JAL-2525 get sequence features for Ontology term(s), tidy feature sort

[jalview.git] / src / jalview / datamodel / features / SequenceFeatures.java

diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java
index 5fa9a3c..73ddac7 100644 (file)
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -1,10 +1,13 @@
 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;
@@ -22,6 +25,29 @@ 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
@@ -38,8 +64,9 @@ 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
      */
-    featureStore = Collections
-            .synchronizedSortedMap(new TreeMap<String, FeatureStore>());
+    // featureStore = Collections
+    // .synchronizedSortedMap(new TreeMap<String, FeatureStore>());
+    featureStore = new TreeMap<String, FeatureStore>();
   }
 
   /**
@@ -102,6 +129,22 @@ public class SequenceFeatures implements SequenceFeaturesI
    * {@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;
@@ -309,20 +352,47 @@ public class SequenceFeatures implements SequenceFeaturesI
    * {@inheritDoc}
    */
   @Override
-  public Set<String> getFeatureTypes()
+  public Set<String> getFeatureTypes(String... soTerm)
   {
     Set<String> types = new HashSet<String>();
     for (Entry<String, FeatureStore> entry : featureStore.entrySet())
     {
-      if (!entry.getValue().isEmpty())
+      String type = entry.getKey();
+      if (!entry.getValue().isEmpty() && isOntologyTerm(type, soTerm))
       {
-        types.add(entry.getKey());
+        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
@@ -341,4 +411,18 @@ public class SequenceFeatures implements SequenceFeaturesI
     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);
+  }
+}
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