X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FMappedFeatures.java;h=d652a97db6edfeef5f25feb347208552b24273f9;hb=30119dce1634085c41372d55b528a7a878b03b23;hp=4b558a5ec16f8d214337af937556b37e111f871a;hpb=650c1e87af071e4fd945e725bcd46995fa67d654;p=jalview.git

diff --git a/src/jalview/datamodel/MappedFeatures.java b/src/jalview/datamodel/MappedFeatures.java
index 4b558a5..d652a97 100644
--- a/src/jalview/datamodel/MappedFeatures.java
+++ b/src/jalview/datamodel/MappedFeatures.java
@@ -1,14 +1,35 @@
+/*
+ * 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;
 
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
 import jalview.io.gff.Gff3Helper;
 import jalview.schemes.ResidueProperties;
+import jalview.util.MapList;
 import jalview.util.MappingUtils;
 import jalview.util.StringUtils;
 
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
 /**
  * A data bean to hold a list of mapped sequence features (e.g. CDS features
  * mapped from protein), and the mapping between the sequences. It also provides
@@ -18,22 +39,26 @@ import java.util.Set;
  */
 public class MappedFeatures
 {
+  /*
+   * VEP CSQ:HGVSp (if present) is a short-cut to the protein variant consequence
+   */
   private static final String HGV_SP = "HGVSp";
 
   private static final String CSQ = "CSQ";
 
   /*
-   * the mapping from one sequence to another
+   * the sequence the mapped features are on
    */
-  public final Mapping mapping;
+  private final SequenceI featureSequence;
 
-  /**
-   * the sequence mapped from
+  /*
+   * the mapping between sequences;
+   * NB this could be in either sense (from or to featureSequence)
    */
-  public final SequenceI fromSeq;
+  private final Mapping mapping;
 
   /*
-   * features on the sequence mapped to that overlap the mapped positions
+   * features on featureSequence that overlap the mapped positions
    */
   public final List<SequenceFeature> features;
 
@@ -60,21 +85,23 @@ public class MappedFeatures
    * Constructor
    * 
    * @param theMapping
-   * @param from
-   *                      the sequence mapped from (e.g. CDS)
+   *          sequence mapping (which may be either to, or from, the sequence
+   *          holding the linked features)
+   * @param featureSeq
+   *          the sequence hosting the virtual features
    * @param pos
-   *                      the residue position in the sequence mapped to
+   *          the residue position in the sequence mapped to
    * @param res
-   *                      the residue character at position pos
+   *          the residue character at position pos
    * @param theFeatures
-   *                      list of mapped features found in the 'from' sequence at
-   *                      the mapped position(s)
+   *          list of mapped features found in the 'featureSeq' sequence at the
+   *          mapped position(s)
    */
-  public MappedFeatures(Mapping theMapping, SequenceI from, int pos,
+  public MappedFeatures(Mapping theMapping, SequenceI featureSeq, int pos,
           char res, List<SequenceFeature> theFeatures)
   {
     mapping = theMapping;
-    fromSeq = from;
+    featureSequence = featureSeq;
     toPosition = pos;
     toResidue = res;
     features = theFeatures;
@@ -90,10 +117,13 @@ public class MappedFeatures
     {
       codonPos = codonPositions;
       baseCodon = new char[3];
-      int cdsStart = fromSeq.getStart();
-      baseCodon[0] = fromSeq.getCharAt(codonPos[0] - cdsStart);
-      baseCodon[1] = fromSeq.getCharAt(codonPos[1] - cdsStart);
-      baseCodon[2] = fromSeq.getCharAt(codonPos[2] - cdsStart);
+      int cdsStart = featureSequence.getStart();
+      baseCodon[0] = Character
+              .toUpperCase(featureSequence.getCharAt(codonPos[0] - cdsStart));
+      baseCodon[1] = Character
+              .toUpperCase(featureSequence.getCharAt(codonPos[1] - cdsStart));
+      baseCodon[2] = Character
+              .toUpperCase(featureSequence.getCharAt(codonPos[2] - cdsStart));
     }
     else
     {
@@ -105,11 +135,14 @@ public class MappedFeatures
   /**
    * Computes and returns comma-delimited HGVS notation peptide variants derived
    * from codon allele variants. If no variants are found, answers an empty
-   * string.
+   * string. The peptide variant is either simply read from the "CSQ:HGVSp"
+   * attribute if present, else computed based on the "alleles" attribute if
+   * present. If neither attribute is found, no variant (empty string) is
+   * returned.
    * 
    * @param sf
-   *             a sequence feature (which must be one of those held in this
-   *             object)
+   *          a sequence feature (which must be one of those held in this
+   *          object)
    * @return
    */
   public String findProteinVariants(SequenceFeature sf)
@@ -230,4 +263,53 @@ public class MappedFeatures
 
     return vars.toString();
   }
+
+  /**
+   * Answers the name of the linked sequence holding any mapped features
+   * 
+   * @return
+   */
+  public String getLinkedSequenceName()
+  {
+    return featureSequence == null ? null : featureSequence.getName();
+  }
+
+  /**
+   * Answers the mapped ranges (as one or more [start, end] positions) which
+   * correspond to the given [begin, end] range of the linked sequence.
+   * 
+   * <pre>
+   * Example: MappedFeatures with CDS features mapped to peptide 
+   * CDS/200-220 gtc aac TGa acGt att AAC tta
+   * mapped to PEP/6-7 WN by mapping [206, 207, 210, 210, 215, 217] to [6, 7]
+   * getMappedPositions(206, 206) should return [6, 6]
+   * getMappedPositions(200, 214) should return [6, 6]
+   * getMappedPositions(210, 215) should return [6, 7]
+   * </pre>
+   * 
+   * @param begin
+   * @param end
+   * @return
+   */
+  public int[] getMappedPositions(int begin, int end)
+  {
+    MapList map = mapping.getMap();
+    return mapping.to == featureSequence ? map.locateInFrom(begin, end)
+            : map.locateInTo(begin, end);
+  }
+
+  /**
+   * Answers true if the linked features are on coding sequence, false if on
+   * peptide
+   * 
+   * @return
+   */
+  public boolean isFromCds()
+  {
+    if (mapping.getMap().getFromRatio() == 3)
+    {
+      return mapping.to != featureSequence;
+    }
+    return mapping.to == featureSequence;
+  }
 }