X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FComparison.java;h=9fea705bade9be1b2442d357808c7f8292a986c9;hb=1f41372a2bda3efcc27abaed092495548135b6b4;hp=c779bb1e9179df755ff7d27b56316d7d6600d599;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git
diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java
old mode 100755
new mode 100644
index c779bb1..9fea705
--- a/src/jalview/util/Comparison.java
+++ b/src/jalview/util/Comparison.java
@@ -1,243 +1,606 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program is free software; you can redistribute it and/or
-* modify it under the terms of the GNU General Public License
-* as published by the Free Software Foundation; either version 2
-* of the License, or (at your option) any later version.
-*
-* This program is distributed in the hope that it will be useful,
-* but WITHOUT ANY WARRANTY; without even the implied warranty of
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-* GNU General Public License for more details.
-*
-* You should have received a copy of the GNU General Public License
-* along with this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-package jalview.util;
-
-import jalview.datamodel.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class Comparison
-{
- /** DOCUMENT ME!! */
- public static String GapChars = " .-";
-
- /**
- * DOCUMENT ME!
- *
- * @param ii DOCUMENT ME!
- * @param jj DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public static float compare(SequenceI ii, SequenceI jj)
- {
- return Comparison.compare(ii, jj, 0, ii.getLength() - 1);
- }
-
- /**
- * this was supposed to be an ungapped pid calculation
- * @param ii SequenceI
- * @param jj SequenceI
- * @param start int
- * @param end int
- * @return float
- */
- public static float compare(SequenceI ii, SequenceI jj, int start, int end)
- {
- String si = ii.getSequence();
- String sj = jj.getSequence();
-
- int ilen = si.length() - 1;
- int jlen = sj.length() - 1;
-
- while (jalview.util.Comparison.isGap(si.charAt(start + ilen)))
- {
- ilen--;
- }
-
- while (jalview.util.Comparison.isGap(sj.charAt(start + jlen)))
- {
- jlen--;
- }
-
- int count = 0;
- int match = 0;
- float pid = -1;
-
- if (ilen > jlen)
- {
- for (int j = 0; j < jlen; j++)
- {
- if (si.substring(start + j, start + j + 1).equals(sj.substring(start +
- j, start + j + 1)))
- {
- match++;
- }
-
- count++;
- }
-
- pid = (float) match / (float) ilen * 100;
- }
- else
- {
- for (int j = 0; j < jlen; j++)
- {
- if (si.substring(start + j, start + j + 1).equals(sj.substring(start +
- j, start + j + 1)))
- {
- match++;
- }
-
- count++;
- }
-
- pid = (float) match / (float) jlen * 100;
- }
-
- return pid;
- }
-
- /**
- * this is a gapped PID calculation
- *
- * @param s1 SequenceI
- * @param s2 SequenceI
- * @return float
- */
- public static float PID(SequenceI s1, SequenceI s2)
- {
- int len;
-
- if (s1.getSequence().length() > s2.getSequence().length())
- {
- len = s1.getSequence().length();
- }
- else
- {
- len = s2.getSequence().length();
- }
-
- int bad = 0;
-
- for (int i = 0; i < len; i++)
- {
- char chr1;
- char chr2;
-
- if (i < s1.getSequence().length())
- {
- chr1 = s1.getSequence().charAt(i);
- }
- else
- {
- chr1 = '.';
- }
-
- if (i < s2.getSequence().length())
- {
- chr2 = s2.getSequence().charAt(i);
- }
- else
- {
- chr2 = '.';
- }
-
- if (!(jalview.util.Comparison.isGap(chr1)) &&
- !(jalview.util.Comparison.isGap(chr2)))
- {
- if (chr1 != chr2)
- {
- bad++;
- }
- }
- }
-
- return ((float) 100 * (len - bad)) / len;
- }
-
- // Another pid with region specification
- public static float PID(SequenceI s1, SequenceI s2, int start, int end)
- {
- int len;
-
- if (s1.getSequence().length() > s2.getSequence().length())
- {
- len = s1.getSequence().length();
- }
- else
- {
- len = s2.getSequence().length();
- }
-
- if (end < len)
- {
- len = end;
- }
-
- if (len < start)
- {
- start = len - 1; // we just use a single residue for the difference
- }
-
- int bad = 0;
-
- for (int i = start; i < len; i++)
- {
- char chr1;
- char chr2;
-
- if (i < s1.getSequence().length())
- {
- chr1 = s1.getSequence().charAt(i);
- }
- else
- {
- chr1 = '.';
- }
-
- if (i < s2.getSequence().length())
- {
- chr2 = s2.getSequence().charAt(i);
- }
- else
- {
- chr2 = '.';
- }
-
- if (!(jalview.util.Comparison.isGap(chr1)) &&
- !(jalview.util.Comparison.isGap(chr2)))
- {
- if (chr1 != chr2)
- {
- bad++;
- }
- }
- }
-
- return ((float) 100 * (len - bad)) / len;
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param c DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public static boolean isGap(char c)
- {
- return ((c != '.') && (c != '-') && (c != ' ')) ? false : true;
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.util;
+
+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.
+ */
+public class Comparison
+{
+ private static final int EIGHTY_FIVE = 85;
+
+ 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 boolean NUCLEOTIDE_AMBIGUITY_DETECTION;
+
+ public static final char GAP_SPACE = ' ';
+
+ public static final char GAP_DOT = '.';
+
+ 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!
+ *
+ * @param ii
+ * DOCUMENT ME!
+ * @param jj
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static final float compare(SequenceI ii, SequenceI jj)
+ {
+ return Comparison.compare(ii, jj, 0, ii.getLength() - 1);
+ }
+
+ /**
+ * this was supposed to be an ungapped pid calculation
+ *
+ * @param ii
+ * SequenceI
+ * @param jj
+ * SequenceI
+ * @param start
+ * int
+ * @param end
+ * int
+ * @return float
+ */
+ public static float compare(SequenceI ii, SequenceI jj, int start,
+ int end)
+ {
+ String si = ii.getSequenceAsString();
+ String sj = jj.getSequenceAsString();
+
+ int ilen = si.length() - 1;
+ int jlen = sj.length() - 1;
+
+ while (Comparison.isGap(si.charAt(start + ilen)))
+ {
+ ilen--;
+ }
+
+ while (Comparison.isGap(sj.charAt(start + jlen)))
+ {
+ jlen--;
+ }
+
+ int match = 0;
+ float pid = -1;
+
+ if (ilen > jlen)
+ {
+ for (int j = 0; j < jlen; j++)
+ {
+ if (si.substring(start + j, start + j + 1)
+ .equals(sj.substring(start + j, start + j + 1)))
+ {
+ match++;
+ }
+ }
+
+ pid = (float) match / (float) ilen * 100;
+ }
+ else
+ {
+ for (int j = 0; j < jlen; j++)
+ {
+ if (si.substring(start + j, start + j + 1)
+ .equals(sj.substring(start + j, start + j + 1)))
+ {
+ match++;
+ }
+ }
+
+ pid = (float) match / (float) jlen * 100;
+ }
+
+ return pid;
+ }
+
+ /**
+ * this is a gapped PID calculation
+ *
+ * @param s1
+ * SequenceI
+ * @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
+ /**
+ * @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);
+ }
+
+ /**
+ * Calculate percent identity for a pair of sequences over a particular range,
+ * with different options for ignoring gaps.
+ *
+ * @param seq1
+ * @param seq2
+ * @param start
+ * - position in seqs
+ * @param end
+ * - position in seqs
+ * @param wcGaps
+ * - if true - gaps match any character, if false, do not match
+ * anything
+ * @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)
+ {
+ int s1len = seq1.length();
+ int s2len = seq2.length();
+
+ int len = Math.min(s1len, s2len);
+
+ if (end < len)
+ {
+ len = end;
+ }
+
+ if (len < start)
+ {
+ start = len - 1; // we just use a single residue for the difference
+ }
+
+ int elen = len - start, bad = 0;
+ char chr1;
+ char chr2;
+ boolean agap;
+ for (int i = start; i < len; i++)
+ {
+ chr1 = seq1.charAt(i);
+
+ chr2 = seq2.charAt(i);
+ agap = isGap(chr1) || isGap(chr2);
+ if ('a' <= chr1 && chr1 <= 'z')
+ {
+ // TO UPPERCASE !!!
+ // Faster than toUpperCase
+ chr1 -= caseShift;
+ }
+ if ('a' <= chr2 && chr2 <= 'z')
+ {
+ // TO UPPERCASE !!!
+ // Faster than toUpperCase
+ chr2 -= caseShift;
+ }
+
+ if (chr1 != chr2)
+ {
+ if (agap)
+ {
+ if (ungappedOnly)
+ {
+ elen--;
+ }
+ else if (!wcGaps)
+ {
+ bad++;
+ }
+ }
+ else
+ {
+ bad++;
+ }
+ }
+
+ }
+ if (elen < 1)
+ {
+ return 0f;
+ }
+ return ((float) 100 * (elen - bad)) / elen;
+ }
+
+ /**
+ * Answers true if the supplied character is a recognised gap character, else
+ * false. Currently hard-coded to recognise '-', '-' or ' ' (hyphen / dot /
+ * space).
+ *
+ * @param c
+ *
+ * @return
+ */
+ public static final boolean isGap(char c)
+ {
+ 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;
+ }
+
+ /**
+ * 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)
+ {
+ 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
+ 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)
+ {
+ return isNucleotide(c, false);
+ }
+
+ /**
+ * 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 'G':
+ case 'T':
+ 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
+ *
+ * @param s
+ * @param allowGaps
+ * @return
+ */
+ 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, includeAmbiguous))
+ {
+ if (!allowGaps || !isGap(c))
+ {
+ return false;
+ }
+ }
+ }
+ return true;
+ }
+
+ /**
+ * Convenience overload of isNucleotide
+ *
+ * @param seqs
+ * @return
+ */
+ public static boolean isNucleotide(SequenceI[][] seqs)
+ {
+ if (seqs == null)
+ {
+ return false;
+ }
+ List flattened = new ArrayList();
+ for (SequenceI[] ss : seqs)
+ {
+ for (SequenceI s : ss)
+ {
+ flattened.add(s);
+ }
+ }
+ 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)
+ {
+ return caseSensitive ? c1 == c2
+ : Character.toUpperCase(c1) == Character.toUpperCase(c2);
+ }
+}