X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeatures.java;h=be9c4f24360948edecd5ed69735fdb46ec33a402;hb=28e9024f09a78a9625ed4defa2012bf342bec51e;hp=8d5ba58c57ceee4d566424597dca01339d66dd24;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git
diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java
index 8d5ba58..be9c4f2 100644
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -1,14 +1,32 @@
+/*
+ * 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.ContiguousI;
import jalview.datamodel.SequenceFeature;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
+import jalview.util.Platform;
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;
@@ -16,6 +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)
@@ -26,35 +46,35 @@ import java.util.TreeMap;
*/
public class SequenceFeatures implements SequenceFeaturesI
{
+
+ /*
+ * map from feature type to structured store of features for that type
+ * null types are permitted (but not a good idea!)
+ */
+ private Map featureStore;
+
/**
- * a comparator for sorting features by start position ascending
+ * original NCList-based IntervalStore
*/
- private static Comparator FORWARD_STRAND = new Comparator()
- {
- @Override
- public int compare(ContiguousI o1, ContiguousI o2)
- {
- return Integer.compare(o1.getBegin(), o2.getBegin());
- }
- };
+ private final static int INTERVAL_STORE_NCLIST = 0;
/**
- * a comparator for sorting features by end position descending
+ * linked-list deferred-sort IntervalStore
*/
- private static Comparator REVERSE_STRAND = new Comparator()
- {
- @Override
- public int compare(ContiguousI o1, ContiguousI o2)
- {
- return Integer.compare(o2.getEnd(), o1.getEnd());
- }
- };
+ private final static int INTERVAL_STORE_NOCLKIST = 1;
- /*
- * map from feature type to structured store of features for that type
- * null types are permitted (but not a good idea!)
+ /**
+ * no-IntervalStore option for JavaScript
*/
- private Map featureStore;
+ private final static int INTERVAL_STORE_LINKED_LIST = -1;
+
+ private final int INTERVAL_STORE_MODE = (
+ // can be set differently for testing, but default is
+ // LINKED_LIST for JalviewJS and NCLIST for Java
+ Platform.isJS() ? //
+ INTERVAL_STORE_LINKED_LIST //
+ : INTERVAL_STORE_NCLIST//
+ );
/**
* Constructor
@@ -66,8 +86,8 @@ public class SequenceFeatures implements SequenceFeaturesI
* ? wrap as a synchronized map for add and delete operations
*/
// featureStore = Collections
- // .synchronizedSortedMap(new TreeMap());
- featureStore = new TreeMap();
+ // .synchronizedSortedMap(new TreeMap());
+ featureStore = new TreeMap<>();
}
/**
@@ -100,11 +120,25 @@ public class SequenceFeatures implements SequenceFeaturesI
if (featureStore.get(type) == null)
{
- featureStore.put(type, new FeatureStore());
+ featureStore.put(type, newFeatureStore());
}
return featureStore.get(type).addFeature(sf);
}
+ private FeatureStoreI newFeatureStore()
+ {
+ switch (INTERVAL_STORE_MODE)
+ {
+ default:
+ case INTERVAL_STORE_NCLIST:
+ return new FeatureStoreImpl(true);
+ case INTERVAL_STORE_NOCLKIST:
+ return new FeatureStoreImpl(false);
+ case INTERVAL_STORE_LINKED_LIST:
+ return new FeatureStoreJS();
+ }
+ }
+
/**
* {@inheritDoc}
*/
@@ -113,12 +147,14 @@ public class SequenceFeatures implements SequenceFeaturesI
String... type)
{
List result = new ArrayList<>();
-
- for (FeatureStore featureSet : varargToTypes(type))
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
- result.addAll(featureSet.findOverlappingFeatures(from, to));
+ // System.err.println("SF findFeature " + System.currentTimeMillis()
+ // + " " + from + " " + to + " "
+ // + featureSet.getPositionalFeatures().get(0).type);
+ //
+ result.addAll(featureSet.findOverlappingFeatures(from, to, null));
}
-
return result;
}
@@ -157,8 +193,8 @@ public class SequenceFeatures implements SequenceFeaturesI
return new ArrayList<>();
}
- return getAllFeatures(featureTypes.toArray(new String[featureTypes
- .size()]));
+ return getAllFeatures(
+ featureTypes.toArray(new String[featureTypes.size()]));
}
/**
@@ -169,7 +205,7 @@ public class SequenceFeatures implements SequenceFeaturesI
{
int result = 0;
- for (FeatureStore featureSet : varargToTypes(type))
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
result += featureSet.getFeatureCount(positional);
}
@@ -184,7 +220,7 @@ public class SequenceFeatures implements SequenceFeaturesI
{
int result = 0;
- for (FeatureStore featureSet : varargToTypes(type))
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
result += featureSet.getTotalFeatureLength();
}
@@ -199,9 +235,9 @@ public class SequenceFeatures implements SequenceFeaturesI
{
List result = new ArrayList<>();
- for (FeatureStore featureSet : varargToTypes(type))
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
- result.addAll(featureSet.getPositionalFeatures());
+ featureSet.getPositionalFeatures(result);
}
return result;
}
@@ -213,7 +249,7 @@ public class SequenceFeatures implements SequenceFeaturesI
* @param type
* @return
*/
- protected Iterable varargToTypes(String... type)
+ protected Iterable varargToTypes(String... type)
{
if (type == null || type.length == 0)
{
@@ -223,9 +259,9 @@ public class SequenceFeatures implements SequenceFeaturesI
return featureStore.values();
}
- List types = new ArrayList<>();
+ List types = new ArrayList<>();
List args = Arrays.asList(type);
- for (Entry featureType : featureStore.entrySet())
+ for (Entry featureType : featureStore.entrySet())
{
if (args.contains(featureType.getKey()))
{
@@ -243,9 +279,9 @@ public class SequenceFeatures implements SequenceFeaturesI
{
List result = new ArrayList<>();
- for (FeatureStore featureSet : varargToTypes(type))
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
- result.addAll(featureSet.getContactFeatures());
+ featureSet.getContactFeatures(result);
}
return result;
}
@@ -258,9 +294,9 @@ public class SequenceFeatures implements SequenceFeaturesI
{
List result = new ArrayList<>();
- for (FeatureStore featureSet : varargToTypes(type))
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
- result.addAll(featureSet.getNonPositionalFeatures());
+ featureSet.getNonPositionalFeatures(result);
}
return result;
}
@@ -271,7 +307,7 @@ public class SequenceFeatures implements SequenceFeaturesI
@Override
public boolean delete(SequenceFeature sf)
{
- for (FeatureStore featureSet : featureStore.values())
+ for (FeatureStoreI featureSet : featureStore.values())
{
if (featureSet.delete(sf))
{
@@ -287,7 +323,7 @@ public class SequenceFeatures implements SequenceFeaturesI
@Override
public boolean hasFeatures()
{
- for (FeatureStore featureSet : featureStore.values())
+ for (FeatureStoreI featureSet : featureStore.values())
{
if (!featureSet.isEmpty())
{
@@ -306,7 +342,7 @@ public class SequenceFeatures implements SequenceFeaturesI
{
Set groups = new HashSet<>();
- for (FeatureStore featureSet : varargToTypes(type))
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
groups.addAll(featureSet.getFeatureGroups(positionalFeatures));
}
@@ -323,10 +359,10 @@ public class SequenceFeatures implements SequenceFeaturesI
{
Set result = new HashSet<>();
- for (Entry featureType : featureStore.entrySet())
+ 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))
@@ -350,7 +386,7 @@ public class SequenceFeatures implements SequenceFeaturesI
public Set getFeatureTypes(String... soTerm)
{
Set types = new HashSet<>();
- for (Entry entry : featureStore.entrySet())
+ for (Entry entry : featureStore.entrySet())
{
String type = entry.getKey();
if (!entry.getValue().isEmpty() && isOntologyTerm(type, soTerm))
@@ -362,9 +398,10 @@ 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
@@ -376,10 +413,10 @@ 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;
}
@@ -393,8 +430,9 @@ 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;
}
/**
@@ -403,8 +441,9 @@ 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;
}
/**
@@ -414,11 +453,10 @@ public class SequenceFeatures implements SequenceFeaturesI
* @param features
* @param forwardStrand
*/
- public static void sortFeatures(List features,
+ public static void sortFeatures(List extends IntervalI> features,
final boolean forwardStrand)
{
- Collections.sort(features, forwardStrand ? FORWARD_STRAND
- : REVERSE_STRAND);
+ IntervalI.sortIntervals(features, forwardStrand);
}
/**
@@ -437,7 +475,7 @@ public class SequenceFeatures implements SequenceFeaturesI
String group, String... type)
{
List result = new ArrayList<>();
- for (FeatureStore featureSet : varargToTypes(type))
+ for (FeatureStoreI featureSet : varargToTypes(type))
{
if (featureSet.getFeatureGroups(positional).contains(group))
{
@@ -451,13 +489,81 @@ 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())
+ for (FeatureStoreI 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)
+ {
+ FeatureStoreI fs = featureStore.get(type);
+ return fs.findOverlappingFeatures(pos, 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);
+ }
+
+}