X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FAlignmentSorter.java;h=8634db68d2bedf572eaa2d94c3ffeece92a33e9e;hb=5ef61dcb1cc4a94ac6f88e90fc186521ce7224c1;hp=b5cefe0baa860082d1fa6093782270c5cf839e69;hpb=be762d8d9c71a7aa3121e845c45911c7192b7827;p=jalview.git diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java index b5cefe0..8634db6 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; @@ -51,40 +53,65 @@ 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 + } + + private 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 static boolean sortByFeatureAscending = true; + private boolean sortByFeatureAscending = true; - private static boolean sortLengthAscending; + private boolean sortLengthAscending; /** * Sorts sequences in the alignment by Percentage Identity with the given @@ -143,8 +170,8 @@ 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++) { @@ -179,10 +206,10 @@ 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++) { @@ -222,7 +249,8 @@ public class AlignmentSorter QuickSort.sort(ids, seqs); - if (sortIdAscending) + AlignmentSorter as = getInstance(); + if (as.sortIdAscending) { setReverseOrder(align, seqs); } @@ -231,7 +259,7 @@ public class AlignmentSorter setOrder(align, seqs); } - sortIdAscending = !sortIdAscending; + as.sortIdAscending = !as.sortIdAscending; } /** @@ -255,7 +283,9 @@ public class AlignmentSorter QuickSort.sort(length, seqs); - if (sortLengthAscending) + AlignmentSorter as = getInstance(); + + if (as.sortLengthAscending) { setReverseOrder(align, seqs); } @@ -264,7 +294,7 @@ public class AlignmentSorter setOrder(align, seqs); } - sortLengthAscending = !sortLengthAscending; + as.sortLengthAscending = !as.sortLengthAscending; } /** @@ -279,16 +309,18 @@ public class AlignmentSorter { // MAINTAINS ORIGNAL SEQUENCE ORDER, // ORDERS BY GROUP SIZE - List groups = new ArrayList(); + List groups = new ArrayList<>(); + + AlignmentSorter as = getInstance(); - if (groups.hashCode() != lastGroupHash) + 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 @@ -315,7 +347,7 @@ 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++) { @@ -328,7 +360,7 @@ public class AlignmentSorter } } - if (sortGroupAscending) + if (as.sortGroupAscending) { setOrder(align, seqs); } @@ -357,7 +389,7 @@ 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()]; @@ -401,16 +433,18 @@ 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); } @@ -436,7 +470,7 @@ public class AlignmentSorter { int nSeq = align.getHeight(); - List tmp = new ArrayList(); + List tmp = new ArrayList<>(); tmp = _sortByTree(tree.getTopNode(), tmp, align.getSequences()); @@ -473,18 +507,20 @@ public class AlignmentSorter { 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); } @@ -658,9 +694,12 @@ 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 @@ -670,18 +709,6 @@ 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"; - - /** * Sort sequences by feature score or density, optionally restricted by * feature types, feature groups, or alignment start/end positions. *

@@ -809,6 +836,8 @@ public class AlignmentSorter } } + boolean doSort = false; + if (FEATURE_SCORE.equals(method)) { if (hasScores == 0) @@ -834,7 +863,7 @@ public class AlignmentSorter } } } - QuickSort.sortByDouble(scores, seqs, sortByFeatureAscending); + doSort = true; } else if (FEATURE_DENSITY.equals(method)) { @@ -846,9 +875,12 @@ 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); } @@ -883,16 +915,17 @@ 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; } }