X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=d04e897e201c49aaa69098d94611582a954baa14;hb=adca107ff292173bc844ad4a5c6c7eba958ad24a;hp=b9119ed2187946080b4b2eef9dceeb7832915430;hpb=47168f025aefdaa044802bd5f8f510ffe43a4808;p=jalview.git diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java index b9119ed..d04e897 100755 --- a/src/jalview/analysis/AlignSeq.java +++ b/src/jalview/analysis/AlignSeq.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -19,13 +19,27 @@ * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.analysis; -import java.util.*; -import java.awt.*; - -import jalview.datamodel.*; -import jalview.schemes.*; -import jalview.util.*; +import jalview.analysis.scoremodels.PIDModel; +import jalview.analysis.scoremodels.ScoreMatrix; +import jalview.analysis.scoremodels.ScoreModels; +import jalview.analysis.scoremodels.SimilarityParams; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.Mapping; +import jalview.datamodel.Sequence; +import jalview.datamodel.SequenceI; +import jalview.util.Comparison; +import jalview.util.Format; +import jalview.util.MapList; +import jalview.util.MessageManager; + +import java.awt.Color; +import java.awt.Graphics; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; +import java.util.StringTokenizer; /** * @@ -39,19 +53,13 @@ public class AlignSeq public static final String DNA = "dna"; - static String[] dna = - { "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", "-" }; + private static final String NEWLINE = System.lineSeparator(); - int[][] score; + float[][] score; - int[][] E; + float[][] E; - int[][] F; + float[][] F; int[][] traceback; @@ -94,7 +102,7 @@ public class AlignSeq int count; /** DOCUMENT ME!! */ - public int maxscore; + public float maxscore; float pid; @@ -104,31 +112,26 @@ public class AlignSeq int gapExtend = 20; - int[][] lookup = ResidueProperties.getBLOSUM62(); - - String[] intToStr = pep; + float[][] lookup; - int defInt = 23; + int gapIndex = 23; StringBuffer output = new StringBuffer(); - String type; + String type; // AlignSeq.PEP or AlignSeq.DNA - private int[] charToInt; + private ScoreMatrix scoreModel; /** * Creates a new AlignSeq object. * - * @param s1 - * DOCUMENT ME! - * @param s2 - * DOCUMENT ME! - * @param type - * DOCUMENT ME! + * @param s1 first sequence for alignment + * @param s2 second sequence for alignment + * @param type molecule type, either AlignSeq.PEP or AlignSeq.DNA */ public AlignSeq(SequenceI s1, SequenceI s2, String type) { - SeqInit(s1, s1.getSequenceAsString(), s2, s2.getSequenceAsString(), + seqInit(s1, s1.getSequenceAsString(), s2, s2.getSequenceAsString(), type); } @@ -145,7 +148,7 @@ public class AlignSeq public AlignSeq(SequenceI s1, String string1, SequenceI s2, String string2, String type) { - SeqInit(s1, string1.toUpperCase(), s2, string2.toUpperCase(), type); + seqInit(s1, string1.toUpperCase(), s2, string2.toUpperCase(), type); } /** @@ -153,7 +156,7 @@ public class AlignSeq * * @return DOCUMENT ME! */ - public int getMaxScore() + public float getMaxScore() { return maxscore; } @@ -249,68 +252,64 @@ public class AlignSeq } /** - * DOCUMENT ME! * - * @return DOCUMENT ME! + * @return aligned instance of Seq 1 */ - public SequenceI getS1() + public SequenceI getAlignedSeq1() { - return s1; + SequenceI alSeq1 = new Sequence(s1.getName(), getAStr1()); + alSeq1.setStart(s1.getStart() + getSeq1Start() - 1); + alSeq1.setEnd(s1.getStart() + getSeq1End() - 1); + alSeq1.setDatasetSequence(s1.getDatasetSequence() == null ? s1 : s1 + .getDatasetSequence()); + return alSeq1; } /** - * DOCUMENT ME! * - * @return DOCUMENT ME! + * @return aligned instance of Seq 2 */ - public SequenceI getS2() + public SequenceI getAlignedSeq2() { - return s2; + SequenceI alSeq2 = new Sequence(s2.getName(), getAStr2()); + alSeq2.setStart(s2.getStart() + getSeq2Start() - 1); + alSeq2.setEnd(s2.getStart() + getSeq2End() - 1); + alSeq2.setDatasetSequence(s2.getDatasetSequence() == null ? s2 : s2 + .getDatasetSequence()); + return alSeq2; } /** * Construct score matrix for sequences with standard DNA or PEPTIDE matrix - * @param s1 - sequence 1 - * @param string1 - string to use for s1 - * @param s2 - sequence 2 - * @param string2 - string to use for s2 + * + * @param s1 + * - sequence 1 + * @param string1 + * - string to use for s1 + * @param s2 + * - sequence 2 + * @param string2 + * - string to use for s2 * @param type * DNA or PEPTIDE */ - public void SeqInit(SequenceI s1, String string1, SequenceI s2, + public void seqInit(SequenceI s1, String string1, SequenceI s2, String string2, String type) { this.s1 = s1; this.s2 = s2; setDefaultParams(type); - SeqInit(string1, string2); - } - - /** - * Construct score matrix for sequences with custom substitution matrix - * @param s1 - sequence 1 - * @param string1 - string to use for s1 - * @param s2 - sequence 2 - * @param string2 - string to use for s2 - * @param scoreMatrix - substitution matrix to use for alignment - */ - public void SeqInit(SequenceI s1, String string1, SequenceI s2, - String string2, ScoreMatrix scoreMatrix) - { - this.s1 = s1; - this.s2 = s2; - setType(scoreMatrix.isDNA() ? AlignSeq.DNA : AlignSeq.PEP); - lookup = scoreMatrix.getMatrix(); + seqInit(string1, string2); } /** * construct score matrix for string1 and string2 (after removing any existing * gaps * - * @param string1 + * @param string1 * @param string2 */ - private void SeqInit(String string1, String string2) + private void seqInit(String string1, String string2) { s1str = extractGaps(jalview.util.Comparison.GapChars, string1); s2str = extractGaps(jalview.util.Comparison.GapChars, string2); @@ -323,84 +322,37 @@ public class AlignSeq return; } - // System.out.println("lookuip " + rt.freeMemory() + " "+ rt.totalMemory()); seq1 = new int[s1str.length()]; - // System.out.println("seq1 " + rt.freeMemory() +" " + rt.totalMemory()); seq2 = new int[s2str.length()]; - // System.out.println("seq2 " + rt.freeMemory() + " " + rt.totalMemory()); - score = new int[s1str.length()][s2str.length()]; + score = new float[s1str.length()][s2str.length()]; - // System.out.println("score " + rt.freeMemory() + " " + rt.totalMemory()); - E = new int[s1str.length()][s2str.length()]; + E = new float[s1str.length()][s2str.length()]; - // System.out.println("E " + rt.freeMemory() + " " + rt.totalMemory()); - F = new int[s1str.length()][s2str.length()]; + F = new float[s1str.length()][s2str.length()]; traceback = new int[s1str.length()][s2str.length()]; - // System.out.println("F " + rt.freeMemory() + " " + rt.totalMemory()); - seq1 = stringToInt(s1str, type); - - // 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(); - // tstart = System.currentTimeMillis(); - // traceAlignment(); - // tend = System.currentTimeMillis(); - // System.out.println("Time take to traceback alignment = " + (tend-tstart) - // + " ms"); - } - - private void setDefaultParams(String type) - { - setType(type); + seq1 = indexEncode(s1str); - if (type.equals(AlignSeq.PEP)) - { - lookup = ResidueProperties.getDefaultPeptideMatrix(); - } - else if (type.equals(AlignSeq.DNA)) - { - lookup = ResidueProperties.getDefaultDnaMatrix(); - } + seq2 = indexEncode(s2str); } - private void setType(String type2) + private void setDefaultParams(String moleculeType) { - this.type = type2; - if (type.equals(AlignSeq.PEP)) - { - intToStr = pep; - charToInt = ResidueProperties.aaIndex; - defInt = ResidueProperties.maxProteinIndex; - } - else if (type.equals(AlignSeq.DNA)) - { - intToStr = dna; - charToInt = ResidueProperties.nucleotideIndex; - defInt = ResidueProperties.maxNucleotideIndex; - } - else + if (!PEP.equals(moleculeType) && !DNA.equals(moleculeType)) { 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(MessageManager.formatMessage( + "error.unknown_type_dna_or_pep", + new String[] { moleculeType })); } + + type = moleculeType; + scoreModel = ScoreModels.getInstance().getDefaultModel( + PEP.equals(type)); + lookup = scoreModel.getMatrix(); + gapIndex = scoreModel.getGapIndex(); } /** @@ -409,7 +361,7 @@ public class AlignSeq public void traceAlignment() { // Find the maximum score along the rhs or bottom row - int max = -9999; + float max = -Float.MAX_VALUE; for (int i = 0; i < seq1.length; i++) { @@ -443,21 +395,17 @@ public class AlignSeq aseq1 = new int[seq1.length + seq2.length]; aseq2 = new int[seq1.length + seq2.length]; + StringBuilder sb1 = new StringBuilder(aseq1.length); + StringBuilder sb2 = new StringBuilder(aseq2.length); + count = (seq1.length + seq2.length) - 1; - while ((i > 0) && (j > 0)) + while (i > 0 && j > 0) { - if ((aseq1[count] != defInt) && (i >= 0)) - { - aseq1[count] = seq1[i]; - astr1 = s1str.charAt(i) + astr1; - } - - if ((aseq2[count] != defInt) && (j > 0)) - { - aseq2[count] = seq2[j]; - astr2 = s2str.charAt(j) + astr2; - } + aseq1[count] = seq1[i]; + sb1.append(s1str.charAt(i)); + aseq2[count] = seq2[j]; + sb2.append(s2str.charAt(j)); trace = findTrace(i, j); @@ -469,14 +417,14 @@ public class AlignSeq else if (trace == 1) { j--; - aseq1[count] = defInt; - astr1 = "-" + astr1.substring(1); + aseq1[count] = gapIndex; + sb1.replace(sb1.length() - 1, sb1.length(), "-"); } else if (trace == -1) { i--; - aseq2[count] = defInt; - astr2 = "-" + astr2.substring(1); + aseq2[count] = gapIndex; + sb2.replace(sb2.length() - 1, sb2.length(), "-"); } count--; @@ -485,17 +433,24 @@ public class AlignSeq seq1start = i + 1; seq2start = j + 1; - if (aseq1[count] != defInt) + if (aseq1[count] != gapIndex) { aseq1[count] = seq1[i]; - astr1 = s1str.charAt(i) + astr1; + sb1.append(s1str.charAt(i)); } - if (aseq2[count] != defInt) + if (aseq2[count] != gapIndex) { aseq2[count] = seq2[j]; - astr2 = s2str.charAt(j) + astr2; + sb2.append(s2str.charAt(j)); } + + /* + * we built the character strings backwards, so now + * reverse them to convert to sequence strings + */ + astr1 = sb1.reverse().toString(); + astr2 = sb2.reverse().toString(); } /** @@ -526,24 +481,34 @@ public class AlignSeq } } int len = 72 - maxid - 1; - int nochunks = ((aseq1.length - count) / len) + 1; + int nochunks = ((aseq1.length - count) / len) + + ((aseq1.length - count) % len > 0 ? 1 : 0); pid = 0; - output.append("Score = " + score[maxi][maxj] + "\n"); - output.append("Length of alignment = " + (aseq1.length - count) + "\n"); + output.append("Score = ").append(score[maxi][maxj]).append(NEWLINE); + output.append("Length of alignment = ") + .append(String.valueOf(aseq1.length - count)).append(NEWLINE); 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(" : ").append(String.valueOf(s1.getStart())) + .append(" - ").append(String.valueOf(s1.getEnd())); + output.append(" (Sequence length = ") + .append(String.valueOf(s1str.length())).append(")") + .append(NEWLINE); 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(" : ").append(String.valueOf(s2.getStart())) + .append(" - ").append(String.valueOf(s2.getEnd())); + output.append(" (Sequence length = ") + .append(String.valueOf(s2str.length())).append(")") + .append(NEWLINE).append(NEWLINE); + + ScoreMatrix pam250 = ScoreModels.getInstance().getPam250(); for (int j = 0; j < nochunks; j++) { // Print the first aligned sequence - output.append(new Format("%" + (maxid) + "s").form(s1id) + " "); + output.append(new Format("%" + (maxid) + "s").form(s1id)).append(" "); for (int i = 0; i < len; i++) { @@ -553,25 +518,30 @@ public class AlignSeq } } - output.append("\n"); - output.append(new Format("%" + (maxid) + "s").form(" ") + " "); + output.append(NEWLINE); + output.append(new Format("%" + (maxid) + "s").form(" ")).append(" "); - // Print out the matching chars + /* + * Print out the match symbols: + * | for exact match (ignoring case) + * . if PAM250 score is positive + * else a space + */ for (int i = 0; i < len; i++) { 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)))) + char c1 = astr1.charAt(i + (j * len)); + char c2 = astr2.charAt(i + (j * len)); + boolean sameChar = Comparison.isSameResidue(c1, c2, false); + if (sameChar && !Comparison.isGap(c1)) { pid++; output.append("|"); } else if (type.equals("pep")) { - if (ResidueProperties.getPAM250(astr1.charAt(i + (j * len)), - astr2.charAt(i + (j * len))) > 0) + if (pam250.getPairwiseScore(c1, c2) > 0) { output.append("."); } @@ -588,9 +558,9 @@ public class AlignSeq } // Now print the second aligned sequence - output = output.append("\n"); - output = output.append(new Format("%" + (maxid) + "s").form(s2id) - + " "); + output = output.append(NEWLINE); + output = output.append(new Format("%" + (maxid) + "s").form(s2id)) + .append(" "); for (int i = 0; i < len; i++) { @@ -600,13 +570,11 @@ public class AlignSeq } } - output = output.append("\n\n"); + output.append(NEWLINE).append(NEWLINE); } - pid = pid / (float) (aseq1.length - count) * 100; - output = output.append(new Format("Percentage ID = %2.2f\n\n") - .form(pid)); - + pid = pid / (aseq1.length - count) * 100; + output = output.append(new Format("Percentage ID = %2.2f\n").form(pid)); try { os.print(output.toString()); @@ -618,46 +586,6 @@ public class AlignSeq /** * DOCUMENT ME! * - * @param mat - * DOCUMENT ME! - */ - public void printScoreMatrix(int[][] mat) - { - int n = seq1.length; - int m = seq2.length; - - for (int i = 0; i < n; i++) - { - // Print the top sequence - if (i == 0) - { - Format.print(System.out, "%8s", s2str.substring(0, 1)); - - for (int jj = 1; jj < m; jj++) - { - Format.print(System.out, "%5s", s2str.substring(jj, jj + 1)); - } - - System.out.println(); - } - - for (int j = 0; j < m; j++) - { - if (j == 0) - { - Format.print(System.out, "%3s", s1str.substring(i, i + 1)); - } - - Format.print(System.out, "%3d ", mat[i][j] / 10); - } - - System.out.println(); - } - } - - /** - * DOCUMENT ME! - * * @param i * DOCUMENT ME! * @param j @@ -668,7 +596,7 @@ public class AlignSeq public int findTrace(int i, int j) { int t = 0; - int max = score[i - 1][j - 1] + (lookup[seq1[i]][seq2[j]] * 10); + float max = score[i - 1][j - 1] + (lookup[seq1[i]][seq2[j]] * 10); if (F[i][j] > max) { @@ -754,19 +682,23 @@ public class AlignSeq } /** - * DOCUMENT ME! + * Returns the given sequence with all of the given gap characters removed. * - * @param gapChar - * DOCUMENT ME! + * @param gapChars + * a string of characters to be treated as gaps * @param seq - * DOCUMENT ME! + * the input sequence * - * @return DOCUMENT ME! + * @return */ - public static String extractGaps(String gapChar, String seq) + public static String extractGaps(String gapChars, String seq) { - StringTokenizer str = new StringTokenizer(seq, gapChar); - StringBuffer newString = new StringBuffer(); + if (gapChars == null || seq == null) + { + return null; + } + StringTokenizer str = new StringTokenizer(seq, gapChars); + StringBuilder newString = new StringBuilder(seq.length()); while (str.hasMoreTokens()) { @@ -779,27 +711,27 @@ public class AlignSeq /** * DOCUMENT ME! * - * @param i1 + * @param f1 * DOCUMENT ME! - * @param i2 + * @param f2 * DOCUMENT ME! - * @param i3 + * @param f3 * DOCUMENT ME! * * @return DOCUMENT ME! */ - public int max(int i1, int i2, int i3) + private static float max(float f1, float f2, float f3) { - int max = i1; + float max = f1; - if (i2 > i1) + if (f2 > f1) { - max = i2; + max = f2; } - if (i3 > max) + if (f3 > max) { - max = i3; + max = f3; } return max; @@ -808,65 +740,44 @@ public class AlignSeq /** * DOCUMENT ME! * - * @param i1 + * @param f1 * DOCUMENT ME! - * @param i2 + * @param f2 * DOCUMENT ME! * * @return DOCUMENT ME! */ - public int max(int i1, int i2) + private static float max(float f1, float f2) { - int max = i1; + float max = f1; - if (i2 > i1) + if (f2 > f1) { - max = i2; + max = f2; } return max; } /** - * DOCUMENT ME! + * Converts the character string to an array of integers which are the + * corresponding indices to the characters in the score matrix * * @param s - * DOCUMENT ME! - * @param type - * DOCUMENT ME! * - * @return DOCUMENT ME! + * @return */ - public int[] stringToInt(String s, String type) + int[] indexEncode(String s) { - int[] seq1 = new int[s.length()]; + int[] encoded = new int[s.length()]; for (int i = 0; i < s.length(); i++) { - // String ss = s.substring(i, i + 1).toUpperCase(); char c = s.charAt(i); - if ('a' <= c && c <= 'z') - { - // TO UPPERCASE !!! - c -= ('a' - 'A'); - } - - try - { - 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] = defInt; - } - - } catch (Exception e) - { - seq1[i] = defInt; - } + encoded[i] = scoreModel.getMatrixIndex(c); } - return seq1; + return encoded; } /** @@ -886,6 +797,7 @@ public class AlignSeq public static void displayMatrix(Graphics g, int[][] mat, int n, int m, int psize) { + // TODO method dosen't seem to be referenced anywhere delete?? int max = -1000; int min = 1000; @@ -970,22 +882,29 @@ public class AlignSeq if (allowmismatch || c1 == c2) { - lastmatch = true; - // extend mapping interval. - if (lp1 + 1 != alignpos || lp2+1 !=pdbpos) + // extend mapping interval + if (lp1 + 1 != alignpos || lp2 + 1 != pdbpos) { as1.add(Integer.valueOf(alignpos)); as2.add(Integer.valueOf(pdbpos)); } + lastmatch = true; lp1 = alignpos; lp2 = pdbpos; } else { + // extend mapping interval + if (lastmatch) + { + as1.add(Integer.valueOf(lp1)); + as2.add(Integer.valueOf(lp2)); + } lastmatch = false; } } // construct range pairs + int[] mapseq1 = new int[as1.size() + (lastmatch ? 1 : 0)], mapseq2 = new int[as2 .size() + (lastmatch ? 1 : 0)]; int i = 0; @@ -1013,6 +932,104 @@ public class AlignSeq } /** + * matches ochains against al and populates seqs with the best match between + * each ochain and the set in al + * + * @param ochains + * @param al + * @param dnaOrProtein + * @param removeOldAnnots + * when true, old annotation is cleared before new annotation + * transferred + * @return List originals, List replacement, + * List alignment between each> + */ + public static List> replaceMatchingSeqsWith( + List seqs, List annotations, + List ochains, AlignmentI al, String dnaOrProtein, + boolean removeOldAnnots) + { + List orig = new ArrayList(), repl = new ArrayList(); + List aligs = new ArrayList(); + if (al != null && al.getHeight() > 0) + { + ArrayList matches = new ArrayList(); + ArrayList aligns = new ArrayList(); + + for (SequenceI sq : ochains) + { + SequenceI bestm = null; + AlignSeq bestaseq = null; + float bestscore = 0; + for (SequenceI msq : al.getSequences()) + { + AlignSeq aseq = doGlobalNWAlignment(msq, sq, dnaOrProtein); + if (bestm == null || aseq.getMaxScore() > bestscore) + { + bestscore = aseq.getMaxScore(); + bestaseq = aseq; + bestm = msq; + } + } + System.out.println("Best Score for " + (matches.size() + 1) + " :" + + bestscore); + matches.add(bestm); + aligns.add(bestaseq); + al.deleteSequence(bestm); + } + for (int p = 0, pSize = seqs.size(); p < pSize; p++) + { + SequenceI sq, sp = seqs.get(p); + int q; + if ((q = ochains.indexOf(sp)) > -1) + { + seqs.set(p, sq = matches.get(q)); + orig.add(sp); + repl.add(sq); + sq.setName(sp.getName()); + sq.setDescription(sp.getDescription()); + Mapping sp2sq; + sq.transferAnnotation(sp, + sp2sq = aligns.get(q).getMappingFromS1(false)); + aligs.add(aligns.get(q)); + int inspos = -1; + for (int ap = 0; ap < annotations.size();) + { + if (annotations.get(ap).sequenceRef == sp) + { + if (inspos == -1) + { + inspos = ap; + } + if (removeOldAnnots) + { + annotations.remove(ap); + } + else + { + AlignmentAnnotation alan = annotations.remove(ap); + alan.liftOver(sq, sp2sq); + alan.setSequenceRef(sq); + sq.addAlignmentAnnotation(alan); + } + } + else + { + ap++; + } + } + if (sq.getAnnotation() != null && sq.getAnnotation().length > 0) + { + annotations.addAll(inspos == -1 ? annotations.size() : inspos, + Arrays.asList(sq.getAnnotation())); + } + } + } + } + return Arrays.asList(orig, repl, aligs); + } + + /** * compute the PID vector used by the redundancy filter. * * @param originalSequences @@ -1044,6 +1061,8 @@ public class AlignSeq // long start = System.currentTimeMillis(); + SimilarityParams pidParams = new SimilarityParams(true, true, true, + true); float pid; String seqi, seqj; for (int i = 0; i < height; i++) @@ -1084,7 +1103,7 @@ public class AlignSeq seqj = ug; } } - pid = Comparison.PID(seqi, seqj); + pid = (float) PIDModel.computePID(seqi, seqj, pidParams); // use real sequence length rather than string length if (lngth[j] < lngth[i])