X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeatures.java;h=0d29184ea135d66ce8ffebd7406a843c33e363ce;hb=3d4ead4880755ec949de0300c232544ba965e60d;hp=8f6d49697eef4dc5abf315fb71569ce620a38737;hpb=807f5945ffa954c38f07cbf9d2a4ebc22cfe5eb9;p=jalview.git
diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java
index 8f6d496..0d29184 100644
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -1,14 +1,31 @@
+/*
+ * 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 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 +33,8 @@ 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)
@@ -26,29 +45,6 @@ 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
@@ -67,7 +63,7 @@ public class SequenceFeatures implements SequenceFeaturesI
*/
// featureStore = Collections
// .synchronizedSortedMap(new TreeMap());
- featureStore = new TreeMap();
+ featureStore = new TreeMap<>();
}
/**
@@ -112,17 +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));
- }
+ result.addAll(featureSet.findOverlappingFeatures(from, to));
}
-
return result;
}
@@ -132,7 +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));
@@ -149,10 +139,18 @@ public class SequenceFeatures implements SequenceFeaturesI
{
if (ontologyTerm == null || ontologyTerm.length == 0)
{
- return new ArrayList();
+ return new ArrayList<>();
}
Set featureTypes = getFeatureTypes(ontologyTerm);
+ if (featureTypes.isEmpty())
+ {
+ /*
+ * no features of the specified type or any sub-type
+ */
+ return new ArrayList<>();
+ }
+
return getAllFeatures(featureTypes.toArray(new String[featureTypes
.size()]));
}
@@ -165,13 +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;
}
@@ -184,16 +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;
-
}
/**
@@ -202,45 +191,42 @@ 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());
- }
+ result.addAll(featureSet.getPositionalFeatures());
}
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
- * sort in alphabetical order for consistent output behaviour
- */
- List types = new ArrayList(Arrays.asList(type));
- types.remove(null);
- Collections.sort(types);
+
+ 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;
}
@@ -250,15 +236,11 @@ 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());
- }
+ result.addAll(featureSet.getContactFeatures());
}
return result;
}
@@ -269,15 +251,11 @@ 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());
- }
+ result.addAll(featureSet.getNonPositionalFeatures());
}
return result;
}
@@ -321,17 +299,11 @@ 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;
@@ -344,7 +316,7 @@ 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())
{
@@ -372,7 +344,7 @@ 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();
@@ -385,9 +357,10 @@ 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
@@ -399,10 +372,10 @@ 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;
}
@@ -437,11 +410,10 @@ 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);
}
/**
@@ -459,20 +431,12 @@ public class SequenceFeatures implements SequenceFeaturesI
public List getFeaturesForGroup(boolean positional,
String group, String... type)
{
- List result = new ArrayList();
- Iterable types = varargToTypes(type);
-
- for (String featureType : types)
+ List result = new ArrayList<>();
+ for (FeatureStore featureSet : varargToTypes(type))
{
- /*
- * check whether the feature type is present, and also
- * whether it has features for the specified group
- */
- FeatureStore features = featureStore.get(featureType);
- if (features != null
- && features.getFeatureGroups(positional).contains(group))
+ if (featureSet.getFeatureGroups(positional).contains(group))
{
- result.addAll(features.getFeaturesForGroup(positional, group));
+ result.addAll(featureSet.getFeaturesForGroup(positional, group));
}
}
return result;
@@ -482,13 +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);
+ }
+
+}