X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2Ffeatures%2FSequenceFeatures.java;h=fcf1b536409a3579a74c2fe1556d6c0b074d5dac;hb=c0d7fb852ebfdb0b4322c636dd379a031de665c8;hp=ff570b1ada2e9f742e708e8466751bae2c9c8f0a;hpb=1ec8fc3e8bc982115e5ba1b16a101d239a2df591;p=jalview.git

diff --git a/src/jalview/datamodel/features/SequenceFeatures.java b/src/jalview/datamodel/features/SequenceFeatures.java
index ff570b1..fcf1b53 100644
--- a/src/jalview/datamodel/features/SequenceFeatures.java
+++ b/src/jalview/datamodel/features/SequenceFeatures.java
@@ -1,5 +1,26 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.datamodel.features;
 
+import jalview.datamodel.ContiguousI;
 import jalview.datamodel.SequenceFeature;
 import jalview.io.gff.SequenceOntologyFactory;
 import jalview.io.gff.SequenceOntologyI;
@@ -62,7 +83,7 @@ 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
+     * ? wrap as a synchronized map for add and delete operations
      */
     // featureStore = Collections
     // .synchronizedSortedMap(new TreeMap<String, FeatureStore>());
@@ -70,6 +91,21 @@ public class SequenceFeatures implements SequenceFeaturesI
   }
 
   /**
+   * Constructor given a list of features
+   */
+  public SequenceFeatures(List<SequenceFeature> features)
+  {
+    this();
+    if (features != null)
+    {
+      for (SequenceFeature feature : features)
+      {
+        add(feature);
+      }
+    }
+  }
+
+  /**
    * {@inheritDoc}
    */
   @Override
@@ -96,15 +132,11 @@ public class SequenceFeatures implements SequenceFeaturesI
   public List<SequenceFeature> findFeatures(int from, int to,
           String... type)
   {
-    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+    List<SequenceFeature> result = new ArrayList<>();
 
-    for (String featureType : varargToTypes(type))
+    for (FeatureStore featureSet : varargToTypes(type))
     {
-      FeatureStore features = featureStore.get(featureType);
-      if (features != null)
-      {
-        result.addAll(features.findOverlappingFeatures(from, to));
-      }
+      result.addAll(featureSet.findOverlappingFeatures(from, to));
     }
 
     return result;
@@ -116,7 +148,7 @@ public class SequenceFeatures implements SequenceFeaturesI
   @Override
   public List<SequenceFeature> getAllFeatures(String... type)
   {
-    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+    List<SequenceFeature> result = new ArrayList<>();
 
     result.addAll(getPositionalFeatures(type));
 
@@ -133,10 +165,18 @@ public class SequenceFeatures implements SequenceFeaturesI
   {
     if (ontologyTerm == null || ontologyTerm.length == 0)
     {
-      return new ArrayList<SequenceFeature>();
+      return new ArrayList<>();
     }
 
     Set<String> featureTypes = getFeatureTypes(ontologyTerm);
+    if (featureTypes.isEmpty())
+    {
+      /*
+       * no features of the specified type or any sub-type
+       */
+      return new ArrayList<>();
+    }
+
     return getAllFeatures(featureTypes.toArray(new String[featureTypes
             .size()]));
   }
@@ -149,13 +189,9 @@ public class SequenceFeatures implements SequenceFeaturesI
   {
     int result = 0;
 
-    for (String featureType : varargToTypes(type))
+    for (FeatureStore featureSet : varargToTypes(type))
     {
-      FeatureStore featureSet = featureStore.get(featureType);
-      if (featureSet != null)
-      {
-        result += featureSet.getFeatureCount(positional);
-      }
+      result += featureSet.getFeatureCount(positional);
     }
     return result;
   }
@@ -168,16 +204,11 @@ public class SequenceFeatures implements SequenceFeaturesI
   {
     int result = 0;
 
-    for (String featureType : varargToTypes(type))
+    for (FeatureStore featureSet : varargToTypes(type))
     {
-      FeatureStore featureSet = featureStore.get(featureType);
-      if (featureSet != null)
-      {
-        result += featureSet.getTotalFeatureLength();
-      }
+      result += featureSet.getTotalFeatureLength();
     }
     return result;
-
   }
 
   /**
@@ -186,45 +217,41 @@ public class SequenceFeatures implements SequenceFeaturesI
   @Override
   public List<SequenceFeature> getPositionalFeatures(String... type)
   {
-    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+    List<SequenceFeature> result = new ArrayList<>();
 
-    for (String featureType : varargToTypes(type))
+    for (FeatureStore featureSet : varargToTypes(type))
     {
-      FeatureStore featureSet = featureStore.get(featureType);
-      if (featureSet != null)
-      {
-        result.addAll(featureSet.getPositionalFeatures());
-      }
+      result.addAll(featureSet.getPositionalFeatures());
     }
     return result;
   }
 
   /**
    * A convenience method that converts a vararg for feature types to an
-   * Iterable, replacing the value with the stored feature types if it is null
-   * or empty
+   * Iterable over matched feature sets in key order
    * 
    * @param type
    * @return
    */
-  protected Iterable<String> varargToTypes(String... type)
+  protected Iterable<FeatureStore> varargToTypes(String... type)
   {
     if (type == null || type.length == 0)
     {
       /*
-       * no vararg parameter supplied
+       * no vararg parameter supplied - return all
        */
-      return featureStore.keySet();
+      return featureStore.values();
     }
 
-    /*
-     * 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);
+    List<FeatureStore> types = new ArrayList<>();
+    List<String> args = Arrays.asList(type);
+    for (Entry<String, FeatureStore> featureType : featureStore.entrySet())
+    {
+      if (args.contains(featureType.getKey()))
+      {
+        types.add(featureType.getValue());
+      }
+    }
     return types;
   }
 
@@ -234,15 +261,11 @@ public class SequenceFeatures implements SequenceFeaturesI
   @Override
   public List<SequenceFeature> getContactFeatures(String... type)
   {
-    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+    List<SequenceFeature> result = new ArrayList<>();
 
-    for (String featureType : varargToTypes(type))
+    for (FeatureStore featureSet : varargToTypes(type))
     {
-      FeatureStore featureSet = featureStore.get(featureType);
-      if (featureSet != null)
-      {
-        result.addAll(featureSet.getContactFeatures());
-      }
+      result.addAll(featureSet.getContactFeatures());
     }
     return result;
   }
@@ -253,15 +276,11 @@ public class SequenceFeatures implements SequenceFeaturesI
   @Override
   public List<SequenceFeature> getNonPositionalFeatures(String... type)
   {
-    List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+    List<SequenceFeature> result = new ArrayList<>();
 
-    for (String featureType : varargToTypes(type))
+    for (FeatureStore featureSet : varargToTypes(type))
     {
-      FeatureStore featureSet = featureStore.get(featureType);
-      if (featureSet != null)
-      {
-        result.addAll(featureSet.getNonPositionalFeatures());
-      }
+      result.addAll(featureSet.getNonPositionalFeatures());
     }
     return result;
   }
@@ -305,17 +324,11 @@ public class SequenceFeatures implements SequenceFeaturesI
   public Set<String> getFeatureGroups(boolean positionalFeatures,
           String... type)
   {
-    Set<String> groups = new HashSet<String>();
-
-    Iterable<String> types = varargToTypes(type);
+    Set<String> groups = new HashSet<>();
 
-    for (String featureType : types)
+    for (FeatureStore featureSet : varargToTypes(type))
     {
-      FeatureStore featureSet = featureStore.get(featureType);
-      if (featureSet != null)
-      {
-        groups.addAll(featureSet.getFeatureGroups(positionalFeatures));
-      }
+      groups.addAll(featureSet.getFeatureGroups(positionalFeatures));
     }
 
     return groups;
@@ -328,7 +341,7 @@ public class SequenceFeatures implements SequenceFeaturesI
   public Set<String> getFeatureTypesForGroups(boolean positionalFeatures,
           String... groups)
   {
-    Set<String> result = new HashSet<String>();
+    Set<String> result = new HashSet<>();
 
     for (Entry<String, FeatureStore> featureType : featureStore.entrySet())
     {
@@ -356,7 +369,7 @@ public class SequenceFeatures implements SequenceFeaturesI
   @Override
   public Set<String> getFeatureTypes(String... soTerm)
   {
-    Set<String> types = new HashSet<String>();
+    Set<String> types = new HashSet<>();
     for (Entry<String, FeatureStore> entry : featureStore.entrySet())
     {
       String type = entry.getKey();
@@ -443,22 +456,28 @@ public class SequenceFeatures implements SequenceFeaturesI
   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)
+    List<SequenceFeature> result = new ArrayList<>();
+    for (FeatureStore featureSet : varargToTypes(type))
     {
-      /*
-       * 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))
+      if (featureSet.getFeatureGroups(positional).contains(group))
       {
-        result.addAll(features.getFeaturesForGroup(positional, group));
+        result.addAll(featureSet.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