X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignSeq.java;h=34a21e690670b0d49197a1e523607a38dc5974b3;hb=8213e48c6973494f7a6e22e1a97290520a461d1b;hp=ceca6d6fcd207c2a468c1ccc6385ff3445eb08b8;hpb=69b6e688c0a87bffc1fc7ae970fa0f8cd2976007;p=jalview.git diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java index ceca6d6..34a21e6 100755 --- a/src/jalview/analysis/AlignSeq.java +++ b/src/jalview/analysis/AlignSeq.java @@ -20,8 +20,10 @@ */ package jalview.analysis; +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; @@ -110,22 +112,23 @@ public class AlignSeq int gapExtend = 20; - float[][] lookup; - - int gapIndex = 23; - StringBuffer output = new StringBuffer(); String type; // AlignSeq.PEP or AlignSeq.DNA - private ScoreMatrix scoreModel; + private ScoreMatrix scoreMatrix; + + private static final int GAP_INDEX = -1; /** * Creates a new AlignSeq object. * - * @param s1 first sequence for alignment - * @param s2 second sequence for alignment - * @param type molecule type, either AlignSeq.PEP or AlignSeq.DNA + * @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) { @@ -258,8 +261,8 @@ 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; } @@ -272,8 +275,8 @@ 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; } @@ -314,16 +317,12 @@ 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; } - seq1 = new int[s1str.length()]; - - seq2 = new int[s2str.length()]; - score = new float[s1str.length()][s2str.length()]; E = new float[s1str.length()][s2str.length()]; @@ -341,16 +340,14 @@ public class AlignSeq 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[] { moleculeType })); + 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.getMatrixIndex(' '); + scoreMatrix = ScoreModels.getInstance() + .getDefaultModel(PEP.equals(type)); } /** @@ -415,13 +412,13 @@ public class AlignSeq else if (trace == 1) { j--; - aseq1[count] = gapIndex; + aseq1[count] = GAP_INDEX; sb1.replace(sb1.length() - 1, sb1.length(), "-"); } else if (trace == -1) { i--; - aseq2[count] = gapIndex; + aseq2[count] = GAP_INDEX; sb2.replace(sb2.length() - 1, sb2.length(), "-"); } @@ -431,13 +428,13 @@ public class AlignSeq seq1start = i + 1; seq2start = j + 1; - if (aseq1[count] != gapIndex) + if (aseq1[count] != GAP_INDEX) { aseq1[count] = seq1[i]; sb1.append(s1str.charAt(i)); } - if (aseq2[count] != gapIndex) + if (aseq2[count] != GAP_INDEX) { aseq2[count] = seq2[j]; sb2.append(s2str.charAt(j)); @@ -594,7 +591,10 @@ public class AlignSeq public int findTrace(int i, int j) { int t = 0; - float max = score[i - 1][j - 1] + (lookup[seq1[i]][seq2[j]] * 10); + // float pairwiseScore = lookup[seq1[i]][seq2[j]]; + float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(i), + s2str.charAt(j)); + float max = score[i - 1][j - 1] + (pairwiseScore * 10); if (F[i][j] > max) { @@ -638,7 +638,8 @@ public class AlignSeq int m = seq2.length; // top left hand element - score[0][0] = lookup[seq1[0]][seq2[0]] * 10; + score[0][0] = scoreMatrix.getPairwiseScore(s1str.charAt(0), + s2str.charAt(0)) * 10; E[0][0] = -gapExtend; F[0][0] = 0; @@ -649,7 +650,9 @@ 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); + float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(0), + s2str.charAt(j)); + score[0][j] = max(pairwiseScore * 10, -gapOpen, -gapExtend); traceback[0][j] = 1; } @@ -660,7 +663,9 @@ public class AlignSeq E[i][0] = -gapOpen; F[i][0] = max(score[i - 1][0] - gapOpen, F[i - 1][0] - gapExtend); - 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; } @@ -672,8 +677,10 @@ public class AlignSeq 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]); + 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); } } @@ -772,7 +779,7 @@ public class AlignSeq for (int i = 0; i < s.length(); i++) { char c = s.charAt(i); - encoded[i] = scoreModel.getMatrixIndex(c); + encoded[i] = scoreMatrix.getMatrixIndex(c); } return encoded; @@ -795,7 +802,7 @@ 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?? + // TODO method doesn't seem to be referenced anywhere delete?? int max = -1000; int min = 1000; @@ -859,7 +866,8 @@ 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; @@ -903,8 +911,8 @@ 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) { @@ -947,7 +955,8 @@ 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) { @@ -969,8 +978,8 @@ 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); @@ -1059,6 +1068,8 @@ 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++) @@ -1099,7 +1110,7 @@ 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])