i < s.length(); i++)
+ {
+ char c = s.charAt(i);
+ if (!isNucleotide(c))
+ {
+ if (!allowGaps || !isGap(c))
+ {
+ return false;
+ }
+ }
+ }
+ return true;
}
/**
flattened.add(s);
}
}
- final SequenceI[] oneDArray = flattened.toArray(new SequenceI[flattened
- .size()]);
+ final SequenceI[] oneDArray = flattened
+ .toArray(new SequenceI[flattened.size()]);
return isNucleotide(oneDArray);
}
+
+ /**
+ * Compares two residues either case sensitively or case insensitively
+ * depending on the caseSensitive flag
+ *
+ * @param c1
+ * first char
+ * @param c2
+ * second char to compare with
+ * @param caseSensitive
+ * if true comparison will be case sensitive otherwise its not
+ * @return
+ */
+ public static boolean isSameResidue(char c1, char c2,
+ boolean caseSensitive)
+ {
+ if (caseSensitive)
+ {
+ return (c1 == c2);
+ }
+ else
+ {
+ return Character.toUpperCase(c1) == Character.toUpperCase(c2);
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff