X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=03cdc15ecba02e2bd677df853c65d177a99aa922;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=4ef250b2cf6b10d564fd938b9b85557144eae437;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java index 4ef250b..03cdc15 100755 --- a/src/jalview/analysis/AAFrequency.java +++ b/src/jalview/analysis/AAFrequency.java @@ -1,35 +1,30 @@ /* -* 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 -*/ + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 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.*; +import jalview.datamodel.*; /** - * 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. + * 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 $author$ @@ -37,98 +32,125 @@ import java.util.*; */ 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) + //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++) { - Vector result = new Vector(); + 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 (int i = start; i <= end; i++) + for (v = 'A'; v < 'Z'; v++) + { + if (values[v] < 2 || values[v] < maxCount) { - Hashtable residueHash = new Hashtable(); - int maxCount = 0; - String maxResidue = "-"; - int nongap = 0; - - for (int j = 0; j < sequences.size(); j++) - { - if (sequences.elementAt(j) instanceof Sequence) - { - Sequence s = (Sequence) sequences.elementAt(j); - - if (s.getSequence().length() > i) - { - String res = s.getSequence().charAt(i) + ""; - - if (!jalview.util.Comparison.isGap(res.charAt(0))) - { - nongap++; - } - else - { - res = "-"; // we always use this for gaps in the property vectors - } - - if (residueHash.containsKey(res)) - { - int 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("-")) - { - int count = ((Integer) residueHash.get("-")).intValue(); - count++; - residueHash.put("-", new Integer(count)); - } - else - { - residueHash.put("-", new Integer(1)); - } - } - } - } - - residueHash.put("maxCount", new Integer(maxCount)); - - if (maxCount < 0) - { - System.out.println("asasa " + maxCount); - } - - residueHash.put("maxResidue", maxResidue); - residueHash.put("size", new Integer(sequences.size())); - residueHash.put("nongap", new Integer(nongap)); - result.addElement(residueHash); + continue; } - return result; + 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; } + } }