X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Futil%2FComparison.java;h=4f2c0a70fda0274cc137a2a495bfe5a808de30c0;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=50472a53ac0851542b951933e39c1927807f3eb5;hpb=6c4bc68ae8b1c5005e79661bb2d8246515cb787d;p=jalview.git diff --git a/src/jalview/util/Comparison.java b/src/jalview/util/Comparison.java old mode 100755 new mode 100644 index 50472a5..4f2c0a7 --- a/src/jalview/util/Comparison.java +++ b/src/jalview/util/Comparison.java @@ -1,222 +1,276 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2006 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 final String GapChars = " .-"; - - /** - * 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 (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 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) - { - - 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 bad = 0; - char chr1; - char chr2; - - - for (int i = start; i < len; i++) - { - chr1 = seq1.charAt(i) ; - - chr2 = seq2.charAt(i) ; - - 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 && !isGap(chr1) && !isGap(chr2) ) - { - bad++; - } - } - - return ( (float) 100 * (len - bad)) / len; - } - - /** - * DOCUMENT ME! - * - * @param c DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public static final boolean isGap(char c) - { - return (c == '-' || c == '.' || c == ' ') ? true : false; - } - - public static final boolean isNucleotide(SequenceI [] seqs) - { - int i = 0, iSize = seqs.length, j, jSize; - float nt = 0, aa = 0; - char c; - while (i < iSize) - { - jSize = seqs[i].getLength(); - for (j = 0; j < jSize; j++) - { - c = seqs[i].getCharAt(j); - if ('a' <= c && c <= 'z') - c -= ('a' - 'A'); - - if (c == 'A' || c == 'G' || c == 'C' || c == 'T' || c == 'U') - nt++; - else if (!jalview.util.Comparison.isGap( seqs[i].getCharAt(j))) - { - aa++; - } - } - i++; - } - - if ( (nt / (nt + aa)) > 0.85f) - return true; - else - return false; - - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1) + * Copyright (C) 2014 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 jalview.datamodel.*; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class Comparison +{ + /** DOCUMENT ME!! */ + public static final String GapChars = " .-"; + + /** + * 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 (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 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) + { + 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 + */ + 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; + } + + /** + * DOCUMENT ME! + * + * @param c + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public static final boolean isGap(char c) + { + return (c == '-' || c == '.' || c == ' ') ? true : false; + } + + public static final boolean isNucleotide(SequenceI[] seqs) + { + int i = 0, iSize = seqs.length, j, jSize; + float nt = 0, aa = 0; + char c; + while (i < iSize) + { + jSize = seqs[i].getLength(); + for (j = 0; j < jSize; j++) + { + c = seqs[i].getCharAt(j); + if ('a' <= c && c <= 'z') + { + c -= ('a' - 'A'); + } + + if (c == 'A' || c == 'G' || c == 'C' || c == 'T' || c == 'U') + { + nt++; + } + else if (!jalview.util.Comparison.isGap(seqs[i].getCharAt(j))) + { + aa++; + } + } + i++; + } + + if ((nt / (nt + aa)) > 0.85f) + { + return true; + } + else + { + return false; + } + + } +}