X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeatures.java;h=c75dbe0511533b46673f8862f9a408d6b7e28383;hb=b690e55cf50b5d253ec5545ee21cd93fc381f8c1;hp=fcf1b536409a3579a74c2fe1556d6c0b074d5dac;hpb=0dc22d603ad9d58a4ed951fc2146f7a027917a2c;p=jalview.git diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java index fcf1b53..c75dbe0 100644 --- a/src/jalview/datamodel/features/SequenceFeatures.java +++ b/src/jalview/datamodel/features/SequenceFeatures.java @@ -20,7 +20,6 @@ */ package jalview.datamodel.features; -import jalview.datamodel.ContiguousI; import jalview.datamodel.SequenceFeature; import jalview.io.gff.SequenceOntologyFactory; import jalview.io.gff.SequenceOntologyI; @@ -28,7 +27,6 @@ import jalview.io.gff.SequenceOntologyI; import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; -import java.util.Comparator; import java.util.HashSet; import java.util.List; import java.util.Map; @@ -36,6 +34,8 @@ import java.util.Map.Entry; import java.util.Set; import java.util.TreeMap; +import intervalstore.api.IntervalI; + /** * A class that stores sequence features in a way that supports efficient * querying by type and location (overlap). Intended for (but not limited to) @@ -46,30 +46,6 @@ import java.util.TreeMap; */ public class SequenceFeatures implements SequenceFeaturesI { - /** - * a comparator for sorting features by start position ascending - */ - private static Comparator FORWARD_STRAND = new Comparator() - { - @Override - public int compare(ContiguousI o1, ContiguousI o2) - { - return Integer.compare(o1.getBegin(), o2.getBegin()); - } - }; - - /** - * a comparator for sorting features by end position descending - */ - private static Comparator REVERSE_STRAND = new Comparator() - { - @Override - public int compare(ContiguousI o1, ContiguousI o2) - { - return Integer.compare(o2.getEnd(), o1.getEnd()); - } - }; - /* * map from feature type to structured store of features for that type * null types are permitted (but not a good idea!) @@ -87,7 +63,7 @@ public class SequenceFeatures implements SequenceFeaturesI */ // featureStore = Collections // .synchronizedSortedMap(new TreeMap()); - featureStore = new TreeMap(); + featureStore = new TreeMap<>(); } /** @@ -133,12 +109,10 @@ public class SequenceFeatures implements SequenceFeaturesI String... type) { List result = new ArrayList<>(); - for (FeatureStore featureSet : varargToTypes(type)) { - result.addAll(featureSet.findOverlappingFeatures(from, to)); + featureSet.findFeatures(from, to, result); } - return result; } @@ -177,8 +151,8 @@ public class SequenceFeatures implements SequenceFeaturesI return new ArrayList<>(); } - return getAllFeatures(featureTypes.toArray(new String[featureTypes - .size()])); + return getAllFeatures( + featureTypes.toArray(new String[featureTypes.size()])); } /** @@ -221,7 +195,7 @@ public class SequenceFeatures implements SequenceFeaturesI for (FeatureStore featureSet : varargToTypes(type)) { - result.addAll(featureSet.getPositionalFeatures()); + featureSet.getPositionalFeatures(result); } return result; } @@ -265,7 +239,7 @@ public class SequenceFeatures implements SequenceFeaturesI for (FeatureStore featureSet : varargToTypes(type)) { - result.addAll(featureSet.getContactFeatures()); + featureSet.getContactFeatures(result); } return result; } @@ -280,7 +254,7 @@ public class SequenceFeatures implements SequenceFeaturesI for (FeatureStore featureSet : varargToTypes(type)) { - result.addAll(featureSet.getNonPositionalFeatures()); + featureSet.getNonPositionalFeatures(result); } return result; } @@ -345,8 +319,8 @@ public class SequenceFeatures implements SequenceFeaturesI for (Entry featureType : featureStore.entrySet()) { - Set featureGroups = featureType.getValue().getFeatureGroups( - positionalFeatures); + Set featureGroups = featureType.getValue() + .getFeatureGroups(positionalFeatures); for (String group : groups) { if (featureGroups.contains(group)) @@ -382,9 +356,10 @@ public class SequenceFeatures implements SequenceFeaturesI } /** - * Answers true if the given type is one of the specified sequence ontology - * terms (or a sub-type of one), or if no terms are supplied. Answers false if - * filter terms are specified and the given term does not match any of them. + * Answers true if the given type matches one of the specified terms (or is a + * sub-type of one in the Sequence Ontology), or if no terms are supplied. + * Answers false if filter terms are specified and the given term does not + * match any of them. * * @param type * @param soTerm @@ -396,10 +371,10 @@ public class SequenceFeatures implements SequenceFeaturesI { return true; } - SequenceOntologyI so = SequenceOntologyFactory.getInstance(); + SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology(); for (String term : soTerm) { - if (so.isA(type, term)) + if (type.equals(term) || so.isA(type, term)) { return true; } @@ -413,8 +388,9 @@ public class SequenceFeatures implements SequenceFeaturesI @Override public float getMinimumScore(String type, boolean positional) { - return featureStore.containsKey(type) ? featureStore.get(type) - .getMinimumScore(positional) : Float.NaN; + return featureStore.containsKey(type) + ? featureStore.get(type).getMinimumScore(positional) + : Float.NaN; } /** @@ -423,8 +399,9 @@ public class SequenceFeatures implements SequenceFeaturesI @Override public float getMaximumScore(String type, boolean positional) { - return featureStore.containsKey(type) ? featureStore.get(type) - .getMaximumScore(positional) : Float.NaN; + return featureStore.containsKey(type) + ? featureStore.get(type).getMaximumScore(positional) + : Float.NaN; } /** @@ -434,11 +411,12 @@ public class SequenceFeatures implements SequenceFeaturesI * @param features * @param forwardStrand */ - public static void sortFeatures(List features, + public static void sortFeatures(List features, final boolean forwardStrand) { - Collections.sort(features, forwardStrand ? FORWARD_STRAND - : REVERSE_STRAND); + Collections.sort(features, + forwardStrand ? IntervalI.COMPARE_BEGIN_ASC + : IntervalI.COMPARE_END_DESC); } /** @@ -471,13 +449,42 @@ public class SequenceFeatures implements SequenceFeaturesI * {@inheritDoc} */ @Override - public boolean shiftFeatures(int shift) + public boolean shiftFeatures(int fromPosition, int shiftBy) { boolean modified = false; for (FeatureStore fs : featureStore.values()) { - modified |= fs.shiftFeatures(shift); + modified |= fs.shiftFeatures(fromPosition, shiftBy); } return modified; } -} \ No newline at end of file + + /** + * {@inheritDoc} + */ + @Override + public void deleteAll() + { + featureStore.clear(); + } + + @Override + public List findFeatures(int pos, String type, + List list) + { + FeatureStore fs = featureStore.get(type); + if (fs == null) + { + return list == null ? new ArrayList<>() : list; + } + return fs.findFeatures(pos, pos, list); + } + + @Override + public boolean hasFeatures(String type) + { + return featureStore.containsKey(type) + && !featureStore.get(type).isEmpty(); + } + +}