X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeatures.java;h=8f6d49697eef4dc5abf315fb71569ce620a38737;hb=8eaa775e59bf928f8899f9ada5c9811200c2853a;hp=6165d0abb7e0340b8560c0a0636b5f25c9b475fd;hpb=5c10f71b18bb8a9e3320440cc1eaa95350d56120;p=jalview.git

diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java
index 6165d0a..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.HashMap;
+import java.util.Collections;
+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)
     {
@@ -56,15 +106,9 @@ public class SequenceFeatures
   }
 
   /**
-   * Returns a (possibly empty) list of features, optionally restricted to
-   * specified types, which overlap the given (inclusive) sequence position
-   * range
-   * 
-   * @param from
-   * @param to
-   * @param type
-   * @return
+   * {@inheritDoc}
    */
+  @Override
   public List<SequenceFeature> findFeatures(int from, int to,
           String... type)
   {
@@ -83,30 +127,79 @@ public class SequenceFeatures
   }
 
   /**
-   * Answers a list of all features stored, optionally restricted to specified
-   * types, in no particular guaranteed order
-   * 
-   * @param type
-   * @return
+   * {@inheritDoc}
    */
+  @Override
   public List<SequenceFeature> getAllFeatures(String... type)
   {
     List<SequenceFeature> result = new ArrayList<SequenceFeature>();
 
     result.addAll(getPositionalFeatures(type));
 
-    result.addAll(getNonPositionalFeatures(type));
+    result.addAll(getNonPositionalFeatures());
 
     return result;
   }
 
   /**
-   * Answers a list of all positional features, optionally restricted to
-   * specified types, in no particular guaranteed order
-   * 
-   * @param type
-   * @return
+   * {@inheritDoc}
+   */
+  @Override
+  public List<SequenceFeature> getFeaturesByOntology(String... ontologyTerm)
+  {
+    if (ontologyTerm == null || ontologyTerm.length == 0)
+    {
+      return new ArrayList<SequenceFeature>();
+    }
+
+    Set<String> featureTypes = getFeatureTypes(ontologyTerm);
+    return getAllFeatures(featureTypes.toArray(new String[featureTypes
+            .size()]));
+  }
+
+  /**
+   * {@inheritDoc}
    */
+  @Override
+  public int getFeatureCount(boolean positional, String... type)
+  {
+    int result = 0;
+
+    for (String featureType : varargToTypes(type))
+    {
+      FeatureStore featureSet = featureStore.get(featureType);
+      if (featureSet != null)
+      {
+        result += featureSet.getFeatureCount(positional);
+      }
+    }
+    return result;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public int getTotalFeatureLength(String... type)
+  {
+    int result = 0;
+
+    for (String featureType : varargToTypes(type))
+    {
+      FeatureStore featureSet = featureStore.get(featureType);
+      if (featureSet != null)
+      {
+        result += featureSet.getTotalFeatureLength();
+      }
+    }
+    return result;
+
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
   public List<SequenceFeature> getPositionalFeatures(String... type)
   {
     List<SequenceFeature> result = new ArrayList<SequenceFeature>();
@@ -132,16 +225,29 @@ public class SequenceFeatures
    */
   protected Iterable<String> varargToTypes(String... type)
   {
-    return type == null || type.length == 0 ? featureStore
-            .keySet() : Arrays.asList(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;
   }
 
   /**
-   * Answers a list of all contact features, optionally restricted to specified
-   * types, in no particular guaranteed order
-   * 
-   * @return
+   * {@inheritDoc}
    */
+  @Override
   public List<SequenceFeature> getContactFeatures(String... type)
   {
     List<SequenceFeature> result = new ArrayList<SequenceFeature>();
@@ -158,13 +264,9 @@ public class SequenceFeatures
   }
 
   /**
-   * Answers a list of all non-positional features, optionally restricted to
-   * specified types, in no particular guaranteed order
-   * 
-   * @param type
-   *          if no type is specified, all are returned
-   * @return
+   * {@inheritDoc}
    */
+  @Override
   public List<SequenceFeature> getNonPositionalFeatures(String... type)
   {
     List<SequenceFeature> result = new ArrayList<SequenceFeature>();
@@ -181,13 +283,9 @@ public class SequenceFeatures
   }
 
   /**
-   * 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())
@@ -201,10 +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())
@@ -218,16 +315,9 @@ public class SequenceFeatures
   }
 
   /**
-   * Returns a set of the distinct feature groups present in the collection. The
-   * set may include null. The boolean parameter determines whether the groups
-   * for positional or for non-positional features are returned. The optional
-   * type parameter may be used to restrict to groups for specified feature
-   * types.
-   * 
-   * @param positionalFeatures
-   * @param type
-   * @return
+   * {@inheritDoc}
    */
+  @Override
   public Set<String> getFeatureGroups(boolean positionalFeatures,
           String... type)
   {
@@ -248,15 +338,9 @@ public class SequenceFeatures
   }
 
   /**
-   * Answers the set of distinct feature types for which there is at least one
-   * feature with one of the given feature group(s). The parameter determines
-   * whether the groups for positional or for non-positional features are
-   * returned.
-   * 
-   * @param positionalFeatures
-   * @param groups
-   * @return
+   * {@inheritDoc}
    */
+  @Override
   public Set<String> getFeatureTypesForGroups(boolean positionalFeatures,
           String... groups)
   {
@@ -281,4 +365,130 @@ public class SequenceFeatures
 
     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))
+      {
+        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