X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=03cdc15ecba02e2bd677df853c65d177a99aa922;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=15618de9beddc09413c338604d622d8041b3eef1;hpb=d69ea8f1997771890b44e4b332a7ca84fe6f0893;p=jalview.git diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java index 15618de..03cdc15 100755 --- a/src/jalview/analysis/AAFrequency.java +++ b/src/jalview/analysis/AAFrequency.java @@ -1,33 +1,30 @@ /* -* 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 -*/ + * 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.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 $author$ @@ -35,108 +32,125 @@ import java.util.*; */ public class AAFrequency { - /** Takes in a !!ARRAY!! of sequences and column start and column end - * and fills given 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 final Hashtable [] calculate(Vector sequences, int start, int end) - { - SequenceI [] seqs = new SequenceI[sequences.size()]; - int width = 0; - for(int i=0; iwidth) - width = seqs[i].getLength(); - } - - Hashtable [] reply = new Hashtable[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; + //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(); + } + } - int[] values = new int[132]; + Hashtable[] reply = new Hashtable[width]; - for (i = start; i < end; i++) + 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) { - residueHash = new Hashtable(); - maxCount = 0; - maxResidue = "-"; - nongap = 0; - values = new int[132]; + 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 (j = 0; j < jSize; j++) + for (i = start; i < end; i++) { - if (sequences[j].getLength() > i) - { - c = sequences[j].getCharAt(i); + residueHash = new Hashtable(); + maxCount = 0; + maxResidue = ""; + nongap = 0; + values = new int[255]; - if ('a' <= c && c <= 'z') + for (j = 0; j < jSize; j++) + { + seq = sequences[j].getSequence(); + if (seq.length > i) { - c -= ('a' - 'A'); - } + c = seq[i]; + + if (c == '.' || c == ' ') + { + c = '-'; + } + + if (c == '-') + { + values['-']++; + continue; + } + else if ('a' <= c && c <= 'z') + { + c -= 32; //('a' - 'A'); + } + + nongap++; + values[c]++; - if (jalview.util.Comparison.isGap(c)) - { - c = '-'; // we always use this for gaps in the property vectors } else { - nongap++; + values['-']++; } - - values[c]++; - - } - else - { - values['-']++; } - } - - for (v = 'A'; v < 'Z'; v++) - { - if (values[v] == 0 || values[v] < maxCount) - continue; - if (values[v] > maxCount) + for (v = 'A'; v < 'Z'; v++) { - maxResidue = String.valueOf( (char) 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]; } - else if (values[v] == maxCount) + + if (maxResidue.length() == 0) { - maxResidue += String.valueOf( (char) v); + maxResidue = "-"; } - maxCount = values[v]; - } + residueHash.put(MAXCOUNT, new Integer(maxCount)); + residueHash.put(MAXRESIDUE, 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) jSize; - residueHash.put("pid_gaps", new Float(percentage)); - - percentage = ( (float) maxCount * 100) / (float) nongap; - residueHash.put("pid_nogaps", new Float(percentage)); - result[i] = residueHash; + percentage = ( (float) maxCount * 100) / (float) nongap; + residueHash.put(PID_NOGAPS, new Float(percentage)); + result[i] = residueHash; + } } } -} - -