X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeatures.java;h=93ee71b32ea5e54b8cb11d023a152f3e54efefd6;hb=fbf6a124e2ffe81bcde747fda6f004748eb3b479;hp=f263938e05e534500f616145c246cd726cb9944b;hpb=b44349fe3a5f2d70b74a1b110018a753a1036aca;p=jalview.git

diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java
index f263938..93ee71b 100644
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -1,3 +1,23 @@
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel.features;
 
 import jalview.datamodel.SequenceFeature;
@@ -6,8 +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;
@@ -15,6 +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)
@@ -25,29 +45,6 @@ import java.util.TreeMap;
  */
 public class SequenceFeatures implements SequenceFeaturesI
 {
-  /**
-   * a comparator for sorting features by start position ascending
-   */
-  private static Comparator<ContiguousI> FORWARD_STRAND = new Comparator<ContiguousI>()
-  {
-    @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<ContiguousI> REVERSE_STRAND = new Comparator<ContiguousI>()
-  {
-    @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
@@ -62,11 +59,26 @@ 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<String, FeatureStore>());
-    featureStore = new TreeMap<String, FeatureStore>();
+    featureStore = new TreeMap<>();
+  }
+
+  /**
+   * Constructor given a list of features
+   */
+  public SequenceFeatures(List<SequenceFeature> features)
+  {
+    this();
+    if (features != null)
+    {
+      for (SequenceFeature feature : features)
+      {
+        add(feature);
+      }
+    }
   }
 
   /**
@@ -96,17 +108,11 @@ public class SequenceFeatures implements SequenceFeaturesI
   public List<SequenceFeature> findFeatures(int from, int to,
           String... type)
   {
-    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
-
-    for (String featureType : varargToTypes(type))
+    List<SequenceFeature> 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;
   }
 
@@ -116,7 +122,7 @@ public class SequenceFeatures implements SequenceFeaturesI
   @Override
   public List<SequenceFeature> getAllFeatures(String... type)
   {
-    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+    List<SequenceFeature> result = new ArrayList<>();
 
     result.addAll(getPositionalFeatures(type));
 
@@ -133,10 +139,18 @@ public class SequenceFeatures implements SequenceFeaturesI
   {
     if (ontologyTerm == null || ontologyTerm.length == 0)
     {
-      return new ArrayList<SequenceFeature>();
+      return new ArrayList<>();
     }
 
     Set<String> 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()]));
   }
@@ -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<SequenceFeature> getPositionalFeatures(String... type)
   {
-    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+    List<SequenceFeature> 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<String> varargToTypes(String... type)
+  protected Iterable<FeatureStore> 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<String> types = new ArrayList<String>(Arrays.asList(type));
-    types.remove(null);
-    Collections.sort(types);
+
+    List<FeatureStore> types = new ArrayList<>();
+    List<String> args = Arrays.asList(type);
+    for (Entry<String, FeatureStore> featureType : featureStore.entrySet())
+    {
+      if (args.contains(featureType.getKey()))
+      {
+        types.add(featureType.getValue());
+      }
+    }
     return types;
   }
 
@@ -234,15 +236,11 @@ public class SequenceFeatures implements SequenceFeaturesI
   @Override
   public List<SequenceFeature> getContactFeatures(String... type)
   {
-    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+    List<SequenceFeature> 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<SequenceFeature> getNonPositionalFeatures(String... type)
   {
-    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+    List<SequenceFeature> 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<String> getFeatureGroups(boolean positionalFeatures,
           String... type)
   {
-    Set<String> groups = new HashSet<String>();
-
-    Iterable<String> types = varargToTypes(type);
+    Set<String> 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;
@@ -328,7 +316,7 @@ public class SequenceFeatures implements SequenceFeaturesI
   public Set<String> getFeatureTypesForGroups(boolean positionalFeatures,
           String... groups)
   {
-    Set<String> result = new HashSet<String>();
+    Set<String> result = new HashSet<>();
 
     for (Entry<String, FeatureStore> featureType : featureStore.entrySet())
     {
@@ -356,7 +344,7 @@ public class SequenceFeatures implements SequenceFeaturesI
   @Override
   public Set<String> getFeatureTypes(String... soTerm)
   {
-    Set<String> types = new HashSet<String>();
+    Set<String> types = new HashSet<>();
     for (Entry<String, FeatureStore> 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
@@ -383,10 +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;
       }
@@ -421,11 +410,10 @@ public class SequenceFeatures implements SequenceFeaturesI
    * @param features
    * @param forwardStrand
    */
-  public static void sortFeatures(List<SequenceFeature> features,
+  public static void sortFeatures(List<? extends IntervalI> features,
           final boolean forwardStrand)
   {
-    Collections.sort(features, forwardStrand ? FORWARD_STRAND
-            : REVERSE_STRAND);
+    IntervalI.sortIntervals(features, forwardStrand);
   }
 
   /**
@@ -443,20 +431,12 @@ public class SequenceFeatures implements SequenceFeaturesI
   public List<SequenceFeature> getFeaturesForGroup(boolean positional,
           String group, String... type)
   {
-    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
-    Iterable<String> types = varargToTypes(type);
-
-    for (String featureType : types)
+    List<SequenceFeature> 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;
@@ -466,13 +446,39 @@ 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.
+   * 
+   * @author Bob Hanson 2019.07.30
+   */
+  @Override
+  public void findFeatures(int pos, String type, List<SequenceFeature> list)
+  {
+    FeatureStore fs = featureStore.get(type);
+    if (fs != null)
+    {
+      fs.findOverlappingFeatures(pos, list);
+    }
+  }
+
+
+}