X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeatures.java;h=8f965b4237284dd60307d1d75d0a65eed839253d;hb=b83eff8c672cede0305da3c76823dab414749dde;hp=d177566f887d547c22a3c27219426d647893293d;hpb=51728d3951398f9c12d7017c776953f17322cc68;p=jalview.git

diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java
index d177566..8f965b4 100644
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -1,17 +1,78 @@
+/*
+ * 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.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.HashMap;
+import java.util.Comparator;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.TreeMap;
 
-public class SequenceFeatures
+/**
+ * A class that stores sequence features in a way that supports efficient
+ * querying by type and location (overlap). Intended for (but not limited to)
+ * storage of features for one sequence.
+ * 
+ * @author gmcarstairs
+ *
+ */
+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
+   * null types are permitted (but not a good idea!)
    */
   private Map<String, FeatureStore> featureStore;
 
@@ -20,41 +81,413 @@ public class SequenceFeatures
    */
   public SequenceFeatures()
   {
-    featureStore = new HashMap<String, FeatureStore>();
+    /*
+     * use a TreeMap so that features are returned in alphabetical order of type
+     * ? wrap as a synchronized map for add and delete operations
+     */
+    // featureStore = Collections
+    // .synchronizedSortedMap(new TreeMap<String, FeatureStore>());
+    featureStore = new TreeMap<>();
   }
 
   /**
-   * Add one sequence feature to the store
-   * 
-   * @param sf
+   * Constructor given a list of features
    */
-  public void add(SequenceFeature sf)
+  public SequenceFeatures(List<SequenceFeature> features)
+  {
+    this();
+    if (features != null)
+    {
+      for (SequenceFeature feature : features)
+      {
+        add(feature);
+      }
+    }
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public boolean add(SequenceFeature sf)
   {
     String type = sf.getType();
+    if (type == null)
+    {
+      System.err.println("Feature type may not be null: " + sf.toString());
+      return false;
+    }
+
     if (featureStore.get(type) == null)
     {
       featureStore.put(type, new FeatureStore());
     }
-    featureStore.get(type).addFeature(sf);
+    return featureStore.get(type).addFeature(sf);
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public List<SequenceFeature> findFeatures(int from, int to,
+          String... type)
+  {
+    List<SequenceFeature> result = new ArrayList<>();
+
+    for (FeatureStore featureSet : varargToTypes(type))
+    {
+      result.addAll(featureSet.findOverlappingFeatures(from, to));
+    }
+
+    return result;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public List<SequenceFeature> getAllFeatures(String... type)
+  {
+    List<SequenceFeature> result = new ArrayList<>();
+
+    result.addAll(getPositionalFeatures(type));
+
+    result.addAll(getNonPositionalFeatures());
+
+    return result;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public List<SequenceFeature> getFeaturesByOntology(String... ontologyTerm)
+  {
+    if (ontologyTerm == null || ontologyTerm.length == 0)
+    {
+      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()]));
   }
 
   /**
-   * Returns a (possibly empty) list of features of the given type which overlap
-   * the (inclusive) sequence position range
+   * {@inheritDoc}
+   */
+  @Override
+  public int getFeatureCount(boolean positional, String... type)
+  {
+    int result = 0;
+
+    for (FeatureStore featureSet : varargToTypes(type))
+    {
+      result += featureSet.getFeatureCount(positional);
+    }
+    return result;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public int getTotalFeatureLength(String... type)
+  {
+    int result = 0;
+
+    for (FeatureStore featureSet : varargToTypes(type))
+    {
+      result += featureSet.getTotalFeatureLength();
+    }
+    return result;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public List<SequenceFeature> getPositionalFeatures(String... type)
+  {
+    List<SequenceFeature> result = new ArrayList<>();
+
+    for (FeatureStore featureSet : varargToTypes(type))
+    {
+      result.addAll(featureSet.getPositionalFeatures());
+    }
+    return result;
+  }
+
+  /**
+   * A convenience method that converts a vararg for feature types to an
+   * Iterable over matched feature sets in key order
    * 
    * @param type
-   * @param from
-   * @param to
    * @return
    */
-  public List<SequenceFeature> findFeatures(String type, int from,
-          int to)
+  protected Iterable<FeatureStore> varargToTypes(String... type)
+  {
+    if (type == null || type.length == 0)
+    {
+      /*
+       * no vararg parameter supplied - return all
+       */
+      return featureStore.values();
+    }
+
+    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;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public List<SequenceFeature> getContactFeatures(String... type)
   {
-    FeatureStore features = featureStore.get(type);
-    if (features == null)
+    List<SequenceFeature> result = new ArrayList<>();
+
+    for (FeatureStore featureSet : varargToTypes(type))
     {
-      return Collections.emptyList();
+      result.addAll(featureSet.getContactFeatures());
     }
-    return features.findOverlappingFeatures(from, to);
+    return result;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public List<SequenceFeature> getNonPositionalFeatures(String... type)
+  {
+    List<SequenceFeature> result = new ArrayList<>();
+
+    for (FeatureStore featureSet : varargToTypes(type))
+    {
+      result.addAll(featureSet.getNonPositionalFeatures());
+    }
+    return result;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public boolean delete(SequenceFeature sf)
+  {
+    for (FeatureStore featureSet : featureStore.values())
+    {
+      if (featureSet.delete(sf))
+      {
+        return true;
+      }
+    }
+    return false;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public boolean hasFeatures()
+  {
+    for (FeatureStore featureSet : featureStore.values())
+    {
+      if (!featureSet.isEmpty())
+      {
+        return true;
+      }
+    }
+    return false;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public Set<String> getFeatureGroups(boolean positionalFeatures,
+          String... type)
+  {
+    Set<String> groups = new HashSet<>();
+
+    for (FeatureStore featureSet : varargToTypes(type))
+    {
+      groups.addAll(featureSet.getFeatureGroups(positionalFeatures));
+    }
+
+    return groups;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public Set<String> getFeatureTypesForGroups(boolean positionalFeatures,
+          String... groups)
+  {
+    Set<String> result = new HashSet<>();
+
+    for (Entry<String, FeatureStore> featureType : featureStore.entrySet())
+    {
+      Set<String> featureGroups = featureType.getValue().getFeatureGroups(
+              positionalFeatures);
+      for (String group : groups)
+      {
+        if (featureGroups.contains(group))
+        {
+          /*
+           * yes this feature type includes one of the query groups
+           */
+          result.add(featureType.getKey());
+          break;
+        }
+      }
+    }
+
+    return result;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public Set<String> getFeatureTypes(String... soTerm)
+  {
+    Set<String> types = new HashSet<>();
+    for (Entry<String, FeatureStore> entry : featureStore.entrySet())
+    {
+      String type = entry.getKey();
+      if (!entry.getValue().isEmpty() && isOntologyTerm(type, soTerm))
+      {
+        types.add(type);
+      }
+    }
+    return types;
+  }
+
+  /**
+   * 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
+   * @return
+   */
+  protected boolean isOntologyTerm(String type, String... soTerm)
+  {
+    if (soTerm == null || soTerm.length == 0)
+    {
+      return true;
+    }
+    SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+    for (String term : soTerm)
+    {
+      if (type.equals(term) || so.isA(type, term))
+      {
+        return true;
+      }
+    }
+    return false;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public float getMinimumScore(String type, boolean positional)
+  {
+    return featureStore.containsKey(type) ? featureStore.get(type)
+            .getMinimumScore(positional) : Float.NaN;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public float getMaximumScore(String type, boolean positional)
+  {
+    return featureStore.containsKey(type) ? featureStore.get(type)
+            .getMaximumScore(positional) : Float.NaN;
+  }
+
+  /**
+   * A convenience method to sort features by start position ascending (if on
+   * forward strand), or end position descending (if on reverse strand)
+   * 
+   * @param features
+   * @param forwardStrand
+   */
+  public static void sortFeatures(List<SequenceFeature> features,
+          final boolean forwardStrand)
+  {
+    Collections.sort(features, forwardStrand ? FORWARD_STRAND
+            : REVERSE_STRAND);
+  }
+
+  /**
+   * {@inheritDoc} This method is 'semi-optimised': it only inspects features
+   * for types that include the specified group, but has to inspect every
+   * feature of those types for matching feature group. This is efficient unless
+   * a sequence has features that share the same type but are in different
+   * groups - an unlikely case.
+   * <p>
+   * For example, if RESNUM feature is created with group = PDBID, then features
+   * would only be retrieved for those sequences associated with the target
+   * PDBID (group).
+   */
+  @Override
+  public List<SequenceFeature> getFeaturesForGroup(boolean positional,
+          String group, String... type)
+  {
+    List<SequenceFeature> result = new ArrayList<>();
+    for (FeatureStore featureSet : varargToTypes(type))
+    {
+      if (featureSet.getFeatureGroups(positional).contains(group))
+      {
+        result.addAll(featureSet.getFeaturesForGroup(positional, group));
+      }
+    }
+    return result;
+  }
+
+  /**
+   * {@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();
   }
 }