X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeatures.java;h=15c2c071364709f3f5490d79078a2df6bcc405cb;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=e489e4c8bf3811f600149ad2220444b2c3f8ebba;hpb=5929abf0b458a833c936a2f34895e29600354a54;p=jalview.git

diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java
index e489e4c..15c2c07 100644
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -20,15 +20,8 @@
  */
 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.Comparator;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
@@ -36,6 +29,11 @@ import java.util.Map.Entry;
 import java.util.Set;
 import java.util.TreeMap;
 
+import intervalstore.api.IntervalI;
+import jalview.datamodel.SequenceFeature;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyI;
+
 /**
  * A class that stores sequence features in a way that supports efficient
  * querying by type and location (overlap). Intended for (but not limited to)
@@ -46,30 +44,6 @@ 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
    * null types are permitted (but not a good idea!)
@@ -87,7 +61,7 @@ public class SequenceFeatures implements SequenceFeaturesI
      */
     // featureStore = Collections
     // .synchronizedSortedMap(new TreeMap<String, FeatureStore>());
-    featureStore = new TreeMap<String, FeatureStore>();
+    featureStore = new TreeMap<>();
   }
 
   /**
@@ -177,8 +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()]));
   }
 
   /**
@@ -228,7 +202,9 @@ public class SequenceFeatures implements SequenceFeaturesI
 
   /**
    * A convenience method that converts a vararg for feature types to an
-   * Iterable over matched feature sets in key order
+   * Iterable over matched feature sets. If no types are specified, all feature
+   * sets are returned. If one or more types are specified, feature sets for
+   * those types are returned, preserving the order of the types.
    * 
    * @param type
    * @return
@@ -244,12 +220,11 @@ public class SequenceFeatures implements SequenceFeaturesI
     }
 
     List<FeatureStore> types = new ArrayList<>();
-    List<String> args = Arrays.asList(type);
-    for (Entry<String, FeatureStore> featureType : featureStore.entrySet())
+    for (String theType : type)
     {
-      if (args.contains(featureType.getKey()))
+      if (theType != null && featureStore.containsKey(theType))
       {
-        types.add(featureType.getValue());
+        types.add(featureStore.get(theType));
       }
     }
     return types;
@@ -345,8 +320,8 @@ 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))
@@ -382,9 +357,10 @@ public class SequenceFeatures implements SequenceFeaturesI
   }
 
   /**
-   * 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.
+   * 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
@@ -396,10 +372,10 @@ public class SequenceFeatures implements SequenceFeaturesI
     {
       return true;
     }
-    SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+    SequenceOntologyI so = SequenceOntologyFactory.getSequenceOntology();
     for (String term : soTerm)
     {
-      if (so.isA(type, term))
+      if (type.equals(term) || so.isA(type, term))
       {
         return true;
       }
@@ -413,8 +389,9 @@ 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;
   }
 
   /**
@@ -423,8 +400,9 @@ 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;
   }
 
   /**
@@ -434,11 +412,12 @@ 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_END_DESC
+                    : IntervalI.COMPARE_END_DESC);
   }
 
   /**