JAL-3438 spotless for 2.11.2.0

[jalview.git] / src / jalview / ext / ensembl / EnsemblCds.java

diff --git a/src/jalview/ext/ensembl/EnsemblCds.java b/src/jalview/ext/ensembl/EnsemblCds.java
index 58cf8fa..f397412 100644 (file)
--- a/src/jalview/ext/ensembl/EnsemblCds.java
+++ b/src/jalview/ext/ensembl/EnsemblCds.java
@@ -1,25 +1,71 @@
+/*
+ * 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.ext.ensembl;
 
 import jalview.datamodel.SequenceFeature;
-import jalview.io.gff.SequenceOntology;
+import jalview.datamodel.SequenceI;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyI;
 
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * A client for direct fetching of CDS sequences from Ensembl (i.e. that part of
+ * the genomic sequence that is translated to protein)
+ * 
+ * TODO: not currently used as CDS sequences are computed from CDS features on
+ * transcripts - delete this class?
+ * 
+ * @author gmcarstairs
+ *
+ */
 public class EnsemblCds extends EnsemblSeqProxy
 {
   /*
    * fetch cds features on genomic sequence (to identify the CDS regions)
-   * and variation features (to retain)
+   * and exon and variation features (to retain for display)
    */
   private static final EnsemblFeatureType[] FEATURES_TO_FETCH = {
-      EnsemblFeatureType.cds, EnsemblFeatureType.variation };
+      EnsemblFeatureType.cds, EnsemblFeatureType.exon,
+      EnsemblFeatureType.variation };
 
   /**
-   * Constructor
+   * Default constructor (to use rest.ensembl.org)
    */
   public EnsemblCds()
   {
     super();
   }
 
+  /**
+   * Constructor given the target domain to fetch data from
+   * 
+   * @param d
+   */
+  public EnsemblCds(String d)
+  {
+    super(d);
+  }
+
   @Override
   public String getDbName()
   {
@@ -47,32 +93,49 @@ public class EnsemblCds extends EnsemblSeqProxy
   @Override
   protected boolean retainFeature(SequenceFeature sf, String accessionId)
   {
-    if (SequenceOntology.getInstance().isA(sf.getType(),
-            SequenceOntology.CDS))
+    if (SequenceOntologyFactory.getInstance().isA(sf.getType(),
+            SequenceOntologyI.CDS))
     {
       return false;
     }
-    return super.retainFeature(sf, accessionId);
+    return featureMayBelong(sf, accessionId);
   }
 
   /**
-   * Answers true if the sequence feature type is 'CDS' (or a subtype of CDS in
-   * the Sequence Ontology), and the Parent of the feature is the transcript we
-   * are retrieving
+   * Answers a list of sequence features (if any) whose type is 'CDS' (or a
+   * subtype of CDS in the Sequence Ontology), and whose Parent is the
+   * transcript we are retrieving
    */
   @Override
-  protected boolean identifiesSequence(SequenceFeature sf, String accId)
+  protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq,
+          String accId)
   {
-    if (SequenceOntology.getInstance().isA(sf.getType(),
-            SequenceOntology.CDS))
+    List<SequenceFeature> result = new ArrayList<>();
+    List<SequenceFeature> sfs = seq.getFeatures()
+            .getFeaturesByOntology(SequenceOntologyI.CDS);
+    for (SequenceFeature sf : sfs)
     {
       String parentFeature = (String) sf.getValue(PARENT);
-      if (("transcript:" + accId).equals(parentFeature))
+      if (accId.equals(parentFeature))
       {
-        return true;
+        result.add(sf);
       }
     }
-    return false;
+    return result;
+  }
+
+  /**
+   * Overrides this method to trivially return a range which is the whole of the
+   * nucleotide sequence. This is both faster than scanning for CDS features,
+   * and also means we don't need to keep CDS features on CDS sequence (where
+   * they are redundant information).
+   */
+  protected List<int[]> getCdsRanges(SequenceI dnaSeq)
+  {
+    int len = dnaSeq.getLength();
+    List<int[]> ranges = new ArrayList<>();
+    ranges.add(new int[] { 1, len });
+    return ranges;
   }
 
 }