X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAAFrequency.java;h=aadd8f0e82ab8ec034b49f7fd0fd0d00f45bbb9d;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=4ef250b2cf6b10d564fd938b9b85557144eae437;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java index 4ef250b..aadd8f0 100755 --- a/src/jalview/analysis/AAFrequency.java +++ b/src/jalview/analysis/AAFrequency.java @@ -1,134 +1,336 @@ -/* -* 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(); - - for (int i = start; i <= end; i++) - { - 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); - } - - return result; - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * + * 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 . + */ +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 String PROFILE = "P"; + + public static final Hashtable[] calculate(Vector sequences, int start, + int end) + { + return calculate(sequences, start, end, false); + } + + public static final Hashtable[] calculate(Vector sequences, int start, + int end, boolean profile) + { + 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, profile); + + return reply; + } + + public static final void calculate(SequenceI[] sequences, int start, + int end, Hashtable[] result) + { + calculate(sequences, start, end, result, false); + } + + public static final void calculate(SequenceI[] sequences, int start, + int end, Hashtable[] result, boolean profile) + { + 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++) + { + if (sequences[j]==null) + { + System.err.println("WARNING: Consensus skipping null sequence - possible race condition."); + continue; + } + 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 = "-"; + } + if (profile) + { + residueHash.put(PROFILE, new int[][] + { values, new int[] + { jSize, nongap } }); + } + 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; + } + } + + /** + * Compute all or part of the annotation row from the given consensus + * hashtable + * + * @param consensus + * - pre-allocated annotation row + * @param hconsensus + * @param iStart + * @param width + * @param ignoreGapsInConsensusCalculation + * @param includeAllConsSymbols + */ + public static void completeConsensus(AlignmentAnnotation consensus, + Hashtable[] hconsensus, int iStart, int width, + boolean ignoreGapsInConsensusCalculation, + boolean includeAllConsSymbols) + { + completeConsensus(consensus, hconsensus, iStart, width, + ignoreGapsInConsensusCalculation, includeAllConsSymbols, null); // new + // char[] + // { 'A', 'C', 'G', 'T', 'U' }); + } + + public static void completeConsensus(AlignmentAnnotation consensus, + Hashtable[] hconsensus, int iStart, int width, + boolean ignoreGapsInConsensusCalculation, + boolean includeAllConsSymbols, char[] alphabet) + { + float tval, value; + if (consensus == null || consensus.annotations == null + || consensus.annotations.length < width) + { + // called with a bad alignment annotation row - wait for it to be + // initialised properly + return; + } + for (int i = iStart; i < width; i++) + { + if (i >= hconsensus.length) + { + // happens if sequences calculated over were shorter than alignment + // width + consensus.annotations[i] = null; + continue; + } + value = 0; + if (ignoreGapsInConsensusCalculation) + { + value = ((Float) hconsensus[i].get(AAFrequency.PID_NOGAPS)) + .floatValue(); + } + else + { + value = ((Float) hconsensus[i].get(AAFrequency.PID_GAPS)) + .floatValue(); + } + + String maxRes = hconsensus[i].get(AAFrequency.MAXRESIDUE).toString(); + String mouseOver = hconsensus[i].get(AAFrequency.MAXRESIDUE) + " "; + if (maxRes.length() > 1) + { + mouseOver = "[" + maxRes + "] "; + maxRes = "+"; + } + int[][] profile = (int[][]) hconsensus[i].get(AAFrequency.PROFILE); + if (profile != null && includeAllConsSymbols) + { + mouseOver = ""; + if (alphabet != null) + { + for (int c = 0; c < alphabet.length; c++) + { + tval = ((float) profile[0][alphabet[c]]) + * 100f + / (float) profile[1][ignoreGapsInConsensusCalculation ? 1 + : 0]; + mouseOver += ((c == 0) ? "" : "; ") + alphabet[c] + " " + + ((int) tval) + "%"; + } + } + else + { + Object[] ca = new Object[profile[0].length]; + float[] vl = new float[profile[0].length]; + for (int c = 0; c < ca.length; c++) + { + ca[c] = new char[] + { (char) c }; + vl[c] = (float) profile[0][c]; + } + ; + jalview.util.QuickSort.sort(vl, ca); + for (int p = 0, c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--) + { + if (((char[]) ca[c])[0] != '-') + { + tval = ((float) profile[0][((char[]) ca[c])[0]]) + * 100f + / (float) profile[1][ignoreGapsInConsensusCalculation ? 1 + : 0]; + mouseOver += ((p == 0) ? "" : "; ") + ((char[]) ca[c])[0] + + " " + ((int) tval) + "%"; + p++; + + } + } + + } + } + else + { + mouseOver += ((int) value + "%"); + } + consensus.annotations[i] = new Annotation(maxRes, mouseOver, ' ', + value); + } + } + + /** + * get the sorted profile for the given position of the consensus + * + * @param hconsensus + * @return + */ + public static int[] extractProfile(Hashtable hconsensus, + boolean ignoreGapsInConsensusCalculation) + { + int[] rtnval = new int[64]; + int[][] profile = (int[][]) hconsensus.get(AAFrequency.PROFILE); + if (profile == null) + return null; + Object[] ca = new Object[profile[0].length]; + float[] vl = new float[profile[0].length]; + for (int c = 0; c < ca.length; c++) + { + ca[c] = new char[] + { (char) c }; + vl[c] = (float) profile[0][c]; + } + ; + jalview.util.QuickSort.sort(vl, ca); + rtnval[0] = 1; + for (int c = ca.length - 1; profile[0][((char[]) ca[c])[0]] > 0; c--) + { + if (((char[]) ca[c])[0] != '-') + { + rtnval[rtnval[0]++] = ((char[]) ca[c])[0]; + rtnval[rtnval[0]++] = (int) (((float) profile[0][((char[]) ca[c])[0]]) * 100f / (float) profile[1][ignoreGapsInConsensusCalculation ? 1 + : 0]); + } + } + return rtnval; + } +}