X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeatures.java;h=15c2c071364709f3f5490d79078a2df6bcc405cb;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=bd102f6d39d01c561d41c08c4435ea873e2448f5;hpb=81d2ea57ab71c0806a036833f73711bc4ad5c76d;p=jalview.git

diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java
index bd102f6..15c2c07 100644
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -20,14 +20,8 @@
  */
 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;
@@ -36,6 +30,9 @@ 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
@@ -47,30 +44,6 @@ 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!)
@@ -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()]));
   }
 
   /**
@@ -229,7 +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
@@ -245,12 +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;
@@ -346,8 +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))
@@ -398,7 +372,7 @@ 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 +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;
   }
 
   /**
@@ -425,8 +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;
   }
 
   /**
@@ -436,11 +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);
   }
 
   /**
@@ -473,13 +450,22 @@ 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();
+  }
+}