X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeatures.java;h=0d29184ea135d66ce8ffebd7406a843c33e363ce;hb=3d4ead4880755ec949de0300c232544ba965e60d;hp=bd102f6d39d01c561d41c08c4435ea873e2448f5;hpb=81d2ea57ab71c0806a036833f73711bc4ad5c76d;p=jalview.git diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java index bd102f6..0d29184 100644 --- a/src/jalview/datamodel/features/SequenceFeatures.java +++ b/src/jalview/datamodel/features/SequenceFeatures.java @@ -26,8 +26,6 @@ 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; @@ -47,29 +45,6 @@ import intervalstore.api.IntervalI; */ 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(IntervalI o1, IntervalI 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(IntervalI o1, IntervalI o2) - { - return Integer.compare(o2.getEnd(), o1.getEnd()); - } - }; /* * map from feature type to structured store of features for that type @@ -134,12 +109,10 @@ public class SequenceFeatures implements SequenceFeaturesI String... type) { List result = new ArrayList<>(); - for (FeatureStore featureSet : varargToTypes(type)) { result.addAll(featureSet.findOverlappingFeatures(from, to)); } - return result; } @@ -244,6 +217,7 @@ public class SequenceFeatures implements SequenceFeaturesI return featureStore.values(); } + List types = new ArrayList<>(); List args = Arrays.asList(type); for (Entry featureType : featureStore.entrySet()) @@ -398,7 +372,7 @@ public class SequenceFeatures implements SequenceFeaturesI { return true; } - SequenceOntologyI so = SequenceOntologyFactory.getInstance(); + SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology(); for (String term : soTerm) { if (type.equals(term) || so.isA(type, term)) @@ -436,11 +410,10 @@ 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); + IntervalI.sortIntervals(features, forwardStrand); } /** @@ -473,13 +446,88 @@ 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(); + } + + /** + * Simplified find for features associated with a given position. + * + * JavaScript set to not use IntervalI, but easily testable by setting false + * to true in javadoc + * + * FeatureRenderer has checked already that featureStore does contain type. + * + * @author Bob Hanson 2019.07.30 + */ + @Override + public List findFeatures(int pos, String type, + List list) + { + FeatureStore fs = featureStore.get(type); + boolean useIntervalStore = /** + * @j2sNative false && + */ + true; + return (useIntervalStore ? fs.findOverlappingFeatures(pos, pos) + : fs.findOverlappingFeatures(pos, list)); + } + + // Chrome; developer console closed + + // BH 2019.08.01 useIntervalStore true, redraw false: + // Platform: timer mark 13.848 0.367 overviewrender 16000 pixels row:14 + // Platform: timer mark 15.391 0.39 overviewrender 16000 pixels row:14 + // Platform: timer mark 16.498 0.39 overviewrender 16000 pixels row:14 + // Platform: timer mark 17.596 0.401 overviewrender 16000 pixels row:14 + // Platform: timer mark 18.738 0.363 overviewrender 16000 pixels row:14 + // Platform: timer mark 19.659 0.358 overviewrender 16000 pixels row:14 + // Platform: timer mark 20.737 0.359 overviewrender 16000 pixels row:14 + // Platform: timer mark 21.797 0.391 overviewrender 16000 pixels row:14 + // Platform: timer mark 22.851 0.361 overviewrender 16000 pixels row:14 + // Platform: timer mark 24.019 0.395 overviewrender 16000 pixels row:14 + + // BH 2019.08.01 useIntervalStore false, redraw false: + // Platform: timer mark 19.011 0.181 overviewrender 16000 pixels row:14 + // Platform: timer mark 20.311 0.183 overviewrender 16000 pixels row:14 + // Platform: timer mark 21.368 0.175 overviewrender 16000 pixels row:14 + // Platform: timer mark 22.347 0.178 overviewrender 16000 pixels row:14 + // Platform: timer mark 23.605 0.216 overviewrender 16000 pixels row:14 + // Platform: timer mark 24.836 0.191 overviewrender 16000 pixels row:14 + // Platform: timer mark 26.016 0.181 overviewrender 16000 pixels row:14 + // Platform: timer mark 27.278 0.178 overviewrender 16000 pixels row:14 + // Platform: timer mark 28.158 0.181 overviewrender 16000 pixels row:14 + // Platform: timer mark 29.227 0.196 overviewrender 16000 pixels row:14 + // Platform: timer mark 30.1 0.171 overviewrender 16000 pixels row:14 + // Platform: timer mark 31.684 0.196 overviewrender 16000 pixels row:14 + // Platform: timer mark 32.779 0.18 overviewrender 16000 pixels row:14 + // Platform: timer mark 52.355 0.185 overviewrender 16000 pixels row:14 + // Platform: timer mark 53.829 0.186 overviewrender 16000 pixels row:14 + + + + /** + * @author Bob Hanson 2019.08.01 + */ + @Override + public boolean hasFeatures(String type) + { + return featureStore.containsKey(type); + } + +}