/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.
- *
+ * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.util;
-import jalview.datamodel.*;
+import jalview.datamodel.SequenceI;
+
+import java.util.ArrayList;
+import java.util.List;
/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
+ * Assorted methods for analysing or comparing sequences.
*/
public class Comparison
{
- /** DOCUMENT ME!! */
- public static final String GapChars = " .-";
+ private static final int EIGHTY_FIVE = 85;
+
+ private static final int TO_UPPER_CASE = 'a' - 'A';
+
+ private static final char GAP_SPACE = ' ';
+
+ private static final char GAP_DOT = '.';
+
+ private static final char GAP_DASH = '-';
+
+ public static final String GapChars = new String(new char[] { GAP_SPACE,
+ GAP_DOT, GAP_DASH });
/**
* DOCUMENT ME!
int ilen = si.length() - 1;
int jlen = sj.length() - 1;
- while (jalview.util.Comparison.isGap(si.charAt(start + ilen)))
+ while (Comparison.isGap(si.charAt(start + ilen)))
{
ilen--;
}
- while (jalview.util.Comparison.isGap(sj.charAt(start + jlen)))
+ while (Comparison.isGap(sj.charAt(start + jlen)))
{
jlen--;
}
// 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);
+ 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.
+ * 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
+ * @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)
+ 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();
start = len - 1; // we just use a single residue for the difference
}
- int elen=len-start,bad = 0;
+ int elen = len - start, bad = 0;
char chr1;
char chr2;
boolean agap;
// Faster than toUpperCase
chr2 -= caseShift;
}
-
+
if (chr1 != chr2)
{
- if (agap)
- {
- if (ungappedOnly)
- {
- elen--;
- } else if (!wcGaps) {
- bad++;
- }
- } else {
- bad++;
- }
+ if (agap)
+ {
+ if (ungappedOnly)
+ {
+ elen--;
+ }
+ else if (!wcGaps)
+ {
+ bad++;
+ }
+ }
+ else
+ {
+ bad++;
+ }
}
-
+
+ }
+ if (elen < 1)
+ {
+ return 0f;
}
- if (elen<1) { return 0f; }
return ((float) 100 * (elen - bad)) / elen;
}
/**
- * DOCUMENT ME!
+ * Answers true if the supplied character is a recognised gap character, else
+ * false. Currently hard-coded to recognise '-', '-' or ' ' (hyphen / dot /
+ * space).
*
* @param c
- * DOCUMENT ME!
*
- * @return DOCUMENT ME!
+ * @return
*/
public static final boolean isGap(char c)
{
- return (c == '-' || c == '.' || c == ' ') ? true : false;
+ return (c == GAP_DASH || c == GAP_DOT || c == GAP_SPACE) ? true : 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).
+ *
+ * @param seqs
+ * @return
+ */
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)
+ if (seqs == null)
+ {
+ return false;
+ }
+ int ntCount = 0;
+ int aaCount = 0;
+ for (SequenceI seq : seqs)
{
- jSize = seqs[i].getLength();
- for (j = 0; j < jSize; j++)
+ if (seq == null)
+ {
+ continue;
+ }
+ // TODO could possibly make an informed guess just from the first sequence
+ // to save a lengthy calculation
+ for (char c : seq.getSequence())
{
- c = seqs[i].getCharAt(j);
if ('a' <= c && c <= 'z')
{
- c -= ('a' - 'A');
+ c -= TO_UPPER_CASE;
}
if (c == 'A' || c == 'G' || c == 'C' || c == 'T' || c == 'U')
{
- nt++;
+ ntCount++;
}
- else if (!jalview.util.Comparison.isGap(seqs[i].getCharAt(j)))
+ else if (!Comparison.isGap(c))
{
- aa++;
+ aaCount++;
}
}
- i++;
}
- if ((nt / (nt + aa)) > 0.85f)
+ /*
+ * 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;
}
}
}
+
+ /**
+ * Convenience overload of isNucleotide
+ *
+ * @param seqs
+ * @return
+ */
+ public static boolean isNucleotide(SequenceI[][] seqs)
+ {
+ if (seqs == null)
+ {
+ return false;
+ }
+ List<SequenceI> flattened = new ArrayList<SequenceI>();
+ for (SequenceI[] ss : seqs)
+ {
+ for (SequenceI s : ss)
+ {
+ flattened.add(s);
+ }
+ }
+ final SequenceI[] oneDArray = flattened.toArray(new SequenceI[flattened
+ .size()]);
+ return isNucleotide(oneDArray);
+ }
}
git://source.jalview.org / jalview.git / blobdiff