X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=3db44350a0b9173d56cae2343672a41dd791fb00;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=0de81677fa8d7a6a1415095408dbd8155117851b;hpb=85de15725d1b74ba9e0c35a104132206615d8c13;p=jalview.git diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java index 0de8167..3db4435 100755 --- a/src/jalview/analysis/AlignSeq.java +++ b/src/jalview/analysis/AlignSeq.java @@ -1,20 +1,19 @@ /* - * 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 + * 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; @@ -27,40 +26,55 @@ import jalview.schemes.*; import jalview.util.*; /** - * - * + * + * * @author $author$ * @version $Revision$ */ public class AlignSeq { public static final String PEP = "pep"; + public static final String DNA = "dna"; - + static String[] dna = - { - "A", "C", "G", "T", "-"}; - //"C", "T", "A", "G", "-"}; + { "A", "C", "G", "T", "-" }; + + // "C", "T", "A", "G", "-"}; static String[] pep = - { - "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", - "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "-" - }; + { "A", "R", "N", "D", "C", "Q", "E", "G", "H", "I", "L", "K", "M", "F", + "P", "S", "T", "W", "Y", "V", "B", "Z", "X", "-" }; + int[][] score; + int[][] E; + int[][] F; + int[][] traceback; + int[] seq1; + int[] seq2; + SequenceI s1; + SequenceI s2; + public String s1str; + public String s2str; + int maxi; + int maxj; + int[] aseq1; + int[] aseq2; + public String astr1 = ""; + public String astr2 = ""; /** DOCUMENT ME!! */ @@ -74,51 +88,67 @@ public class AlignSeq /** DOCUMENT ME!! */ public int seq2end; + int count; /** DOCUMENT ME!! */ public int maxscore; + float pid; + int prev = 0; + int gapOpen = 120; + int gapExtend = 20; + int[][] lookup = ResidueProperties.getBLOSUM62(); + String[] intToStr = pep; + int defInt = 23; + StringBuffer output = new StringBuffer(); + String type; + private int[] charToInt; + /** * Creates a new AlignSeq object. - * - * @param s1 DOCUMENT ME! - * @param s2 DOCUMENT ME! - * @param type DOCUMENT ME! + * + * @param s1 + * DOCUMENT ME! + * @param s2 + * DOCUMENT ME! + * @param type + * DOCUMENT ME! */ public AlignSeq(SequenceI s1, SequenceI s2, String type) { - SeqInit(s1, s1.getSequenceAsString(), s2, s2.getSequenceAsString(), type); + SeqInit(s1, s1.getSequenceAsString(), s2, s2.getSequenceAsString(), + type); } /** * Creates a new AlignSeq object. - * - * @param s1 DOCUMENT ME! - * @param s2 DOCUMENT ME! - * @param type DOCUMENT ME! + * + * @param s1 + * DOCUMENT ME! + * @param s2 + * DOCUMENT ME! + * @param type + * DOCUMENT ME! */ - public AlignSeq(SequenceI s1, - String string1, - SequenceI s2, - String string2, - String type) + 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); } /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public int getMaxScore() @@ -128,7 +158,7 @@ public class AlignSeq /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public int getSeq2Start() @@ -138,7 +168,7 @@ public class AlignSeq /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public int getSeq2End() @@ -148,7 +178,7 @@ public class AlignSeq /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public int getSeq1Start() @@ -158,7 +188,7 @@ public class AlignSeq /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public int getSeq1End() @@ -168,7 +198,7 @@ public class AlignSeq /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public String getOutput() @@ -178,7 +208,7 @@ public class AlignSeq /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public String getAStr1() @@ -188,7 +218,7 @@ public class AlignSeq /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public String getAStr2() @@ -198,7 +228,7 @@ public class AlignSeq /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public int[] getASeq1() @@ -208,7 +238,7 @@ public class AlignSeq /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public int[] getASeq2() @@ -218,7 +248,7 @@ public class AlignSeq /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public SequenceI getS1() @@ -228,7 +258,7 @@ public class AlignSeq /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public SequenceI getS2() @@ -238,18 +268,20 @@ public class AlignSeq /** * DOCUMENT ME! - * - * @param s1 DOCUMENT ME! - * @param string1 - string to align for sequence1 - * @param s2 sequence 2 - * @param string2 - string to align for sequence2 - * @param type DNA or PEPTIDE + * + * @param s1 + * DOCUMENT ME! + * @param string1 + * - string to align for sequence1 + * @param s2 + * sequence 2 + * @param string2 + * - string to align for sequence2 + * @param type + * DNA or PEPTIDE */ - public void SeqInit(SequenceI s1, - String string1, - SequenceI s2, - String string2, - String type) + public void SeqInit(SequenceI s1, String string1, SequenceI s2, + String string2, String type) { this.s1 = s1; this.s2 = s2; @@ -257,11 +289,8 @@ public class AlignSeq SeqInit(string1, string2); } - public void SeqInit(SequenceI s1, - String string1, - SequenceI s2, - String string2, - ScoreMatrix scoreMatrix) + public void SeqInit(SequenceI s1, String string1, SequenceI s2, + String string2, ScoreMatrix scoreMatrix) { this.s1 = s1; this.s2 = s2; @@ -270,7 +299,9 @@ public class AlignSeq } /** - * construct score matrix for string1 and string2 (after removing any existing gaps + * construct score matrix for string1 and string2 (after removing any existing + * gaps + * * @param string1 * @param string2 */ @@ -281,51 +312,53 @@ public class AlignSeq if (s1str.length() == 0 || s2str.length() == 0) { - output.append("ALL GAPS: " + - (s1str.length() == 0 ? s1.getName() : " ") - + (s2str.length() == 0 ? s2.getName() : "")); + output.append("ALL GAPS: " + + (s1str.length() == 0 ? s1.getName() : " ") + + (s2str.length() == 0 ? s2.getName() : "")); return; } - //System.out.println("lookuip " + rt.freeMemory() + " "+ rt.totalMemory()); + // System.out.println("lookuip " + rt.freeMemory() + " "+ rt.totalMemory()); seq1 = new int[s1str.length()]; - //System.out.println("seq1 " + rt.freeMemory() +" " + rt.totalMemory()); + // System.out.println("seq1 " + rt.freeMemory() +" " + rt.totalMemory()); seq2 = new int[s2str.length()]; - //System.out.println("seq2 " + rt.freeMemory() + " " + rt.totalMemory()); + // System.out.println("seq2 " + rt.freeMemory() + " " + rt.totalMemory()); score = new int[s1str.length()][s2str.length()]; - //System.out.println("score " + rt.freeMemory() + " " + rt.totalMemory()); + // System.out.println("score " + rt.freeMemory() + " " + rt.totalMemory()); E = new int[s1str.length()][s2str.length()]; - //System.out.println("E " + rt.freeMemory() + " " + rt.totalMemory()); + // System.out.println("E " + rt.freeMemory() + " " + rt.totalMemory()); F = new int[s1str.length()][s2str.length()]; traceback = new int[s1str.length()][s2str.length()]; - //System.out.println("F " + rt.freeMemory() + " " + rt.totalMemory()); + // System.out.println("F " + rt.freeMemory() + " " + rt.totalMemory()); seq1 = stringToInt(s1str, type); - //System.out.println("seq1 " + rt.freeMemory() + " " + rt.totalMemory()); + // System.out.println("seq1 " + rt.freeMemory() + " " + rt.totalMemory()); seq2 = stringToInt(s2str, type); - //System.out.println("Seq2 " + rt.freeMemory() + " " + rt.totalMemory()); - // long tstart = System.currentTimeMillis(); - // calcScoreMatrix(); - //long tend = System.currentTimeMillis(); - //System.out.println("Time take to calculate score matrix = " + (tend-tstart) + " ms"); - // printScoreMatrix(score); - //System.out.println(); - //printScoreMatrix(traceback); - //System.out.println(); - // printScoreMatrix(E); - //System.out.println(); - ///printScoreMatrix(F); - //System.out.println(); + // System.out.println("Seq2 " + rt.freeMemory() + " " + rt.totalMemory()); + // long tstart = System.currentTimeMillis(); + // calcScoreMatrix(); + // long tend = System.currentTimeMillis(); + // System.out.println("Time take to calculate score matrix = " + + // (tend-tstart) + " ms"); + // printScoreMatrix(score); + // System.out.println(); + // printScoreMatrix(traceback); + // System.out.println(); + // printScoreMatrix(E); + // System.out.println(); + // /printScoreMatrix(F); + // System.out.println(); // tstart = System.currentTimeMillis(); - //traceAlignment(); - //tend = System.currentTimeMillis(); - //System.out.println("Time take to traceback alignment = " + (tend-tstart) + " ms"); + // traceAlignment(); + // tend = System.currentTimeMillis(); + // System.out.println("Time take to traceback alignment = " + (tend-tstart) + // + " ms"); } private void setDefaultParams(String type) @@ -348,18 +381,20 @@ public class AlignSeq if (type.equals(AlignSeq.PEP)) { intToStr = pep; + charToInt = ResidueProperties.aaIndex; defInt = 23; } else if (type.equals(AlignSeq.DNA)) { intToStr = dna; + charToInt = ResidueProperties.nucleotideIndex; defInt = 4; } else { output.append("Wrong type = dna or pep only"); - throw new Error("Unknown Type " + type2 + - " - dna or pep are the only allowed values."); + throw new Error("Unknown Type " + type2 + + " - dna or pep are the only allowed values."); } } @@ -391,7 +426,7 @@ public class AlignSeq } } - // System.out.println(maxi + " " + maxj + " " + score[maxi][maxj]); + // System.out.println(maxi + " " + maxj + " " + score[maxi][maxj]); int i = maxi; int j = maxj; int trace; @@ -405,15 +440,15 @@ public class AlignSeq count = (seq1.length + seq2.length) - 1; - while ( (i > 0) && (j > 0)) + while ((i > 0) && (j > 0)) { - if ( (aseq1[count] != defInt) && (i >= 0)) + if ((aseq1[count] != defInt) && (i >= 0)) { aseq1[count] = seq1[i]; astr1 = s1str.charAt(i) + astr1; } - if ( (aseq2[count] != defInt) && (j > 0)) + if ((aseq2[count] != defInt) && (j > 0)) { aseq2[count] = seq2[j]; astr2 = s2str.charAt(j) + astr2; @@ -463,42 +498,53 @@ public class AlignSeq */ public void printAlignment(java.io.PrintStream os) { - // TODO: Use original sequence characters rather than re-translated characters in output + // 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; + int nochunks = ((aseq1.length - count) / len) + 1; pid = 0; output.append("Score = " + score[maxi][maxj] + "\n"); output.append("Length of alignment = " + (aseq1.length - count) + "\n"); output.append("Sequence "); output.append(new Format("%" + maxid + "s").form(s1.getName())); - output.append(" : " + s1.getStart() + " - " + s1.getEnd() + - " (Sequence length = " + - s1str.length() + ")\n"); + output.append(" : " + s1.getStart() + " - " + s1.getEnd() + + " (Sequence length = " + s1str.length() + ")\n"); output.append("Sequence "); output.append(new Format("%" + maxid + "s").form(s2.getName())); - output.append(" : " + s2.getStart() + " - " + s2.getEnd() + - " (Sequence length = " + - s2str.length() + ")\n\n"); - + output.append(" : " + s2.getStart() + " - " + s2.getEnd() + + " (Sequence length = " + s2str.length() + ")\n\n"); + 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++) { - if ( (i + (j * len)) < astr1.length()) + if ((i + (j * len)) < astr1.length()) { - output.append(astr1.charAt(i + - (j * len))); + output.append(astr1.charAt(i + (j * len))); } } @@ -508,19 +554,19 @@ public class AlignSeq // Print out the matching chars for (int i = 0; i < len; i++) { - if ( (i + (j * len)) < astr1.length()) + if ((i + (j * len)) < astr1.length()) { - if (astr1.charAt(i + (j * len))==astr2.charAt(i + (j * len)) && - !jalview.util.Comparison.isGap(astr1.charAt(i + (j * len)))) + if (astr1.charAt(i + (j * len)) == astr2.charAt(i + (j * len)) + && !jalview.util.Comparison.isGap(astr1.charAt(i + + (j * len)))) { pid++; output.append("|"); } else if (type.equals("pep")) { - if (ResidueProperties.getPAM250( - astr1.charAt(i + (j * len)), - astr2.charAt(i + (j * len)))>0) + if (ResidueProperties.getPAM250(astr1.charAt(i + (j * len)), + astr2.charAt(i + (j * len))) > 0) { output.append("."); } @@ -538,12 +584,12 @@ 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++) { - if ( (i + (j * len)) < astr2.length()) + if ((i + (j * len)) < astr2.length()) { output.append(astr2.charAt(i + (j * len))); } @@ -553,20 +599,22 @@ public class AlignSeq } pid = pid / (float) (aseq1.length - count) * 100; - output = output.append(new Format("Percentage ID = %2.2f\n\n").form(pid)); + output = output.append(new Format("Percentage ID = %2.2f\n\n") + .form(pid)); try { os.print(output.toString()); + } catch (Exception ex) + { } - catch (Exception ex) - {} } /** * DOCUMENT ME! - * - * @param mat DOCUMENT ME! + * + * @param mat + * DOCUMENT ME! */ public void printScoreMatrix(int[][] mat) { @@ -604,10 +652,12 @@ public class AlignSeq /** * DOCUMENT ME! - * - * @param i DOCUMENT ME! - * @param j DOCUMENT ME! - * + * + * @param i + * DOCUMENT ME! + * @param j + * DOCUMENT ME! + * * @return DOCUMENT ME! */ public int findTrace(int i, int j) @@ -668,8 +718,7 @@ public class AlignSeq E[0][j] = max(score[0][j - 1] - gapOpen, E[0][j - 1] - gapExtend); F[0][j] = -gapExtend; - score[0][j] = max(lookup[seq1[0]][seq2[j]] * 10, -gapOpen, - -gapExtend); + score[0][j] = max(lookup[seq1[0]][seq2[j]] * 10, -gapOpen, -gapExtend); traceback[0][j] = 1; } @@ -689,13 +738,11 @@ public class AlignSeq { for (int j = 1; j < m; j++) { - E[i][j] = max(score[i][j - 1] - gapOpen, E[i][j - 1] - - gapExtend); - F[i][j] = max(score[i - 1][j] - gapOpen, F[i - 1][j] - - gapExtend); + E[i][j] = max(score[i][j - 1] - gapOpen, E[i][j - 1] - gapExtend); + F[i][j] = max(score[i - 1][j] - gapOpen, F[i - 1][j] - gapExtend); - score[i][j] = max(score[i - 1][j - 1] + - (lookup[seq1[i]][seq2[j]] * 10), E[i][j], F[i][j]); + score[i][j] = max(score[i - 1][j - 1] + + (lookup[seq1[i]][seq2[j]] * 10), E[i][j], F[i][j]); traceback[i][j] = findTrace(i, j); } } @@ -703,10 +750,12 @@ public class AlignSeq /** * DOCUMENT ME! - * - * @param gapChar DOCUMENT ME! - * @param seq DOCUMENT ME! - * + * + * @param gapChar + * DOCUMENT ME! + * @param seq + * DOCUMENT ME! + * * @return DOCUMENT ME! */ public static String extractGaps(String gapChar, String seq) @@ -724,11 +773,14 @@ public class AlignSeq /** * DOCUMENT ME! - * - * @param i1 DOCUMENT ME! - * @param i2 DOCUMENT ME! - * @param i3 DOCUMENT ME! - * + * + * @param i1 + * DOCUMENT ME! + * @param i2 + * DOCUMENT ME! + * @param i3 + * DOCUMENT ME! + * * @return DOCUMENT ME! */ public int max(int i1, int i2, int i3) @@ -750,10 +802,12 @@ public class AlignSeq /** * DOCUMENT ME! - * - * @param i1 DOCUMENT ME! - * @param i2 DOCUMENT ME! - * + * + * @param i1 + * DOCUMENT ME! + * @param i2 + * DOCUMENT ME! + * * @return DOCUMENT ME! */ public int max(int i1, int i2) @@ -770,10 +824,12 @@ public class AlignSeq /** * DOCUMENT ME! - * - * @param s DOCUMENT ME! - * @param type DOCUMENT ME! - * + * + * @param s + * DOCUMENT ME! + * @param type + * DOCUMENT ME! + * * @return DOCUMENT ME! */ public int[] stringToInt(String s, String type) @@ -792,34 +848,16 @@ public class AlignSeq try { - if (type.equals("pep")) + 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.aaIndex[c]; - if (seq1[i] > 23) - { - seq1[i] = 23; - } - } - else if (type.equals("dna")) - { - seq1[i] = ResidueProperties.nucleotideIndex[c]; - if (seq1[i] > 4) - { - seq1[i] = 4; - } + seq1[i] = defInt; } - } - catch (Exception e) + } catch (Exception e) { - if (type.equals("dna")) - { - seq1[i] = 4; - } - else - { - seq1[i] = 23; - } + seq1[i] = defInt; } } @@ -828,15 +866,20 @@ public class AlignSeq /** * DOCUMENT ME! - * - * @param g DOCUMENT ME! - * @param mat DOCUMENT ME! - * @param n DOCUMENT ME! - * @param m DOCUMENT ME! - * @param psize DOCUMENT ME! + * + * @param g + * DOCUMENT ME! + * @param mat + * DOCUMENT ME! + * @param n + * DOCUMENT ME! + * @param m + * DOCUMENT ME! + * @param psize + * DOCUMENT ME! */ public static void displayMatrix(Graphics g, int[][] mat, int n, int m, - int psize) + int psize) { int max = -1000; int min = 1000; @@ -866,12 +909,12 @@ public class AlignSeq int x = psize * i; int y = psize * j; - // System.out.println(mat[i][j]); + // System.out.println(mat[i][j]); float score = (float) (mat[i][j] - min) / (float) (max - min); g.setColor(new Color(score, 0, 0)); g.fillRect(x, y, psize, psize); - // System.out.println(x + " " + y + " " + score); + // System.out.println(x + " " + y + " " + score); } } }