X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=e5038ba2f540048ef20ecd7a643d79bd2abd21b2;hb=87256ba36fb105a1115067ffe2563412e9281d2d;hp=007d538d55659bcf9f4f8f4bdb07d46ad73eb762;hpb=d616b0e1ac213a82591cece50ea25c5bfbfa865f;p=jalview.git diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java index 007d538..e5038ba 100755 --- a/src/jalview/analysis/AlignmentSorter.java +++ b/src/jalview/analysis/AlignmentSorter.java @@ -20,6 +20,8 @@ */ package jalview.analysis; +import jalview.analysis.scoremodels.PIDModel; +import jalview.analysis.scoremodels.SimilarityParams; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentOrder; @@ -27,11 +29,12 @@ import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.datamodel.SequenceNode; -import jalview.util.Comparison; -import jalview.util.MessageManager; +import jalview.util.Platform; import jalview.util.QuickSort; import java.util.ArrayList; +import java.util.Collections; +import java.util.Iterator; import java.util.List; /** @@ -51,81 +54,103 @@ import java.util.List; */ public class AlignmentSorter { - /** + + static AlignmentSorter instance; + + public static AlignmentSorter getInstance() + { + + // BH 2019.05.08 need to isolate static fields in JavaScript + + AlignmentSorter i = instance; + @SuppressWarnings("unused") + ThreadGroup g = null; + if (Platform.isJS()) + { + g = Thread.currentThread().getThreadGroup(); + /** + * @j2sNative i = g._jalviewScoreModelsInstance; + * + */ + } + if (i == null) + { + i = new AlignmentSorter(); + + if (Platform.isJS()) + { + /** + * @j2sNative g._jalviewScoreModelsInstance = i; + * + */ + } + else + { + instance = i; + } + } + return i; + } + + /* * todo: refactor searches to follow a basic pattern: (search property, last * search state, current sort direction) */ - static boolean sortIdAscending = true; + boolean sortIdAscending = true; + + int lastGroupHash = 0; - static int lastGroupHash = 0; + boolean sortGroupAscending = true; - static boolean sortGroupAscending = true; + AlignmentOrder lastOrder = null; - static AlignmentOrder lastOrder = null; + boolean sortOrderAscending = true; - static boolean sortOrderAscending = true; + TreeModel lastTree = null; - static NJTree lastTree = null; + boolean sortTreeAscending = true; - static boolean sortTreeAscending = true; /** - * last Annotation Label used by sortByScore + * last Annotation Label used for sort by Annotation score */ - private static String lastSortByScore; - - private static boolean sortByScoreAscending = true; + private String lastSortByAnnotation; /** - * compact representation of last arguments to SortByFeatureScore + * string hash of last arguments to sortByFeature (sort order toggles if this + * is unchanged between sorts) */ - private static String lastSortByFeatureScore; + private String sortByFeatureCriteria; - private static boolean sortByFeatureScoreAscending = true; + private boolean sortByFeatureAscending = true; - private static boolean sortLengthAscending; + private boolean sortLengthAscending; /** - * Sort by Percentage Identity w.r.t. s + * Sorts sequences in the alignment by Percentage Identity with the given + * reference sequence, sorting the highest identity to the top * * @param align * AlignmentI * @param s * SequenceI - * @param tosort - * sequences from align that are to be sorted. - */ - public static void sortByPID(AlignmentI align, SequenceI s, - SequenceI[] tosort) - { - sortByPID(align, s, tosort, 0, -1); - } - - /** - * Sort by Percentage Identity w.r.t. s - * - * @param align - * AlignmentI - * @param s - * SequenceI - * @param tosort - * sequences from align that are to be sorted. - * @param start - * start column (0 for beginning * @param end */ - public static void sortByPID(AlignmentI align, SequenceI s, - SequenceI[] tosort, int start, int end) + public static void sortByPID(AlignmentI align, SequenceI s) { int nSeq = align.getHeight(); float[] scores = new float[nSeq]; SequenceI[] seqs = new SequenceI[nSeq]; + String refSeq = s.getSequenceAsString(); + SimilarityParams pidParams = new SimilarityParams(true, true, true, + true); for (int i = 0; i < nSeq; i++) { - scores[i] = Comparison.PID(align.getSequenceAt(i) - .getSequenceAsString(), s.getSequenceAsString()); + scores[i] = (float) PIDModel.computePID( + align.getSequenceAt(i).getSequenceAsString(), refSeq, + pidParams); seqs[i] = align.getSequenceAt(i); } @@ -158,8 +183,8 @@ public class AlignmentSorter } // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work - List asq; - synchronized (asq = align.getSequences()) + List asq = align.getSequences(); + synchronized (asq) { for (int i = 0; i < len; i++) { @@ -194,10 +219,10 @@ public class AlignmentSorter public static void setOrder(AlignmentI align, SequenceI[] seqs) { // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work - List algn; - synchronized (algn = align.getSequences()) + List algn = align.getSequences(); + synchronized (algn) { - List tmp = new ArrayList(); + List tmp = new ArrayList<>(); for (int i = 0; i < seqs.length; i++) { @@ -237,7 +262,8 @@ public class AlignmentSorter QuickSort.sort(ids, seqs); - if (sortIdAscending) + AlignmentSorter as = getInstance(); + if (as.sortIdAscending) { setReverseOrder(align, seqs); } @@ -246,7 +272,7 @@ public class AlignmentSorter setOrder(align, seqs); } - sortIdAscending = !sortIdAscending; + as.sortIdAscending = !as.sortIdAscending; } /** @@ -270,7 +296,9 @@ public class AlignmentSorter QuickSort.sort(length, seqs); - if (sortLengthAscending) + AlignmentSorter as = getInstance(); + + if (as.sortLengthAscending) { setReverseOrder(align, seqs); } @@ -279,7 +307,7 @@ public class AlignmentSorter setOrder(align, seqs); } - sortLengthAscending = !sortLengthAscending; + as.sortLengthAscending = !as.sortLengthAscending; } /** @@ -294,16 +322,18 @@ public class AlignmentSorter { // MAINTAINS ORIGNAL SEQUENCE ORDER, // ORDERS BY GROUP SIZE - List groups = new ArrayList(); + List groups = new ArrayList<>(); - if (groups.hashCode() != lastGroupHash) + AlignmentSorter as = getInstance(); + + if (groups.hashCode() != as.lastGroupHash) { - sortGroupAscending = true; - lastGroupHash = groups.hashCode(); + as.sortGroupAscending = true; + as.lastGroupHash = groups.hashCode(); } else { - sortGroupAscending = !sortGroupAscending; + as.sortGroupAscending = !as.sortGroupAscending; } // SORTS GROUPS BY SIZE @@ -330,7 +360,7 @@ public class AlignmentSorter // NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER // ///////////////////////////////////////////// - List seqs = new ArrayList(); + List seqs = new ArrayList<>(); for (int i = 0; i < groups.size(); i++) { @@ -343,7 +373,7 @@ public class AlignmentSorter } } - if (sortGroupAscending) + if (as.sortGroupAscending) { setOrder(align, seqs); } @@ -372,7 +402,7 @@ public class AlignmentSorter // tmp2 = tmp.retainAll(mask); // return tmp2.addAll(mask.removeAll(tmp2)) - ArrayList seqs = new ArrayList(); + ArrayList seqs = new ArrayList<>(); int i, idx; boolean[] tmask = new boolean[mask.size()]; @@ -416,22 +446,25 @@ public class AlignmentSorter // Get an ordered vector of sequences which may also be present in align List tmp = order.getOrder(); - if (lastOrder == order) + AlignmentSorter as = getInstance(); + + if (as.lastOrder == order) { - sortOrderAscending = !sortOrderAscending; + as.sortOrderAscending = !as.sortOrderAscending; } else { - sortOrderAscending = true; + as.sortOrderAscending = true; } - if (sortOrderAscending) + if (as.sortOrderAscending) { setOrder(align, tmp); } else { - setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences())); + setReverseOrder(align, + vectorSubsetToArray(tmp, align.getSequences())); } } @@ -446,11 +479,11 @@ public class AlignmentSorter * @return DOCUMENT ME! */ private static List getOrderByTree(AlignmentI align, - NJTree tree) + TreeModel tree) { int nSeq = align.getHeight(); - List tmp = new ArrayList(); + List tmp = new ArrayList<>(); tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences()); @@ -466,12 +499,9 @@ public class AlignmentSorter if (tmp.size() != nSeq) { - System.err - .println("WARNING: tmp.size()=" - + tmp.size() - + " != nseq=" - + nSeq - + " in getOrderByTree - tree contains sequences not in alignment"); + System.err.println("WARNING: tmp.size()=" + tmp.size() + " != nseq=" + + nSeq + + " in getOrderByTree - tree contains sequences not in alignment"); } } @@ -486,28 +516,31 @@ public class AlignmentSorter * @param tree * tree which has */ - public static void sortByTree(AlignmentI align, NJTree tree) + public static void sortByTree(AlignmentI align, TreeModel tree) { List tmp = getOrderByTree(align, tree); + AlignmentSorter as = getInstance(); + // tmp should properly permute align with tree. - if (lastTree != tree) + if (as.lastTree != tree) { - sortTreeAscending = true; - lastTree = tree; + as.sortTreeAscending = true; + as.lastTree = tree; } else { - sortTreeAscending = !sortTreeAscending; + as.sortTreeAscending = !as.sortTreeAscending; } - if (sortTreeAscending) + if (as.sortTreeAscending) { setOrder(align, tmp); } else { - setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences())); + setReverseOrder(align, + vectorSubsetToArray(tmp, align.getSequences())); } } @@ -674,9 +707,12 @@ public class AlignmentSorter } jalview.util.QuickSort.sort(scores, seqs); - if (lastSortByScore != scoreLabel) + + AlignmentSorter as = getInstance(); + + if (as.lastSortByAnnotation != scoreLabel) { - lastSortByScore = scoreLabel; + as.lastSortByAnnotation = scoreLabel; setOrder(alignment, seqs); } else @@ -698,92 +734,40 @@ public class AlignmentSorter public static String FEATURE_DENSITY = "density"; /** - * sort the alignment using the features on each sequence found between start - * and stop with the given featureLabel (and optional group qualifier) + * Sort sequences by feature score or density, optionally restricted by + * feature types, feature groups, or alignment start/end positions. + *

+ * If the sort is repeated for the same combination of types and groups, sort + * order is reversed. * - * @param featureLabel - * (may not be null) - * @param groupLabel - * (may be null) - * @param start - * (-1 to include non-positional features) - * @param stop - * (-1 to only sort on non-positional features) + * @param featureTypes + * a list of feature types to include (or null for all) + * @param groups + * a list of feature groups to include (or null for all) + * @param startCol + * start column position to include (base zero) + * @param endCol + * end column position to include (base zero) * @param alignment - * - aligned sequences containing features + * the alignment to be sorted * @param method - * - one of the string constants FEATURE_SCORE, FEATURE_LABEL, - * FEATURE_DENSITY + * either "average_score" or "density" ("text" not yet implemented) */ - public static void sortByFeature(String featureLabel, String groupLabel, - int start, int stop, AlignmentI alignment, String method) - { - sortByFeature(featureLabel == null ? null - : new String[] { featureLabel }, groupLabel == null ? null - : new String[] { groupLabel }, start, stop, alignment, method); - } - - private static boolean containsIgnoreCase(final String lab, - final String[] labs) - { - if (labs == null) - { - return true; - } - if (lab == null) - { - return false; - } - for (int q = 0; q < labs.length; q++) - { - if (labs[q] != null && lab.equalsIgnoreCase(labs[q])) - { - return true; - } - } - return false; - } - - public static void sortByFeature(String[] featureLabels, - String[] groupLabels, int start, int stop, AlignmentI alignment, - String method) + public static void sortByFeature(List featureTypes, + List groups, final int startCol, final int endCol, + AlignmentI alignment, String method) { if (method != FEATURE_SCORE && method != FEATURE_LABEL && method != FEATURE_DENSITY) { - throw new Error( - MessageManager - .getString("error.implementation_error_sortbyfeature")); + String msg = String + .format("Implementation Error - sortByFeature method must be either '%s' or '%s'", + FEATURE_SCORE, FEATURE_DENSITY); + System.err.println(msg); + return; } - boolean ignoreScore = method != FEATURE_SCORE; - StringBuffer scoreLabel = new StringBuffer(); - scoreLabel.append(start + stop + method); - // This doesn't quite work yet - we'd like to have a canonical ordering that - // can be preserved from call to call - for (int i = 0; featureLabels != null && i < featureLabels.length; i++) - { - scoreLabel.append(featureLabels[i] == null ? "null" - : featureLabels[i]); - } - for (int i = 0; groupLabels != null && i < groupLabels.length; i++) - { - scoreLabel.append(groupLabels[i] == null ? "null" : groupLabels[i]); - } - - /* - * if resorting the same feature, toggle sort order - */ - if (lastSortByFeatureScore == null - || !scoreLabel.toString().equals(lastSortByFeatureScore)) - { - sortByFeatureScoreAscending = true; - } - else - { - sortByFeatureScoreAscending = !sortByFeatureScoreAscending; - } - lastSortByFeatureScore = scoreLabel.toString(); + flipFeatureSortIfUnchanged(method, featureTypes, groups, startCol, endCol); SequenceI[] seqs = alignment.getSequencesArray(); @@ -792,52 +776,44 @@ public class AlignmentSorter int hasScores = 0; // number of scores present on set double[] scores = new double[seqs.length]; int[] seqScores = new int[seqs.length]; - Object[] feats = new Object[seqs.length]; - double min = 0, max = 0; + Object[][] feats = new Object[seqs.length][]; + double min = 0d; + double max = 0d; + for (int i = 0; i < seqs.length; i++) { - SequenceFeature[] sf = seqs[i].getSequenceFeatures(); - if (sf == null) - { - sf = new SequenceFeature[0]; - } - else - { - SequenceFeature[] tmp = new SequenceFeature[sf.length]; - for (int s = 0; s < tmp.length; s++) - { - tmp[s] = sf[s]; - } - sf = tmp; - } - int sstart = (start == -1) ? start : seqs[i].findPosition(start); - int sstop = (stop == -1) ? stop : seqs[i].findPosition(stop); + /* + * get sequence residues overlapping column region + * and features for residue positions and specified types + */ + String[] types = featureTypes == null ? null : featureTypes + .toArray(new String[featureTypes.size()]); + List sfs = seqs[i].findFeatures(startCol + 1, + endCol + 1, types); + seqScores[i] = 0; scores[i] = 0.0; - int n = sf.length; - for (int f = 0; f < sf.length; f++) + + Iterator it = sfs.listIterator(); + while (it.hasNext()) { - // filter for selection criteria - if ( - // ignore features outwith alignment start-stop positions. - (sf[f].end < sstart || sf[f].begin > sstop) || - // or ignore based on selection criteria - (featureLabels != null && !AlignmentSorter - .containsIgnoreCase(sf[f].type, featureLabels)) - || (groupLabels != null - // problem here: we cannot eliminate null feature group features - && (sf[f].getFeatureGroup() != null && !AlignmentSorter - .containsIgnoreCase(sf[f].getFeatureGroup(), - groupLabels)))) + SequenceFeature sf = it.next(); + + /* + * accept all features with null or empty group, otherwise + * check group is one of the currently visible groups + */ + String featureGroup = sf.getFeatureGroup(); + if (groups != null && featureGroup != null + && !"".equals(featureGroup) + && !groups.contains(featureGroup)) { - // forget about this feature - sf[f] = null; - n--; + it.remove(); } else { - // or, also take a look at the scores if necessary. - if (!ignoreScore && !Float.isNaN(sf[f].getScore())) + float score = sf.getScore(); + if (FEATURE_SCORE.equals(method) && !Float.isNaN(score)) { if (seqScores[i] == 0) { @@ -845,33 +821,26 @@ public class AlignmentSorter } seqScores[i]++; hasScore[i] = true; - scores[i] += sf[f].getScore(); // take the first instance of this - // score. + scores[i] += score; + // take the first instance of this score // ?? } } } - SequenceFeature[] fs; - feats[i] = fs = new SequenceFeature[n]; - if (n > 0) + + feats[i] = sfs.toArray(new SequenceFeature[sfs.size()]); + if (!sfs.isEmpty()) { - n = 0; - for (int f = 0; f < sf.length; f++) - { - if (sf[f] != null) - { - ((SequenceFeature[]) feats[i])[n++] = sf[f]; - } - } if (method == FEATURE_LABEL) { - // order the labels by alphabet - String[] labs = new String[fs.length]; - for (int l = 0; l < labs.length; l++) + // order the labels by alphabet (not yet implemented) + String[] labs = new String[sfs.size()]; + for (int l = 0; l < sfs.size(); l++) { - labs[l] = (fs[l].getDescription() != null ? fs[l] - .getDescription() : fs[l].getType()); + SequenceFeature sf = sfs.get(l); + String description = sf.getDescription(); + labs[l] = (description != null ? description : sf.getType()); } - QuickSort.sort(labs, ((Object[]) feats[i])); + QuickSort.sort(labs, feats[i]); } } if (hasScore[i]) @@ -881,23 +850,20 @@ public class AlignmentSorter // update the score bounds. if (hasScores == 1) { - max = min = scores[i]; + min = scores[i]; + max = min; } else { - if (max < scores[i]) - { - max = scores[i]; - } - if (min > scores[i]) - { - min = scores[i]; - } + max = Math.max(max, scores[i]); + min = Math.min(min, scores[i]); } } } - if (method == FEATURE_SCORE) + boolean doSort = false; + + if (FEATURE_SCORE.equals(method)) { if (hasScores == 0) { @@ -922,9 +888,9 @@ public class AlignmentSorter } } } - QuickSort.sortByDouble(scores, seqs, sortByFeatureScoreAscending); + doSort = true; } - else if (method == FEATURE_DENSITY) + else if (FEATURE_DENSITY.equals(method)) { for (int i = 0; i < seqs.length; i++) { @@ -934,18 +900,57 @@ public class AlignmentSorter // System.err.println("Sorting on Density: seq "+seqs[i].getName()+ // " Feats: "+featureCount+" Score : "+scores[i]); } - QuickSort.sortByDouble(scores, seqs, sortByFeatureScoreAscending); + doSort = true; } - else + if (doSort) { - if (method == FEATURE_LABEL) - { - throw new Error( - MessageManager.getString("error.not_yet_implemented")); - } + QuickSort.sortByDouble(scores, seqs, getInstance().sortByFeatureAscending); } - setOrder(alignment, seqs); } + /** + * Builds a string hash of criteria for sorting, and if unchanged from last + * time, reverse the sort order + * + * @param method + * @param featureTypes + * @param groups + * @param startCol + * @param endCol + */ + protected static void flipFeatureSortIfUnchanged(String method, + List featureTypes, List groups, + final int startCol, final int endCol) + { + StringBuilder sb = new StringBuilder(64); + sb.append(startCol).append(method).append(endCol); + if (featureTypes != null) + { + Collections.sort(featureTypes); + sb.append(featureTypes.toString()); + } + if (groups != null) + { + Collections.sort(groups); + sb.append(groups.toString()); + } + String scoreCriteria = sb.toString(); + + /* + * if resorting on the same criteria, toggle sort order + */ + AlignmentSorter as = getInstance(); + if (as.sortByFeatureCriteria == null + || !scoreCriteria.equals(as.sortByFeatureCriteria)) + { + as.sortByFeatureAscending = true; + } + else + { + as.sortByFeatureAscending = !as.sortByFeatureAscending; + } + as.sortByFeatureCriteria = scoreCriteria; + } + }