X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=f2b2222aba7f0c948bc9463b0e725a17ebb7f5fb;hb=7d602d0e4b439e56af3e4551ed71f181a8025534;hp=f22835088f97981669dbf06dc0a40efe2e501004;hpb=9769c798c95dff2006438438706a3e715755cd57;p=jalview.git diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java index f228350..f2b2222 100755 --- a/src/jalview/analysis/AlignmentSorter.java +++ b/src/jalview/analysis/AlignmentSorter.java @@ -22,6 +22,8 @@ package jalview.analysis; import jalview.analysis.scoremodels.PIDModel; import jalview.analysis.scoremodels.SimilarityParams; +import jalview.bin.ApplicationSingletonProvider; +import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.AlignmentOrder; @@ -32,6 +34,7 @@ import jalview.datamodel.SequenceNode; import jalview.util.QuickSort; import java.util.ArrayList; +import java.util.BitSet; import java.util.Collections; import java.util.Iterator; import java.util.List; @@ -51,40 +54,68 @@ import java.util.List; * from the first tobesorted position in the alignment. e.g. (a,tb2,b,tb1,c,tb3 * becomes a,tb1,tb2,tb3,b,c) */ -public class AlignmentSorter +public class AlignmentSorter implements ApplicationSingletonI { + + private AlignmentSorter() + { + // private singleton + } + + public static AlignmentSorter getInstance() + { + return (AlignmentSorter) ApplicationSingletonProvider + .getInstance(AlignmentSorter.class); + } + + /** + * types of feature ordering: Sort by score : average score - or total score - + * over all features in region Sort by feature label text: (or if null - + * feature type text) - numerical or alphabetical Sort by feature density: + * based on counts - ignoring individual text or scores for each feature + */ + public static final String FEATURE_SCORE = "average_score"; + + public static final String FEATURE_LABEL = "text"; + + public static final String FEATURE_DENSITY = "density"; + /* * todo: refactor searches to follow a basic pattern: (search property, last * search state, current sort direction) */ - static boolean sortIdAscending = true; + boolean sortIdAscending = true; - static int lastGroupHash = 0; + int lastGroupHash = 0; - static boolean sortGroupAscending = true; + boolean sortGroupAscending = true; - static AlignmentOrder lastOrder = null; + AlignmentOrder lastOrder = null; - static boolean sortOrderAscending = true; + boolean sortOrderAscending = true; - static TreeModel lastTree = null; + TreeModel lastTree = null; - static boolean sortTreeAscending = true; + boolean sortTreeAscending = true; - /* + /** * last Annotation Label used for sort by Annotation score */ - private static String lastSortByAnnotation; + private String lastSortByAnnotation; - /* - * string hash of last arguments to sortByFeature - * (sort order toggles if this is unchanged between sorts) + /** + * string hash of last arguments to sortByFeature (sort order toggles if this + * is unchanged between sorts) */ - private static String sortByFeatureCriteria; + private String sortByFeatureCriteria; + + private boolean sortByFeatureAscending = true; + + private boolean sortLengthAscending; - private static boolean sortByFeatureAscending = true; + private static boolean sortEValueAscending; - private static boolean sortLengthAscending; + private static boolean sortBitScoreAscending; /** * Sorts sequences in the alignment by Percentage Identity with the given @@ -108,120 +139,97 @@ public class AlignmentSorter true); for (int i = 0; i < nSeq; i++) { - scores[i] = (float) PIDModel.computePID(align.getSequenceAt(i) - .getSequenceAsString(), refSeq, pidParams); + scores[i] = (float) PIDModel.computePID( + align.getSequenceAt(i).getSequenceAsString(), refSeq, + pidParams); seqs[i] = align.getSequenceAt(i); } QuickSort.sort(scores, seqs); - setReverseOrder(align, seqs); } /** - * Reverse the order of the sort + * Sorts by ID. Numbers are sorted before letters. * * @param align - * DOCUMENT ME! - * @param seqs - * DOCUMENT ME! + * The alignment object to sort */ - private static void setReverseOrder(AlignmentI align, SequenceI[] seqs) + public static void sortByID(AlignmentI align) { - int nSeq = seqs.length; - - int len = 0; + int nSeq = align.getHeight(); - if ((nSeq % 2) == 0) - { - len = nSeq / 2; - } - else - { - len = (nSeq + 1) / 2; - } + String[] ids = new String[nSeq]; + SequenceI[] seqs = new SequenceI[nSeq]; - // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work - List asq; - synchronized (asq = align.getSequences()) + for (int i = 0; i < nSeq; i++) { - for (int i = 0; i < len; i++) - { - // SequenceI tmp = seqs[i]; - asq.set(i, seqs[nSeq - i - 1]); - asq.set(nSeq - i - 1, seqs[i]); - } + ids[i] = align.getSequenceAt(i).getName(); + seqs[i] = align.getSequenceAt(i); } - } - /** - * Sets the Alignment object with the given sequences - * - * @param align - * Alignment object to be updated - * @param tmp - * sequences as a vector - */ - private static void setOrder(AlignmentI align, List tmp) - { - setOrder(align, vectorSubsetToArray(tmp, align.getSequences())); + QuickSort.sort(ids, seqs); + AlignmentSorter as = getInstance(); + as.sortIdAscending = !as.sortIdAscending; + set(align, seqs, as.sortIdAscending); } /** - * Sets the Alignment object with the given sequences + * Sorts by sequence length * * @param align - * DOCUMENT ME! - * @param seqs - * sequences as an array + * The alignment object to sort */ - public static void setOrder(AlignmentI align, SequenceI[] seqs) + public static void sortByLength(AlignmentI align) { - // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work - List algn; - synchronized (algn = align.getSequences()) - { - List tmp = new ArrayList(); + int nSeq = align.getHeight(); - for (int i = 0; i < seqs.length; i++) - { - if (algn.contains(seqs[i])) - { - tmp.add(seqs[i]); - } - } + float[] length = new float[nSeq]; + SequenceI[] seqs = new SequenceI[nSeq]; - algn.clear(); - // User may have hidden seqs, then clicked undo or redo - for (int i = 0; i < tmp.size(); i++) - { - algn.add(tmp.get(i)); - } + for (int i = 0; i < nSeq; i++) + { + seqs[i] = align.getSequenceAt(i); + length[i] = (seqs[i].getEnd() - seqs[i].getStart()); } + + QuickSort.sort(length, seqs); + AlignmentSorter as = getInstance(); + as.sortLengthAscending = !as.sortLengthAscending; + set(align, seqs, as.sortLengthAscending); } /** - * Sorts by ID. Numbers are sorted before letters. + * Sorts by sequence evalue. Currently moves all sequences without an evalue to + * the top of the alignment. * * @param align - * The alignment object to sort + * The alignment object to sort */ - public static void sortByID(AlignmentI align) + public static void sortByEValue(AlignmentI align) { int nSeq = align.getHeight(); - String[] ids = new String[nSeq]; + double[] evalue = new double[nSeq]; SequenceI[] seqs = new SequenceI[nSeq]; for (int i = 0; i < nSeq; i++) { - ids[i] = align.getSequenceAt(i).getName(); seqs[i] = align.getSequenceAt(i); + AlignmentAnnotation[] ann = seqs[i].getAnnotation("Search Scores"); + if (ann != null) + { + evalue[i] = ann[0].getEValue(); + } + else + { + evalue[i] = -1; + } } - QuickSort.sort(ids, seqs); + QuickSort.sort(evalue, seqs); - if (sortIdAscending) + if (sortEValueAscending) { setReverseOrder(align, seqs); } @@ -230,31 +238,40 @@ public class AlignmentSorter setOrder(align, seqs); } - sortIdAscending = !sortIdAscending; + sortEValueAscending = !sortEValueAscending; } /** - * Sorts by sequence length + * Sorts by sequence bit score. Currently moves all sequences without a bit + * score to the top of the alignment * * @param align - * The alignment object to sort + * The alignment object to sort */ - public static void sortByLength(AlignmentI align) + public static void sortByBitScore(AlignmentI align) { int nSeq = align.getHeight(); - float[] length = new float[nSeq]; + double[] score = new double[nSeq]; SequenceI[] seqs = new SequenceI[nSeq]; for (int i = 0; i < nSeq; i++) { seqs[i] = align.getSequenceAt(i); - length[i] = (seqs[i].getEnd() - seqs[i].getStart()); + AlignmentAnnotation[] ann = seqs[i].getAnnotation("Search Scores"); + if (ann != null) + { + score[i] = ann[0].getEValue(); + } + else + { + score[i] = -1; + } } - QuickSort.sort(length, seqs); + QuickSort.sort(score, seqs); - if (sortLengthAscending) + if (sortBitScoreAscending) { setReverseOrder(align, seqs); } @@ -263,7 +280,7 @@ public class AlignmentSorter setOrder(align, seqs); } - sortLengthAscending = !sortLengthAscending; + sortBitScoreAscending = !sortBitScoreAscending; } /** @@ -278,16 +295,18 @@ 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 @@ -314,7 +333,7 @@ public class AlignmentSorter // NOW ADD SEQUENCES MAINTAINING ALIGNMENT ORDER // ///////////////////////////////////////////// - List seqs = new ArrayList(); + List tmp = new ArrayList<>(); for (int i = 0; i < groups.size(); i++) { @@ -323,68 +342,10 @@ public class AlignmentSorter for (int j = 0; j < orderedseqs.length; j++) { - seqs.add(orderedseqs[j]); - } - } - - if (sortGroupAscending) - { - setOrder(align, seqs); - } - else - { - setReverseOrder(align, - vectorSubsetToArray(seqs, align.getSequences())); - } - } - - /** - * Select sequences in order from tmp that is present in mask, and any - * remaining sequences in mask not in tmp - * - * @param tmp - * thread safe collection of sequences - * @param mask - * thread safe collection of sequences - * - * @return intersect(tmp,mask)+intersect(complement(tmp),mask) - */ - private static SequenceI[] vectorSubsetToArray(List tmp, - List mask) - { - // or? - // tmp2 = tmp.retainAll(mask); - // return tmp2.addAll(mask.removeAll(tmp2)) - - ArrayList seqs = new ArrayList(); - int i, idx; - boolean[] tmask = new boolean[mask.size()]; - - for (i = 0; i < mask.size(); i++) - { - tmask[i] = true; - } - - for (i = 0; i < tmp.size(); i++) - { - SequenceI sq = tmp.get(i); - idx = mask.indexOf(sq); - if (idx > -1 && tmask[idx]) - { - tmask[idx] = false; - seqs.add(sq); - } - } - - for (i = 0; i < tmask.length; i++) - { - if (tmask[i]) - { - seqs.add(mask.get(i)); + tmp.add(orderedseqs[j]); } } - - return seqs.toArray(new SequenceI[seqs.size()]); + set(align, tmp, as.sortGroupAscending); } /** @@ -400,23 +361,17 @@ public class AlignmentSorter // Get an ordered vector of sequences which may also be present in align List tmp = order.getOrder(); - if (lastOrder == order) - { - sortOrderAscending = !sortOrderAscending; - } - else - { - sortOrderAscending = true; - } + AlignmentSorter as = getInstance(); - if (sortOrderAscending) + if (as.lastOrder == order) { - setOrder(align, tmp); + as.sortOrderAscending = !as.sortOrderAscending; } else { - setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences())); + as.sortOrderAscending = true; } + set(align, tmp, as.sortOrderAscending); } /** @@ -434,7 +389,7 @@ public class AlignmentSorter { int nSeq = align.getHeight(); - List tmp = new ArrayList(); + List tmp = new ArrayList<>(); tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences()); @@ -450,12 +405,9 @@ 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"); } } @@ -474,25 +426,19 @@ public class AlignmentSorter { List tmp = getOrderByTree(align, tree); - // tmp should properly permute align with tree. - if (lastTree != tree) - { - sortTreeAscending = true; - lastTree = tree; - } - else - { - sortTreeAscending = !sortTreeAscending; - } + AlignmentSorter as = getInstance(); - if (sortTreeAscending) + // tmp should properly permute align with tree. + if (as.lastTree != tree) { - setOrder(align, tmp); + as.sortTreeAscending = true; + as.lastTree = tree; } else { - setReverseOrder(align, vectorSubsetToArray(tmp, align.getSequences())); + as.sortTreeAscending = !as.sortTreeAscending; } + set(align, tmp, as.sortTreeAscending); } /** @@ -586,7 +532,7 @@ public class AlignmentSorter for (int i = 0; i < alignment.length; i++) { - ids[i] = (new Float(alignment[i].getName().substring(8))) + ids[i] = (Float.valueOf(alignment[i].getName().substring(8))) .floatValue(); } @@ -658,9 +604,12 @@ public class AlignmentSorter } jalview.util.QuickSort.sort(scores, seqs); - if (lastSortByAnnotation != scoreLabel) + + AlignmentSorter as = getInstance(); + + if (as.lastSortByAnnotation != scoreLabel) { - lastSortByAnnotation = scoreLabel; + as.lastSortByAnnotation = scoreLabel; setOrder(alignment, seqs); } else @@ -670,39 +619,6 @@ public class AlignmentSorter } /** - * types of feature ordering: Sort by score : average score - or total score - - * over all features in region Sort by feature label text: (or if null - - * feature type text) - numerical or alphabetical Sort by feature density: - * based on counts - ignoring individual text or scores for each feature - */ - public static String FEATURE_SCORE = "average_score"; - - public static String FEATURE_LABEL = "text"; - - public static String FEATURE_DENSITY = "density"; - - private static boolean containsIgnoreCase(final String lab, - final List labs) - { - if (labs == null) - { - return true; - } - if (lab == null) - { - return false; - } - for (String label : labs) - { - if (lab.equalsIgnoreCase(label)) - { - return true; - } - } - return false; - } - - /** * Sort sequences by feature score or density, optionally restricted by * feature types, feature groups, or alignment start/end positions. *

@@ -729,14 +645,15 @@ public class AlignmentSorter if (method != FEATURE_SCORE && method != FEATURE_LABEL && method != FEATURE_DENSITY) { - String msg = String - .format("Implementation Error - sortByFeature method must be either '%s' or '%s'", - FEATURE_SCORE, FEATURE_DENSITY); + String msg = String.format( + "Implementation Error - sortByFeature method must be either '%s' or '%s'", + FEATURE_SCORE, FEATURE_DENSITY); System.err.println(msg); return; } - flipFeatureSortIfUnchanged(method, featureTypes, groups, startCol, endCol); + flipFeatureSortIfUnchanged(method, featureTypes, groups, startCol, + endCol); SequenceI[] seqs = alignment.getSequencesArray(); @@ -755,13 +672,10 @@ public class AlignmentSorter * get sequence residues overlapping column region * and features for residue positions and specified types */ - // TODO new method findPositions(startCol, endCol)? JAL-2544 - int startResidue = seqs[i].findPosition(startCol); - int endResidue = seqs[i].findPosition(endCol); - String[] types = featureTypes == null ? null : featureTypes - .toArray(new String[featureTypes.size()]); - List sfs = seqs[i].getFeatures().findFeatures( - startResidue, endResidue, 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; @@ -772,19 +686,12 @@ public class AlignmentSorter SequenceFeature sf = it.next(); /* - * double-check feature overlaps columns (JAL-2544) - * (could avoid this with a findPositions(fromCol, toCol) method) - * findIndex returns base 1 column values, startCol/endCol are base 0 + * accept all features with null or empty group, otherwise + * check group is one of the currently visible groups */ - if (seqs[i].findIndex(sf.getBegin()) > endCol + 1 - || seqs[i].findIndex(sf.getEnd()) < startCol + 1) - { - it.remove(); - continue; - } - String featureGroup = sf.getFeatureGroup(); if (groups != null && featureGroup != null + && !"".equals(featureGroup) && !groups.contains(featureGroup)) { it.remove(); @@ -840,6 +747,8 @@ public class AlignmentSorter } } + boolean doSort = false; + if (FEATURE_SCORE.equals(method)) { if (hasScores == 0) @@ -865,7 +774,7 @@ public class AlignmentSorter } } } - QuickSort.sortByDouble(scores, seqs, sortByFeatureAscending); + doSort = true; } else if (FEATURE_DENSITY.equals(method)) { @@ -877,9 +786,13 @@ public class AlignmentSorter // System.err.println("Sorting on Density: seq "+seqs[i].getName()+ // " Feats: "+featureCount+" Score : "+scores[i]); } - QuickSort.sortByDouble(scores, seqs, sortByFeatureAscending); + doSort = true; + } + if (doSort) + { + QuickSort.sortByDouble(scores, seqs, + getInstance().sortByFeatureAscending); } - setOrder(alignment, seqs); } @@ -914,16 +827,177 @@ public class AlignmentSorter /* * if resorting on the same criteria, toggle sort order */ - if (sortByFeatureCriteria == null - || !scoreCriteria.equals(sortByFeatureCriteria)) + AlignmentSorter as = getInstance(); + if (as.sortByFeatureCriteria == null + || !scoreCriteria.equals(as.sortByFeatureCriteria)) { - sortByFeatureAscending = true; + as.sortByFeatureAscending = true; } else { - sortByFeatureAscending = !sortByFeatureAscending; + as.sortByFeatureAscending = !as.sortByFeatureAscending; } - sortByFeatureCriteria = scoreCriteria; + as.sortByFeatureCriteria = scoreCriteria; + } + + /** + * Set the alignment's sequences list to contain the sequences from a + * temporary list, first adding all the elements from the tmp list, then adding all sequences in the alignment that + * are not in the list. Option to do the final sort either in order or in reverse order. + * + * @param align The alignment being sorted + * @param tmp + * the temporary sequence list + * @param ascending + * false for reversed order; only sequences already in + * the alignment will be used (which is actually already guaranteed + * by vectorSubsetToArray) + */ + private static void set(AlignmentI align, List tmp, + boolean ascending) + { + set(align, vectorSubsetToArray(align.getSequences(), tmp), ascending); + } + + /** + * Set the alignment's sequences list to contain these sequences, either in + * this order or its reverse. + * + * @param align + * @param seqs + * the new sequence array + * @param ascending + * false for reversed order; if ascending, only sequences already in + * the alignment will be used; if descending, then a direct 1:1 + * replacement is made + */ + private static void set(AlignmentI align, SequenceI[] seqs, + boolean ascending) + { + if (ascending) + { + setOrder(align, seqs); + } + else + { + setReverseOrder(align, seqs); + } + + } + + /** + * Replace the alignment's sequences with values in an array, clearing the + * alignment's sequence list and filtering for sequences that are actually in + * the alignment already. + * + * @param align + * the Alignment + * @param seqs + * the array of replacement values, of any length + */ + public static void setOrder(AlignmentI align, SequenceI[] seqs) + { + // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work + List seqList = align.getSequences(); + synchronized (seqList) + { + List tmp = new ArrayList<>(); + + for (int i = 0; i < seqs.length; i++) + { + if (seqList.contains(seqs[i])) + { + tmp.add(seqs[i]); + } + } + + seqList.clear(); + // User may have hidden seqs, then clicked undo or redo + for (int i = 0; i < tmp.size(); i++) + { + seqList.add(tmp.get(i)); + } + } + } + + /** + * Replace the alignment's sequences or a subset of those sequences with + * values in an array in reverse order. All sequences are replaced; no check + * is made that these sequences are in the alignment already. + * + * @param align + * the Alignment + * @param seqs + * the array of replacement values, length must be less than or equal + * to Alignment.sequences.size() + */ + private static void setReverseOrder(AlignmentI align, SequenceI[] seqs) + { + int nSeq = seqs.length; + + int len = (nSeq + (nSeq % 2)) / 2; + // int len = 0; + // + // if ((nSeq % 2) == 0) + // { + // len = nSeq / 2; + // } + // else + // { + // len = (nSeq + 1) / 2; + // } + + // NOTE: DO NOT USE align.setSequenceAt() here - it will NOT work + List seqList = align.getSequences(); + synchronized (seqList) + { + for (int i = 0; i < len; i++) + { + // SequenceI tmp = seqs[i]; + seqList.set(i, seqs[nSeq - i - 1]); + seqList.set(nSeq - i - 1, seqs[i]); + } + } + } + + /** + * Create and array of reordered sequences in order first from tmp that are + * present in seqList already, then, after that, any remaining sequences in + * seqList not in tmp. Any sequences in tmp that are not in seqList already + * are discarded. + * + * @param seqList + * thread safe collection of sequences originally in the alignment + * @param tmp + * thread safe collection of sequences or subsequences possibly in + * seqList + * + * @return intersect(tmp,seqList)+intersect(complement(tmp),seqList) + */ + private static SequenceI[] vectorSubsetToArray(List seqList, + List tmp) + { + ArrayList seqs = new ArrayList<>(); + int n = seqList.size(); + BitSet bs = new BitSet(n); + bs.set(0, n); + for (int i = 0, nt = tmp.size(); i < nt; i++) + { + SequenceI sq = tmp.get(i); + int idx = seqList.indexOf(sq); + if (idx >= 0 && bs.get(idx)) + { + seqs.add(sq); + bs.clear(idx); + } + } + + for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i + 1)) + { + seqs.add(seqList.get(i)); + } + + return seqs.toArray(new SequenceI[seqs.size()]); } }