X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeatures.java;h=8f6d49697eef4dc5abf315fb71569ce620a38737;hb=807f5945ffa954c38f07cbf9d2a4ebc22cfe5eb9;hp=ff5f32c30b61de6e6f524406dfb2972aa576ab3c;hpb=b770e33934a49a8286b82a863aec8b2ca3b0d94b;p=jalview.git

diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java
index ff5f32c..8f6d496 100644
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -1,15 +1,20 @@
 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;
 
 /**
  * A class that stores sequence features in a way that supports efficient
@@ -19,8 +24,31 @@ import java.util.Set;
  * @author gmcarstairs
  *
  */
-public class SequenceFeatures
+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
@@ -33,20 +61,42 @@ 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<String, FeatureStore>();
   }
 
   /**
-   * Adds one sequence feature to the store, and returns true, unless the
-   * feature is already contained in the store, in which case this method
-   * returns false. Containment is determined by SequenceFeature.equals()
-   * comparison.
-   * 
-   * @param sf
+   * Constructor given a list of features
+   */
+  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)
     {
@@ -56,132 +106,186 @@ public class SequenceFeatures
   }
 
   /**
-   * Returns a (possibly empty) list of features of the given type which overlap
-   * the (inclusive) sequence position range
-   * 
-   * @param type
-   * @param from
-   * @param to
-   * @return
+   * {@inheritDoc}
    */
-  public List<SequenceFeature> findFeatures(String type, int from,
-          int to)
+  @Override
+  public List<SequenceFeature> findFeatures(int from, int to,
+          String... type)
   {
-    FeatureStore features = featureStore.get(type);
-    if (features == null)
+    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+
+    for (String featureType : varargToTypes(type))
     {
-      return Collections.emptyList();
+      FeatureStore features = featureStore.get(featureType);
+      if (features != null)
+      {
+        result.addAll(features.findOverlappingFeatures(from, to));
+      }
     }
-    return features.findOverlappingFeatures(from, to);
+
+    return result;
   }
 
   /**
-   * Answers a list of all features stored (including non-positional), in no
-   * particular guaranteed order
-   * 
-   * @return
+   * {@inheritDoc}
    */
-  public List<SequenceFeature> getFeatures()
+  @Override
+  public List<SequenceFeature> getAllFeatures(String... type)
   {
     List<SequenceFeature> result = new ArrayList<SequenceFeature>();
-    for (FeatureStore featureSet : featureStore.values())
+
+    result.addAll(getPositionalFeatures(type));
+
+    result.addAll(getNonPositionalFeatures());
+
+    return result;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public List<SequenceFeature> getFeaturesByOntology(String... ontologyTerm)
+  {
+    if (ontologyTerm == null || ontologyTerm.length == 0)
     {
-      result.addAll(featureSet.getFeatures());
+      return new ArrayList<SequenceFeature>();
     }
-    return result;
+
+    Set<String> featureTypes = getFeatureTypes(ontologyTerm);
+    return getAllFeatures(featureTypes.toArray(new String[featureTypes
+            .size()]));
   }
 
   /**
-   * Answers a list of all non-positional features stored, in no particular
-   * guaranteed order
-   * 
-   * @return
+   * {@inheritDoc}
    */
-  public List<SequenceFeature> getNonPositionalFeatures()
+  @Override
+  public int getFeatureCount(boolean positional, String... type)
   {
-    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
-    for (FeatureStore featureSet : featureStore.values())
+    int result = 0;
+
+    for (String featureType : varargToTypes(type))
     {
-      result.addAll(featureSet.getNonPositionalFeatures());
+      FeatureStore featureSet = featureStore.get(featureType);
+      if (featureSet != null)
+      {
+        result += featureSet.getFeatureCount(positional);
+      }
     }
     return result;
   }
 
   /**
-   * Answers a list of all contact features stored, in no particular guaranteed
-   * order
-   * 
-   * @return
+   * {@inheritDoc}
    */
-  public List<SequenceFeature> getContactFeatures()
+  @Override
+  public int getTotalFeatureLength(String... type)
   {
-    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
-    for (FeatureStore featureSet : featureStore.values())
+    int result = 0;
+
+    for (String featureType : varargToTypes(type))
     {
-      result.addAll(featureSet.getContactFeatures());
+      FeatureStore featureSet = featureStore.get(featureType);
+      if (featureSet != null)
+      {
+        result += featureSet.getTotalFeatureLength();
+      }
     }
     return result;
+
   }
 
   /**
-   * Answers a list of all features of the given type (including
-   * non-positional), in no particular guaranteed order
-   * 
-   * @return
+   * {@inheritDoc}
    */
-  public List<SequenceFeature> getFeatures(String type)
+  @Override
+  public List<SequenceFeature> getPositionalFeatures(String... type)
   {
     List<SequenceFeature> result = new ArrayList<SequenceFeature>();
-    FeatureStore featureSet = featureStore.get(type);
-    if (featureSet != null)
+
+    for (String featureType : varargToTypes(type))
     {
-      result.addAll(featureSet.getFeatures());
+      FeatureStore featureSet = featureStore.get(featureType);
+      if (featureSet != null)
+      {
+        result.addAll(featureSet.getPositionalFeatures());
+      }
     }
     return result;
   }
 
   /**
-   * Answers a list of all contact features of the given type, in no particular
-   * guaranteed order
+   * 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
    * 
+   * @param type
    * @return
    */
-  public List<SequenceFeature> getContactFeatures(String type)
+  protected Iterable<String> varargToTypes(String... type)
+  {
+    if (type == null || type.length == 0)
+    {
+      /*
+       * no vararg parameter supplied
+       */
+      return featureStore.keySet();
+    }
+
+    /*
+     * 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);
+    return types;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public List<SequenceFeature> getContactFeatures(String... type)
   {
     List<SequenceFeature> result = new ArrayList<SequenceFeature>();
-    FeatureStore featureSet = featureStore.get(type);
-    if (featureSet != null)
+
+    for (String featureType : varargToTypes(type))
     {
-      result.addAll(featureSet.getContactFeatures());
+      FeatureStore featureSet = featureStore.get(featureType);
+      if (featureSet != null)
+      {
+        result.addAll(featureSet.getContactFeatures());
+      }
     }
     return result;
   }
 
   /**
-   * Answers a list of all non-positional features of the given type, in no
-   * particular guaranteed order
-   * 
-   * @return
+   * {@inheritDoc}
    */
-  public List<SequenceFeature> getNonPositionalFeatures(String type)
+  @Override
+  public List<SequenceFeature> getNonPositionalFeatures(String... type)
   {
     List<SequenceFeature> result = new ArrayList<SequenceFeature>();
-    FeatureStore featureSet = featureStore.get(type);
-    if (featureSet != null)
+
+    for (String featureType : varargToTypes(type))
     {
-      result.addAll(featureSet.getNonPositionalFeatures());
+      FeatureStore featureSet = featureStore.get(featureType);
+      if (featureSet != null)
+      {
+        result.addAll(featureSet.getNonPositionalFeatures());
+      }
     }
     return result;
   }
 
   /**
-   * Deletes the given feature from the store, returning true if it was found
-   * (and deleted), else false. This method makes no assumption that the feature
-   * is in the 'expected' place in the store, in case it has been modified since
-   * it was added.
-   * 
-   * @param sf
+   * {@inheritDoc}
    */
+  @Override
   public boolean delete(SequenceFeature sf)
   {
     for (FeatureStore featureSet : featureStore.values())
@@ -195,10 +299,9 @@ public class SequenceFeatures
   }
 
   /**
-   * Answers true if this store contains at least one feature, else false
-   * 
-   * @return
+   * {@inheritDoc}
    */
+  @Override
   public boolean hasFeatures()
   {
     for (FeatureStore featureSet : featureStore.values())
@@ -212,42 +315,180 @@ public class SequenceFeatures
   }
 
   /**
-   * Returns a set of the distinct feature groups present in the collection. The
-   * set may include null.
-   * 
-   * @return
+   * {@inheritDoc}
    */
-  public Set<String> getFeatureGroups()
+  @Override
+  public Set<String> getFeatureGroups(boolean positionalFeatures,
+          String... type)
   {
     Set<String> groups = new HashSet<String>();
-    for (FeatureStore featureSet : featureStore.values())
+
+    Iterable<String> types = varargToTypes(type);
+
+    for (String featureType : types)
     {
-      groups.addAll(featureSet.getFeatureGroups());
+      FeatureStore featureSet = featureStore.get(featureType);
+      if (featureSet != null)
+      {
+        groups.addAll(featureSet.getFeatureGroups(positionalFeatures));
+      }
     }
+
     return groups;
   }
 
   /**
-   * Answers the set of distinct feature types for which there is at least one
-   * feature with the given feature group
-   * 
-   * @param group
-   * @return
+   * {@inheritDoc}
    */
-  public Set<String> getFeatureTypesForGroup(String group)
+  @Override
+  public Set<String> getFeatureTypesForGroups(boolean positionalFeatures,
+          String... groups)
   {
     Set<String> result = new HashSet<String>();
+
     for (Entry<String, FeatureStore> featureType : featureStore.entrySet())
     {
-      if (featureType.getValue().getFeatureGroups().contains(group))
+      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<String>();
+    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 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.
+   * 
+   * @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 (so.isA(type, term))
       {
-        /*
-         * yes this feature type includes the query group
-         */
-        result.add(featureType.getKey());
+        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<SequenceFeature>();
+    Iterable<String> types = varargToTypes(type);
+
+    for (String featureType : types)
+    {
+      /*
+       * 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))
+      {
+        result.addAll(features.getFeaturesForGroup(positional, group));
+      }
+    }
     return result;
   }
-}
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public boolean shiftFeatures(int shift)
+  {
+    boolean modified = false;
+    for (FeatureStore fs : featureStore.values())
+    {
+      modified |= fs.shiftFeatures(shift);
+    }
+    return modified;
+  }
+}
\ No newline at end of file