X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=36534a36a9eaed2a7da3acb49c312974dc1e948a;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=0841bf21304df1290ece958777c6fe340af8eafe;hpb=5e0d83cae421154f0cd70e2296ce6dbcbc4207a4;p=jalview.git diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java index 0841bf2..36534a3 100755 --- a/src/jalview/analysis/AAFrequency.java +++ b/src/jalview/analysis/AAFrequency.java @@ -1,141 +1,159 @@ -/* -* 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.analysis; - -import jalview.analysis.*; - -import jalview.datamodel.*; - -import java.util.*; - - -/** - * Takes in a vector of sequences and column start and column end - * and returns a vector of size (end-start+1). Each element of the - * vector contains a hashtable with the keys being residues and - * the values being the count of each residue in that column. - * This class is used extensively in calculating alignment colourschemes - * that depend on the amount of conservation in each alignment column. - * @author $author$ - * @version $Revision$ - */ -public class AAFrequency -{ - /** Takes in a vector of sequences and column start and column end - * and returns a vector of size (end-start+1). Each element of the - * vector contains a hashtable with the keys being residues and - * the values being the count of each residue in that column. - * This class is used extensively in calculating alignment colourschemes - * that depend on the amount of conservation in each alignment column. */ - public static Vector calculate(Vector sequences, int start, int end) - { - Vector result = new Vector(); - Hashtable residueHash; - int count, maxCount, nongap, i, j, jSize = sequences.size(); - String maxResidue, sequence, res; - float percentage; - - for (i = start; i <= end; i++) - { - residueHash = new Hashtable(); - maxCount = 0; - maxResidue = "-"; - nongap = 0; - - for (j = 0; j < jSize; j++) - { - if (sequences.elementAt(j) instanceof Sequence) - { - sequence = ((Sequence) sequences.elementAt(j)).getSequence(); - - if (sequence.length() > i) - { - res = sequence.substring(i,i+1); - - if (jalview.util.Comparison.isGap(res.charAt(0))) - { - res = "-"; // we always use this for gaps in the property vectors - } - else - { nongap++; } - - if (residueHash.containsKey(res)) - { - count = ((Integer) residueHash.get(res)).intValue(); - count++; - - if (!jalview.util.Comparison.isGap(res.charAt(0)) && - (count >= maxCount)) - { - if (count > maxCount) - { - maxResidue = res; - } - else if (maxResidue.indexOf(res) == -1) - { - maxResidue += res; - } - - maxCount = count; - } - - residueHash.put(res, new Integer(count)); - } - else - { - residueHash.put(res, new Integer(1)); - } - } - else - { - if (residueHash.containsKey("-")) - { - count = ((Integer) residueHash.get("-")).intValue(); - count++; - residueHash.put("-", new Integer(count)); - } - else - { - residueHash.put("-", new Integer(1)); - } - } - } - } - - residueHash.put("maxCount", new Integer(maxCount)); - residueHash.put("maxResidue", maxResidue); - - - //Size is redundant at present if we calculate percentage here - //residueHash.put("size", new Integer(jSize)); - //residueHash.put("nogaps", new Integer(nongap)); - - percentage = ((float)maxCount*100) / (float)jSize; - residueHash.put("pid_gaps", new Float(percentage) ); - - percentage = ((float)maxCount*100) / (float)nongap; - residueHash.put("pid_nogaps", new Float(percentage) ); - result.addElement(residueHash); - } - - - - return result; - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) + * Copyright (C) 2008 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.analysis; + +import java.util.*; + +import jalview.datamodel.*; + +/** + * Takes in a vector or array of sequences and column start and column end and + * returns a new Hashtable[] of size maxSeqLength, if Hashtable not supplied. + * This class is used extensively in calculating alignment colourschemes that + * depend on the amount of conservation in each alignment column. + * + * @author $author$ + * @version $Revision$ + */ +public class AAFrequency +{ + // No need to store 1000s of strings which are not + // visible to the user. + public static final String MAXCOUNT = "C"; + + public static final String MAXRESIDUE = "R"; + + public static final String PID_GAPS = "G"; + + public static final String PID_NOGAPS = "N"; + + public static final Hashtable[] calculate(Vector sequences, int start, + int end) + { + SequenceI[] seqs = new SequenceI[sequences.size()]; + int width = 0; + for (int i = 0; i < sequences.size(); i++) + { + seqs[i] = (SequenceI) sequences.elementAt(i); + if (seqs[i].getLength() > width) + { + width = seqs[i].getLength(); + } + } + + Hashtable[] reply = new Hashtable[width]; + + if (end >= width) + { + end = width; + } + + calculate(seqs, start, end, reply); + + return reply; + } + + public static final void calculate(SequenceI[] sequences, int start, + int end, Hashtable[] result) + { + Hashtable residueHash; + int maxCount, nongap, i, j, v, jSize = sequences.length; + String maxResidue; + char c; + float percentage; + + int[] values = new int[255]; + + char[] seq; + + for (i = start; i < end; i++) + { + residueHash = new Hashtable(); + maxCount = 0; + maxResidue = ""; + nongap = 0; + values = new int[255]; + + for (j = 0; j < jSize; j++) + { + seq = sequences[j].getSequence(); + if (seq.length > i) + { + c = seq[i]; + + if (c == '.' || c == ' ') + { + c = '-'; + } + + if (c == '-') + { + values['-']++; + continue; + } + else if ('a' <= c && c <= 'z') + { + c -= 32; // ('a' - 'A'); + } + + nongap++; + values[c]++; + + } + else + { + values['-']++; + } + } + + for (v = 'A'; v < 'Z'; v++) + { + if (values[v] < 2 || values[v] < maxCount) + { + continue; + } + + if (values[v] > maxCount) + { + maxResidue = String.valueOf((char) v); + } + else if (values[v] == maxCount) + { + maxResidue += String.valueOf((char) v); + } + maxCount = values[v]; + } + + if (maxResidue.length() == 0) + { + maxResidue = "-"; + } + + residueHash.put(MAXCOUNT, new Integer(maxCount)); + residueHash.put(MAXRESIDUE, maxResidue); + + percentage = ((float) maxCount * 100) / (float) jSize; + residueHash.put(PID_GAPS, new Float(percentage)); + + percentage = ((float) maxCount * 100) / (float) nongap; + residueHash.put(PID_NOGAPS, new Float(percentage)); + result[i] = residueHash; + } + } +}