X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeatures.java;h=e747d5f9ec64a5fa4954c74ac6e935f9bd454b5b;hb=08b87509ada06ac8614424247346daef4054b41a;hp=af99adac305ffc821335299b74360877d4b172df;hpb=f782e40f6f1b3f2bb22927891493c5faf318625b;p=jalview.git diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java index af99ada..e747d5f 100644 --- a/src/jalview/datamodel/features/SequenceFeatures.java +++ b/src/jalview/datamodel/features/SequenceFeatures.java @@ -1,3 +1,23 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.datamodel.features; import jalview.datamodel.SequenceFeature; @@ -7,7 +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; @@ -15,6 +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) @@ -25,30 +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!) @@ -62,11 +59,26 @@ public class SequenceFeatures implements SequenceFeaturesI { /* * use a TreeMap so that features are returned in alphabetical order of type - * wrap as a synchronized map for add and delete operations + * ? wrap as a synchronized map for add and delete operations */ // featureStore = Collections // .synchronizedSortedMap(new TreeMap()); - featureStore = new TreeMap(); + featureStore = new TreeMap<>(); + } + + /** + * Constructor given a list of features + */ + public SequenceFeatures(List features) + { + this(); + if (features != null) + { + for (SequenceFeature feature : features) + { + add(feature); + } + } } /** @@ -96,17 +108,11 @@ public class SequenceFeatures implements SequenceFeaturesI public List findFeatures(int from, int to, String... type) { - List result = new ArrayList(); - - for (String featureType : varargToTypes(type)) + List result = new ArrayList<>(); + for (FeatureStore featureSet : varargToTypes(type)) { - FeatureStore features = featureStore.get(featureType); - if (features != null) - { - result.addAll(features.findOverlappingFeatures(from, to)); - } + featureSet.findOverlappingFeatures(from, to, result); } - return result; } @@ -116,7 +122,7 @@ public class SequenceFeatures implements SequenceFeaturesI @Override public List getAllFeatures(String... type) { - List result = new ArrayList(); + List result = new ArrayList<>(); result.addAll(getPositionalFeatures(type)); @@ -133,12 +139,20 @@ public class SequenceFeatures implements SequenceFeaturesI { if (ontologyTerm == null || ontologyTerm.length == 0) { - return new ArrayList(); + return new ArrayList<>(); } Set featureTypes = getFeatureTypes(ontologyTerm); - return getAllFeatures(featureTypes.toArray(new String[featureTypes - .size()])); + if (featureTypes.isEmpty()) + { + /* + * no features of the specified type or any sub-type + */ + return new ArrayList<>(); + } + + return getAllFeatures( + featureTypes.toArray(new String[featureTypes.size()])); } /** @@ -149,13 +163,9 @@ public class SequenceFeatures implements SequenceFeaturesI { int result = 0; - for (String featureType : varargToTypes(type)) + for (FeatureStore featureSet : varargToTypes(type)) { - FeatureStore featureSet = featureStore.get(featureType); - if (featureSet != null) - { - result += featureSet.getFeatureCount(positional); - } + result += featureSet.getFeatureCount(positional); } return result; } @@ -168,16 +178,11 @@ public class SequenceFeatures implements SequenceFeaturesI { int result = 0; - for (String featureType : varargToTypes(type)) + for (FeatureStore featureSet : varargToTypes(type)) { - FeatureStore featureSet = featureStore.get(featureType); - if (featureSet != null) - { - result += featureSet.getTotalFeatureLength(); - } + result += featureSet.getTotalFeatureLength(); } return result; - } /** @@ -186,43 +191,41 @@ public class SequenceFeatures implements SequenceFeaturesI @Override public List getPositionalFeatures(String... type) { - List result = new ArrayList(); + List result = new ArrayList<>(); - for (String featureType : varargToTypes(type)) + for (FeatureStore featureSet : varargToTypes(type)) { - FeatureStore featureSet = featureStore.get(featureType); - if (featureSet != null) - { - result.addAll(featureSet.getPositionalFeatures()); - } + featureSet.getPositionalFeatures(result); } return result; } /** * A convenience method that converts a vararg for feature types to an - * Iterable, replacing the value with the stored feature types if it is null - * or empty + * Iterable over matched feature sets in key order * * @param type * @return */ - protected Iterable varargToTypes(String... type) + protected Iterable varargToTypes(String... type) { if (type == null || type.length == 0) { /* - * no vararg parameter supplied + * no vararg parameter supplied - return all */ - return featureStore.keySet(); + return featureStore.values(); } - /* - * else make a copy of the list, and remove any null value just in case, - * as it would cause errors looking up the features Map - */ - List types = new ArrayList(Arrays.asList(type)); - types.remove(null); + List types = new ArrayList<>(); + List args = Arrays.asList(type); + for (Entry featureType : featureStore.entrySet()) + { + if (args.contains(featureType.getKey())) + { + types.add(featureType.getValue()); + } + } return types; } @@ -232,15 +235,11 @@ public class SequenceFeatures implements SequenceFeaturesI @Override public List getContactFeatures(String... type) { - List result = new ArrayList(); + List result = new ArrayList<>(); - for (String featureType : varargToTypes(type)) + for (FeatureStore featureSet : varargToTypes(type)) { - FeatureStore featureSet = featureStore.get(featureType); - if (featureSet != null) - { - result.addAll(featureSet.getContactFeatures()); - } + featureSet.getContactFeatures(result); } return result; } @@ -251,15 +250,11 @@ public class SequenceFeatures implements SequenceFeaturesI @Override public List getNonPositionalFeatures(String... type) { - List result = new ArrayList(); + List result = new ArrayList<>(); - for (String featureType : varargToTypes(type)) + for (FeatureStore featureSet : varargToTypes(type)) { - FeatureStore featureSet = featureStore.get(featureType); - if (featureSet != null) - { - result.addAll(featureSet.getNonPositionalFeatures()); - } + featureSet.getNonPositionalFeatures(result); } return result; } @@ -303,17 +298,11 @@ public class SequenceFeatures implements SequenceFeaturesI public Set getFeatureGroups(boolean positionalFeatures, String... type) { - Set groups = new HashSet(); - - Iterable types = varargToTypes(type); + Set groups = new HashSet<>(); - for (String featureType : types) + for (FeatureStore featureSet : varargToTypes(type)) { - FeatureStore featureSet = featureStore.get(featureType); - if (featureSet != null) - { - groups.addAll(featureSet.getFeatureGroups(positionalFeatures)); - } + groups.addAll(featureSet.getFeatureGroups(positionalFeatures)); } return groups; @@ -326,12 +315,12 @@ public class SequenceFeatures implements SequenceFeaturesI public Set getFeatureTypesForGroups(boolean positionalFeatures, String... groups) { - Set result = new HashSet(); + Set result = new HashSet<>(); 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)) @@ -354,7 +343,7 @@ public class SequenceFeatures implements SequenceFeaturesI @Override public Set getFeatureTypes(String... soTerm) { - Set types = new HashSet(); + Set types = new HashSet<>(); for (Entry entry : featureStore.entrySet()) { String type = entry.getKey(); @@ -367,9 +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 @@ -381,10 +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; } @@ -398,8 +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; } /** @@ -408,8 +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; } /** @@ -419,10 +411,75 @@ 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); + } + + /** + * {@inheritDoc} This method is 'semi-optimised': it only inspects features + * for types that include the specified group, but has to inspect every + * feature of those types for matching feature group. This is efficient unless + * a sequence has features that share the same type but are in different + * groups - an unlikely case. + *

+ * For example, if RESNUM feature is created with group = PDBID, then features + * would only be retrieved for those sequences associated with the target + * PDBID (group). + */ + @Override + public List getFeaturesForGroup(boolean positional, + String group, String... type) + { + List result = new ArrayList<>(); + for (FeatureStore featureSet : varargToTypes(type)) + { + if (featureSet.getFeatureGroups(positional).contains(group)) + { + result.addAll(featureSet.getFeaturesForGroup(positional, group)); + } + } + return result; + } + + /** + * {@inheritDoc} + */ + @Override + public boolean shiftFeatures(int fromPosition, int shiftBy) + { + boolean modified = false; + for (FeatureStore fs : featureStore.values()) + { + 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); + return fs.findOverlappingFeatures(pos, pos, list); + } + + @Override + public boolean hasFeatures(String type) + { + return featureStore.containsKey(type); + } + +}