X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeatures.java;h=905fd8b4ce4677d77a7f7db8f2ee8d0ad8c9483f;hb=15a605b8a12026b453e252477b416b2c82b6344a;hp=ff570b1ada2e9f742e708e8466751bae2c9c8f0a;hpb=1ec8fc3e8bc982115e5ba1b16a101d239a2df591;p=jalview.git
diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java
index ff570b1..905fd8b 100644
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -1,13 +1,27 @@
+/*
+ * 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;
-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;
@@ -15,6 +29,11 @@ import java.util.Map.Entry;
import java.util.Set;
import java.util.TreeMap;
+import intervalstore.api.IntervalI;
+import jalview.datamodel.SequenceFeature;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyI;
+
/**
* 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 +44,6 @@ 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 +57,26 @@ 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);
+ }
+ }
}
/**
@@ -96,15 +106,11 @@ public class SequenceFeatures implements SequenceFeaturesI
public List findFeatures(int from, int to,
String... type)
{
- List result = new ArrayList();
+ List result = new ArrayList<>();
- for (String featureType : varargToTypes(type))
+ 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;
@@ -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;
-
}
/**
@@ -186,45 +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. If no types are specified, all feature
+ * sets are returned. If one or more types are specified, feature sets for
+ * those types are returned, preserving the order of the types.
*
* @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<>();
+ for (String theType : type)
+ {
+ if (theType != null && featureStore.containsKey(theType))
+ {
+ types.add(featureStore.get(theType));
+ }
+ }
return types;
}
@@ -234,15 +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;
}
@@ -253,15 +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;
}
@@ -305,17 +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;
@@ -328,12 +316,12 @@ 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))
@@ -356,7 +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();
@@ -369,9 +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
@@ -386,7 +375,7 @@ public class SequenceFeatures implements SequenceFeaturesI
SequenceOntologyI so = SequenceOntologyFactory.getInstance();
for (String term : soTerm)
{
- if (so.isA(type, term))
+ if (type.equals(term) || so.isA(type, term))
{
return true;
}
@@ -400,8 +389,9 @@ 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;
}
/**
@@ -410,8 +400,9 @@ 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;
}
/**
@@ -421,11 +412,12 @@ 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_END_DESC
+ : IntervalI.COMPARE_END_DESC);
}
/**
@@ -443,22 +435,37 @@ 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;
}
-}
\ No newline at end of file
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public boolean shiftFeatures(int fromPosition, int shiftBy)
+ {
+ boolean modified = false;
+ for (FeatureStore fs : featureStore.values())
+ {
+ modified |= fs.shiftFeatures(fromPosition, shiftBy);
+ }
+ return modified;
+ }
+
+ /**
+ * {@inheritDoc}
+ */
+ @Override
+ public void deleteAll()
+ {
+ featureStore.clear();
+ }
+}