JAL-3397 impl.IntervalStore and nonc.IntervalStore unified api

[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 bd102f6..e747d5f 100644 (file)
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -27,7 +27,6 @@ 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;
@@ -47,30 +46,6 @@ import intervalstore.api.IntervalI;
  */
 public class SequenceFeatures implements SequenceFeaturesI
 {
-  /**
-   * a comparator for sorting features by start position ascending
-   */
-  private static Comparator<IntervalI> FORWARD_STRAND = new Comparator<IntervalI>()
-  {
-    @Override
-    public int compare(IntervalI o1, IntervalI o2)
-    {
-      return Integer.compare(o1.getBegin(), o2.getBegin());
-    }
-  };
-
-  /**
-   * a comparator for sorting features by end position descending
-   */
-  private static Comparator<IntervalI> REVERSE_STRAND = new Comparator<IntervalI>()
-  {
-    @Override
-    public int compare(IntervalI o1, IntervalI 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!)
@@ -134,12 +109,10 @@ public class SequenceFeatures implements SequenceFeaturesI
           String... type)
   {
     List<SequenceFeature> result = new ArrayList<>();
-
     for (FeatureStore featureSet : varargToTypes(type))
     {
-      result.addAll(featureSet.findOverlappingFeatures(from, to));
+      featureSet.findOverlappingFeatures(from, to, result);
     }
-
     return result;
   }
 
@@ -178,8 +151,8 @@ public class SequenceFeatures implements SequenceFeaturesI
       return new ArrayList<>();
     }
 
-    return getAllFeatures(featureTypes.toArray(new String[featureTypes
-            .size()]));
+    return getAllFeatures(
+            featureTypes.toArray(new String[featureTypes.size()]));
   }
 
   /**
@@ -222,7 +195,7 @@ public class SequenceFeatures implements SequenceFeaturesI
 
     for (FeatureStore featureSet : varargToTypes(type))
     {
-      result.addAll(featureSet.getPositionalFeatures());
+      featureSet.getPositionalFeatures(result);
     }
     return result;
   }
@@ -266,7 +239,7 @@ public class SequenceFeatures implements SequenceFeaturesI
 
     for (FeatureStore featureSet : varargToTypes(type))
     {
-      result.addAll(featureSet.getContactFeatures());
+      featureSet.getContactFeatures(result);
     }
     return result;
   }
@@ -281,7 +254,7 @@ public class SequenceFeatures implements SequenceFeaturesI
 
     for (FeatureStore featureSet : varargToTypes(type))
     {
-      result.addAll(featureSet.getNonPositionalFeatures());
+      featureSet.getNonPositionalFeatures(result);
     }
     return result;
   }
@@ -346,8 +319,8 @@ public class SequenceFeatures implements SequenceFeaturesI
 
     for (Entry<String, FeatureStore> featureType : featureStore.entrySet())
     {
-      Set<String> featureGroups = featureType.getValue().getFeatureGroups(
-              positionalFeatures);
+      Set<String> featureGroups = featureType.getValue()
+              .getFeatureGroups(positionalFeatures);
       for (String group : groups)
       {
         if (featureGroups.contains(group))
@@ -398,7 +371,7 @@ public class SequenceFeatures implements SequenceFeaturesI
     {
       return true;
     }
-    SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+    SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
     for (String term : soTerm)
     {
       if (type.equals(term) || so.isA(type, term))
@@ -415,8 +388,9 @@ public class SequenceFeatures implements SequenceFeaturesI
   @Override
   public float getMinimumScore(String type, boolean positional)
   {
-    return featureStore.containsKey(type) ? featureStore.get(type)
-            .getMinimumScore(positional) : Float.NaN;
+    return featureStore.containsKey(type)
+            ? featureStore.get(type).getMinimumScore(positional)
+            : Float.NaN;
   }
 
   /**
@@ -425,8 +399,9 @@ public class SequenceFeatures implements SequenceFeaturesI
   @Override
   public float getMaximumScore(String type, boolean positional)
   {
-    return featureStore.containsKey(type) ? featureStore.get(type)
-            .getMaximumScore(positional) : Float.NaN;
+    return featureStore.containsKey(type)
+            ? featureStore.get(type).getMaximumScore(positional)
+            : Float.NaN;
   }
 
   /**
@@ -436,11 +411,12 @@ 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);
+    Collections.sort(features,
+            forwardStrand ? IntervalI.COMPARE_BEGIN_ASC
+                    : IntervalI.COMPARE_END_DESC);
   }
 
   /**
@@ -473,13 +449,37 @@ 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();
+  }
+
+  @Override
+  public List<SequenceFeature> findFeatures(int pos, String type,
+          List<SequenceFeature> list)
+  {
+    FeatureStore fs = featureStore.get(type);
+    return fs.findOverlappingFeatures(pos, pos, list);
+  }
+
+  @Override
+  public boolean hasFeatures(String type)
+  {
+    return featureStore.containsKey(type);
+  }
+
+}