X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=65fd1100b8e8a7f2cdc33f1d1a90f80aaa3076bf;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=3ca3d90a952de177844cee8148b42c3509de42cc;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java index 3ca3d90..65fd110 100755 --- a/src/jalview/analysis/AlignSeq.java +++ b/src/jalview/analysis/AlignSeq.java @@ -20,13 +20,17 @@ */ package jalview.analysis; +import java.util.Locale; + +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.schemes.ResidueProperties; -import jalview.schemes.ScoreMatrix; import jalview.util.Comparison; import jalview.util.Format; import jalview.util.MapList; @@ -34,6 +38,7 @@ import jalview.util.MessageManager; import java.awt.Color; import java.awt.Graphics; +import java.io.PrintStream; import java.util.ArrayList; import java.util.Arrays; import java.util.List; @@ -47,25 +52,27 @@ import java.util.StringTokenizer; */ public class AlignSeq { + private static final int MAX_NAME_LENGTH = 30; + + private static final int GAP_OPEN_COST = 120; + + private static final int GAP_EXTEND_COST = 20; + + private static final int GAP_INDEX = -1; + public static final String PEP = "pep"; public static final String DNA = "dna"; private static final String NEWLINE = System.lineSeparator(); - 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", "-" }; + float[][] score; - int[][] score; + float[][] E; - int[][] E; + float[][] F; - int[][] F; - - int[][] traceback; + int[][] traceback; // todo is this actually used? int[] seq1; @@ -100,47 +107,33 @@ public class AlignSeq /** DOCUMENT ME!! */ public int seq2start; - /** DOCUMENT ME!! */ public int seq2end; int count; - /** DOCUMENT ME!! */ - public int maxscore; - - float pid; + public float maxscore; 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; + String type; // AlignSeq.PEP or AlignSeq.DNA - private int[] charToInt; + private ScoreMatrix scoreMatrix; /** * Creates a new AlignSeq object. * * @param s1 - * DOCUMENT ME! + * first sequence for alignment * @param s2 - * DOCUMENT ME! + * second sequence for alignment * @param type - * DOCUMENT ME! + * 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); } @@ -157,7 +150,8 @@ 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(Locale.ROOT), s2, + string2.toUpperCase(Locale.ROOT), type); } /** @@ -165,7 +159,7 @@ public class AlignSeq * * @return DOCUMENT ME! */ - public int getMaxScore() + public float getMaxScore() { return maxscore; } @@ -261,26 +255,6 @@ public class AlignSeq } /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public SequenceI getS1() - { - return s1; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public SequenceI getS2() - { - return s2; - } - - /** * * @return aligned instance of Seq 1 */ @@ -289,8 +263,8 @@ public class AlignSeq 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()); + alSeq1.setDatasetSequence( + s1.getDatasetSequence() == null ? s1 : s1.getDatasetSequence()); return alSeq1; } @@ -303,8 +277,8 @@ public class AlignSeq 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()); + alSeq2.setDatasetSequence( + s2.getDatasetSequence() == null ? s2 : s2.getDatasetSequence()); return alSeq2; } @@ -322,36 +296,13 @@ public class AlignSeq * @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); } /** @@ -361,97 +312,44 @@ public class AlignSeq * @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); 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()); - seq1 = new int[s1str.length()]; - - // System.out.println("seq1 " + rt.freeMemory() +" " + rt.totalMemory()); - seq2 = new int[s2str.length()]; + score = new float[s1str.length()][s2str.length()]; - // System.out.println("seq2 " + rt.freeMemory() + " " + rt.totalMemory()); - score = new int[s1str.length()][s2str.length()]; + E = new float[s1str.length()][s2str.length()]; - // System.out.println("score " + rt.freeMemory() + " " + rt.totalMemory()); - E = new int[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(MessageManager.formatMessage( - "error.unknown_type_dna_or_pep", new String[] { type2 })); + throw new Error(MessageManager + .formatMessage("error.unknown_type_dna_or_pep", new String[] + { moleculeType })); } + + type = moleculeType; + scoreMatrix = ScoreModels.getInstance() + .getDefaultModel(PEP.equals(type)); } /** @@ -460,7 +358,7 @@ 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++) { @@ -482,11 +380,10 @@ public class AlignSeq } } - // System.out.println(maxi + " " + maxj + " " + score[maxi][maxj]); int i = maxi; int j = maxj; int trace; - maxscore = score[i][j] / 10; + maxscore = score[i][j] / 10f; seq1end = maxi + 1; seq2end = maxj + 1; @@ -494,21 +391,17 @@ 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); @@ -520,14 +413,14 @@ public class AlignSeq else if (trace == 1) { j--; - aseq1[count] = defInt; - astr1 = "-" + astr1.substring(1); + aseq1[count] = GAP_INDEX; + sb1.replace(sb1.length() - 1, sb1.length(), "-"); } else if (trace == -1) { i--; - aseq2[count] = defInt; - astr2 = "-" + astr2.substring(1); + aseq2[count] = GAP_INDEX; + sb2.replace(sb2.length() - 1, sb2.length(), "-"); } count--; @@ -536,72 +429,81 @@ public class AlignSeq seq1start = i + 1; seq2start = j + 1; - if (aseq1[count] != defInt) + if (aseq1[count] != GAP_INDEX) { aseq1[count] = seq1[i]; - astr1 = s1str.charAt(i) + astr1; + sb1.append(s1str.charAt(i)); } - if (aseq2[count] != defInt) + if (aseq2[count] != GAP_INDEX) { 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(); } /** * DOCUMENT ME! */ - public void printAlignment(java.io.PrintStream os) + public void printAlignment(PrintStream os) { // 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) + String s1id = getAlignedSeq1().getDisplayId(true); + String s2id = getAlignedSeq2().getDisplayId(true); + int nameLength = Math.max(s1id.length(), s2id.length()); + if (nameLength > MAX_NAME_LENGTH) { - maxid = 30; + int truncateBy = nameLength - MAX_NAME_LENGTH; + nameLength = MAX_NAME_LENGTH; // JAL-527 - truncate the sequence ids - if (s1.getName().length() > maxid) + if (s1id.length() > nameLength) { - s1id = s1.getName().substring(0, 30); + int slashPos = s1id.lastIndexOf('/'); + s1id = s1id.substring(0, slashPos - truncateBy) + + s1id.substring(slashPos); } - if (s2.getName().length() > maxid) + if (s2id.length() > nameLength) { - s2id = s2.getName().substring(0, 30); + int slashPos = s2id.lastIndexOf('/'); + s2id = s2id.substring(0, slashPos - truncateBy) + + s2id.substring(slashPos); } } - int len = 72 - maxid - 1; - int nochunks = ((aseq1.length - count) / len) + 1; - pid = 0; + int len = 72 - nameLength - 1; + int nochunks = ((aseq1.length - count) / len) + + ((aseq1.length - count) % len > 0 ? 1 : 0); + float pid = 0f; 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(" : ").append(String.valueOf(s1.getStart())) - .append(" - ").append(String.valueOf(s1.getEnd())); + Format nameFormat = new Format("%" + nameLength + "s"); + output.append(nameFormat.form(s1id)); 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(" : ").append(String.valueOf(s2.getStart())) - .append(" - ").append(String.valueOf(s2.getEnd())); + output.append(nameFormat.form(s2id)); 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)).append(" "); + output.append(nameFormat.form(s1id)).append(" "); for (int i = 0; i < len; i++) { @@ -612,24 +514,29 @@ public class AlignSeq } output.append(NEWLINE); - output.append(new Format("%" + (maxid) + "s").form(" ")).append(" "); - - // Print out the matching chars + output.append(nameFormat.form(" ")).append(" "); + + /* + * 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")) + else if (PEP.equals(type)) { - if (ResidueProperties.getPAM250(astr1.charAt(i + (j * len)), - astr2.charAt(i + (j * len))) > 0) + if (pam250.getPairwiseScore(c1, c2) > 0) { output.append("."); } @@ -647,8 +554,7 @@ public class AlignSeq // Now print the second aligned sequence output = output.append(NEWLINE); - output = output.append(new Format("%" + (maxid) + "s").form(s2id)) - .append(" "); + output = output.append(nameFormat.form(s2id)).append(" "); for (int i = 0; i < len; i++) { @@ -662,9 +568,8 @@ public class AlignSeq } pid = pid / (aseq1.length - count) * 100; - output = output.append(new Format("Percentage ID = %2.2f\n\n") - .form(pid)); - + output.append(new Format("Percentage ID = %3.2f\n").form(pid)); + output.append(NEWLINE); try { os.print(output.toString()); @@ -676,46 +581,6 @@ 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 @@ -726,7 +591,9 @@ 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 pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i), + s2str.charAt(j)); + float max = score[i - 1][j - 1] + (pairwiseScore * 10); if (F[i][j] > max) { @@ -770,18 +637,23 @@ public class AlignSeq int m = seq2.length; // top left hand element - score[0][0] = lookup[seq1[0]][seq2[0]] * 10; - E[0][0] = -gapExtend; + score[0][0] = scoreMatrix.getPairwiseScore(s1str.charAt(0), + s2str.charAt(0)) * 10; + E[0][0] = -GAP_EXTEND_COST; F[0][0] = 0; // Calculate the top row first for (int j = 1; j < m; j++) { // What should these values be? 0 maybe - E[0][j] = max(score[0][j - 1] - gapOpen, E[0][j - 1] - gapExtend); - F[0][j] = -gapExtend; + E[0][j] = max(score[0][j - 1] - GAP_OPEN_COST, + E[0][j - 1] - GAP_EXTEND_COST); + F[0][j] = -GAP_EXTEND_COST; - score[0][j] = max(lookup[seq1[0]][seq2[j]] * 10, -gapOpen, -gapExtend); + float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(0), + s2str.charAt(j)); + score[0][j] = max(pairwiseScore * 10, -GAP_OPEN_COST, + -GAP_EXTEND_COST); traceback[0][j] = 1; } @@ -789,10 +661,13 @@ public class AlignSeq // Now do the left hand column for (int i = 1; i < n; i++) { - E[i][0] = -gapOpen; - F[i][0] = max(score[i - 1][0] - gapOpen, F[i - 1][0] - gapExtend); + E[i][0] = -GAP_OPEN_COST; + F[i][0] = max(score[i - 1][0] - GAP_OPEN_COST, + F[i - 1][0] - GAP_EXTEND_COST); - score[i][0] = max(lookup[seq1[i]][seq2[0]] * 10, E[i][0], F[i][0]); + float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i), + s2str.charAt(0)); + score[i][0] = max(pairwiseScore * 10, E[i][0], F[i][0]); traceback[i][0] = -1; } @@ -801,11 +676,15 @@ 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); - - score[i][j] = max(score[i - 1][j - 1] - + (lookup[seq1[i]][seq2[j]] * 10), E[i][j], F[i][j]); + E[i][j] = max(score[i][j - 1] - GAP_OPEN_COST, + E[i][j - 1] - GAP_EXTEND_COST); + F[i][j] = max(score[i - 1][j] - GAP_OPEN_COST, + F[i - 1][j] - GAP_EXTEND_COST); + + float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i), + s2str.charAt(j)); + score[i][j] = max(score[i - 1][j - 1] + (pairwiseScore * 10), + E[i][j], F[i][j]); traceback[i][j] = findTrace(i, j); } } @@ -841,27 +720,27 @@ 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; @@ -870,65 +749,44 @@ 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] = scoreMatrix.getMatrixIndex(c); } - return seq1; + return encoded; } /** @@ -948,6 +806,7 @@ public class AlignSeq public static void displayMatrix(Graphics g, int[][] mat, int n, int m, int psize) { + // TODO method doesn't seem to be referenced anywhere delete?? int max = -1000; int min = 1000; @@ -1011,7 +870,8 @@ public class AlignSeq */ public jalview.datamodel.Mapping getMappingFromS1(boolean allowmismatch) { - ArrayList as1 = new ArrayList(), as2 = new ArrayList(); + ArrayList as1 = new ArrayList(), + as2 = new ArrayList(); int pdbpos = s2.getStart() + getSeq2Start() - 2; int alignpos = s1.getStart() + getSeq1Start() - 2; int lp2 = pdbpos - 3, lp1 = alignpos - 3; @@ -1055,8 +915,8 @@ public class AlignSeq } // construct range pairs - int[] mapseq1 = new int[as1.size() + (lastmatch ? 1 : 0)], mapseq2 = new int[as2 - .size() + (lastmatch ? 1 : 0)]; + int[] mapseq1 = new int[as1.size() + (lastmatch ? 1 : 0)], + mapseq2 = new int[as2.size() + (lastmatch ? 1 : 0)]; int i = 0; for (Integer ip : as1) { @@ -1099,7 +959,8 @@ public class AlignSeq List ochains, AlignmentI al, String dnaOrProtein, boolean removeOldAnnots) { - List orig = new ArrayList(), repl = new ArrayList(); + List orig = new ArrayList(), + repl = new ArrayList(); List aligs = new ArrayList(); if (al != null && al.getHeight() > 0) { @@ -1110,7 +971,7 @@ public class AlignSeq { SequenceI bestm = null; AlignSeq bestaseq = null; - int bestscore = 0; + float bestscore = 0; for (SequenceI msq : al.getSequences()) { AlignSeq aseq = doGlobalNWAlignment(msq, sq, dnaOrProtein); @@ -1121,8 +982,8 @@ public class AlignSeq bestm = msq; } } - System.out.println("Best Score for " + (matches.size() + 1) + " :" - + bestscore); + // System.out.println("Best Score for " + (matches.size() + 1) + " :" + // + bestscore); matches.add(bestm); aligns.add(bestaseq); al.deleteSequence(bestm); @@ -1211,6 +1072,8 @@ 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++) @@ -1251,7 +1114,7 @@ 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])