X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeatures.java;h=c75dbe0511533b46673f8862f9a408d6b7e28383;hb=b690e55cf50b5d253ec5545ee21cd93fc381f8c1;hp=24f2081103afb4ebb6b73ec7ddfc36226434e368;hpb=5fc820296bd27badf71036b9d79980277d1dd095;p=jalview.git
diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java
index 24f2081..c75dbe0 100644
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -1,6 +1,25 @@
+/*
+ * 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;
@@ -8,7 +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;
@@ -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)
@@ -26,30 +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!)
@@ -67,7 +63,7 @@ public class SequenceFeatures implements SequenceFeaturesI
*/
// featureStore = Collections
// .synchronizedSortedMap(new TreeMap());
- featureStore = new TreeMap();
+ featureStore = new TreeMap<>();
}
/**
@@ -113,12 +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;
}
@@ -149,8 +143,16 @@ public class SequenceFeatures implements SequenceFeaturesI
}
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()]));
}
/**
@@ -193,7 +195,7 @@ public class SequenceFeatures implements SequenceFeaturesI
for (FeatureStore featureSet : varargToTypes(type))
{
- result.addAll(featureSet.getPositionalFeatures());
+ featureSet.getPositionalFeatures(result);
}
return result;
}
@@ -237,7 +239,7 @@ public class SequenceFeatures implements SequenceFeaturesI
for (FeatureStore featureSet : varargToTypes(type))
{
- result.addAll(featureSet.getContactFeatures());
+ featureSet.getContactFeatures(result);
}
return result;
}
@@ -252,7 +254,7 @@ public class SequenceFeatures implements SequenceFeaturesI
for (FeatureStore featureSet : varargToTypes(type))
{
- result.addAll(featureSet.getNonPositionalFeatures());
+ featureSet.getNonPositionalFeatures(result);
}
return result;
}
@@ -317,8 +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))
@@ -354,9 +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
@@ -368,10 +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;
}
@@ -385,8 +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;
}
/**
@@ -395,8 +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;
}
/**
@@ -406,11 +411,12 @@ 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);
+ Collections.sort(features,
+ forwardStrand ? IntervalI.COMPARE_BEGIN_ASC
+ : IntervalI.COMPARE_END_DESC);
}
/**
@@ -452,4 +458,33 @@ public class SequenceFeatures implements SequenceFeaturesI
}
return modified;
}
+
+ /**
+ * {@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();
+ }
+
}