X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=4a8955bee6bf8ee3f8d4da23bc5cffd6a50392d5;hb=e498cc04385671872ab98220219aaeac2ec245f2;hp=c9a8077edd925da6dd7237f8ac03efad20345bbd;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java index c9a8077..4a8955b 100755 --- a/src/jalview/analysis/AlignSeq.java +++ b/src/jalview/analysis/AlignSeq.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 file is part of Jalview. * - * 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. + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.analysis; @@ -113,15 +112,17 @@ public class AlignSeq String type; + private int[] charToInt; + /** * Creates a new AlignSeq object. * * @param s1 - * DOCUMENT ME! + * DOCUMENT ME! * @param s2 - * DOCUMENT ME! + * DOCUMENT ME! * @param type - * DOCUMENT ME! + * DOCUMENT ME! */ public AlignSeq(SequenceI s1, SequenceI s2, String type) { @@ -133,16 +134,16 @@ public class AlignSeq * Creates a new AlignSeq object. * * @param s1 - * DOCUMENT ME! + * DOCUMENT ME! * @param s2 - * DOCUMENT ME! + * DOCUMENT ME! * @param type - * DOCUMENT ME! + * DOCUMENT ME! */ public AlignSeq(SequenceI s1, String string1, SequenceI s2, String string2, String type) { - SeqInit(s1, string1, s2, string2, type); + SeqInit(s1, string1.toUpperCase(), s2, string2.toUpperCase(), type); } /** @@ -269,15 +270,15 @@ public class AlignSeq * DOCUMENT ME! * * @param s1 - * DOCUMENT ME! - * @param string1 - - * string to align for sequence1 + * DOCUMENT ME! + * @param string1 + * - string to align for sequence1 * @param s2 - * sequence 2 - * @param string2 - - * string to align for sequence2 + * sequence 2 + * @param string2 + * - string to align for sequence2 * @param type - * DNA or PEPTIDE + * DNA or PEPTIDE */ public void SeqInit(SequenceI s1, String string1, SequenceI s2, String string2, String type) @@ -380,12 +381,14 @@ public class AlignSeq if (type.equals(AlignSeq.PEP)) { intToStr = pep; - defInt = 23; + charToInt = ResidueProperties.aaIndex; + defInt = ResidueProperties.maxProteinIndex; } else if (type.equals(AlignSeq.DNA)) { intToStr = dna; - defInt = 4; + charToInt = ResidueProperties.nucleotideIndex; + defInt = ResidueProperties.maxNucleotideIndex; } else { @@ -498,12 +501,25 @@ public class AlignSeq // TODO: Use original sequence characters rather than re-translated // characters in output // Find the biggest id length for formatting purposes + String s1id = s1.getName(), s2id = s2.getName(); int maxid = s1.getName().length(); if (s2.getName().length() > maxid) { maxid = s2.getName().length(); } - + if (maxid > 30) + { + maxid = 30; + // JAL-527 - truncate the sequence ids + if (s1.getName().length() > maxid) + { + s1id = s1.getName().substring(0, 30); + } + if (s2.getName().length() > maxid) + { + s2id = s2.getName().substring(0, 30); + } + } int len = 72 - maxid - 1; int nochunks = ((aseq1.length - count) / len) + 1; pid = 0; @@ -522,8 +538,7 @@ public class AlignSeq for (int j = 0; j < nochunks; j++) { // Print the first aligned sequence - output.append(new Format("%" + (maxid) + "s").form(s1.getName()) - + " "); + output.append(new Format("%" + (maxid) + "s").form(s1id) + " "); for (int i = 0; i < len; i++) { @@ -569,8 +584,7 @@ public class AlignSeq // Now print the second aligned sequence output = output.append("\n"); - output = output.append(new Format("%" + (maxid) + "s").form(s2 - .getName()) + output = output.append(new Format("%" + (maxid) + "s").form(s2id) + " "); for (int i = 0; i < len; i++) @@ -600,7 +614,7 @@ public class AlignSeq * DOCUMENT ME! * * @param mat - * DOCUMENT ME! + * DOCUMENT ME! */ public void printScoreMatrix(int[][] mat) { @@ -640,9 +654,9 @@ public class AlignSeq * DOCUMENT ME! * * @param i - * DOCUMENT ME! + * DOCUMENT ME! * @param j - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -738,9 +752,9 @@ public class AlignSeq * DOCUMENT ME! * * @param gapChar - * DOCUMENT ME! + * DOCUMENT ME! * @param seq - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -761,11 +775,11 @@ public class AlignSeq * DOCUMENT ME! * * @param i1 - * DOCUMENT ME! + * DOCUMENT ME! * @param i2 - * DOCUMENT ME! + * DOCUMENT ME! * @param i3 - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -790,9 +804,9 @@ public class AlignSeq * DOCUMENT ME! * * @param i1 - * DOCUMENT ME! + * DOCUMENT ME! * @param i2 - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -812,9 +826,9 @@ public class AlignSeq * DOCUMENT ME! * * @param s - * DOCUMENT ME! + * DOCUMENT ME! * @param type - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -834,33 +848,16 @@ public class AlignSeq try { - if (type.equals("pep")) - { - seq1[i] = ResidueProperties.aaIndex[c]; - if (seq1[i] > 23) - { - seq1[i] = 23; - } - } - else if (type.equals("dna")) + seq1[i] = charToInt[c]; // set accordingly from setType + if (seq1[i] < 0 || seq1[i] > defInt) // set from setType: 23 for + // peptides, or 4 for NA. { - seq1[i] = ResidueProperties.nucleotideIndex[c]; - if (seq1[i] > 4) - { - seq1[i] = 4; - } + seq1[i] = defInt; } } catch (Exception e) { - if (type.equals("dna")) - { - seq1[i] = 4; - } - else - { - seq1[i] = 23; - } + seq1[i] = defInt; } } @@ -871,15 +868,15 @@ public class AlignSeq * DOCUMENT ME! * * @param g - * DOCUMENT ME! + * DOCUMENT ME! * @param mat - * DOCUMENT ME! + * DOCUMENT ME! * @param n - * DOCUMENT ME! + * DOCUMENT ME! * @param m - * DOCUMENT ME! + * DOCUMENT ME! * @param psize - * DOCUMENT ME! + * DOCUMENT ME! */ public static void displayMatrix(Graphics g, int[][] mat, int n, int m, int psize) @@ -921,4 +918,93 @@ public class AlignSeq } } } + + /** + * compute the PID vector used by the redundancy filter. + * + * @param originalSequences + * - sequences in alignment that are to filtered + * @param omitHidden + * - null or strings to be analysed (typically, visible portion of + * each sequence in alignment) + * @param start + * - first column in window for calculation + * @param end + * - last column in window for calculation + * @param ungapped + * - if true then use ungapped sequence to compute PID + * @return vector containing maximum PID for i-th sequence and any sequences + * longer than that seuqence + */ + public static float[] computeRedundancyMatrix( + SequenceI[] originalSequences, String[] omitHidden, int start, + int end, boolean ungapped) + { + int height = originalSequences.length; + float[] redundancy = new float[height]; + int[] lngth = new int[height]; + for (int i = 0; i < height; i++) + { + redundancy[i] = 0f; + lngth[i] = -1; + } + + // long start = System.currentTimeMillis(); + + float pid; + String seqi, seqj; + for (int i = 0; i < height; i++) + { + + for (int j = 0; j < i; j++) + { + if (i == j) + { + continue; + } + + if (omitHidden == null) + { + seqi = originalSequences[i].getSequenceAsString(start, end); + seqj = originalSequences[j].getSequenceAsString(start, end); + } + else + { + seqi = omitHidden[i]; + seqj = omitHidden[j]; + } + if (lngth[i] == -1) + { + String ug = AlignSeq.extractGaps(Comparison.GapChars, seqi); + lngth[i] = ug.length(); + if (ungapped) + { + seqi = ug; + } + } + if (lngth[j] == -1) + { + String ug = AlignSeq.extractGaps(Comparison.GapChars, seqj); + lngth[j] = ug.length(); + if (ungapped) + { + seqj = ug; + } + } + pid = Comparison.PID(seqi, seqj); + + // use real sequence length rather than string length + if (lngth[j] < lngth[i]) + { + redundancy[j] = Math.max(pid, redundancy[j]); + } + else + { + redundancy[i] = Math.max(pid, redundancy[i]); + } + + } + } + return redundancy; + } }