From 9e97e05a07a7b5b58b54431325c663f2df31cd06 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 8 Jan 2021 16:06:59 +0000 Subject: [PATCH] JAL-3794 X and N are counted as DNA characters, but we also check how many Ns - if there were no real nucleotide characters we always return protein for poly-asparagine --- src/jalview/util/Comparison.java | 43 +++++++++++++++++++++++++++++++------- 1 file changed, 35 insertions(+), 8 deletions(-) diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java index 286bfb2..0d945ac 100644 --- a/src/jalview/util/Comparison.java +++ b/src/jalview/util/Comparison.java @@ -261,7 +261,7 @@ public class Comparison /** * 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 @@ -274,27 +274,32 @@ public class Comparison } long ntCount = 0; long aaCount = 0; + long nCount = 0; int len = seq.getLength(); for (int i = 0; i < len; i++) { char c = seq.getCharAt(i); - if (isNucleotide(c)) + if (isNucleotide(c) || isX(c)) { ntCount++; } else if (!isGap(c)) { aaCount++; + if (isN(c)) + { + nCount++; + } } } /* * 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)) + if ((ntCount+nCount) * 100 > EIGHTY_FIVE * (ntCount + aaCount)) { - return true; + return ntCount>0; // all N is considered protein. Could use a threshold here too } else { @@ -317,17 +322,18 @@ public class Comparison return false; } // true if we have seen a nucleotide sequence - boolean na=false; + boolean na = false; for (SequenceI seq : seqs) { if (seq == null) { continue; } - na=true; + na = true; // TODO could possibly make an informed guess just from the first sequence // to save a lengthy calculation - if (seq.isProtein()) { + if (seq.isProtein()) + { // if even one looks like protein, the alignment is protein return false; } @@ -347,7 +353,6 @@ public class Comparison { c -= TO_UPPER_CASE; } - switch (c) { case 'A': @@ -360,6 +365,28 @@ public class Comparison 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 -- 1.7.10.2