JAL-3251 SequenceToSequenceMapping now SequenceMapping, MappingType++

[jalview.git] / src / jalview / analysis / AlignmentUtils.java

diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 7a082be..f1084a7 100644 (file)
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -24,7 +24,6 @@ import static jalview.io.gff.GffConstants.CLINICAL_SIGNIFICANCE;
 
 import jalview.datamodel.AlignedCodon;
 import jalview.datamodel.AlignedCodonFrame;
-import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -36,6 +35,7 @@ import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.SequenceMapping;
 import jalview.datamodel.features.SequenceFeatures;
 import jalview.io.gff.Gff3Helper;
 import jalview.io.gff.SequenceOntologyI;
@@ -74,12 +74,15 @@ import java.util.TreeMap;
  */
 public class AlignmentUtils
 {
-
   private static final int CODON_LENGTH = 3;
 
   private static final String SEQUENCE_VARIANT = "sequence_variant:";
 
-  private static final String ID = "ID";
+  /*
+   * the 'id' attribute is provided for variant features fetched from
+   * Ensembl using its REST service with JSON format 
+   */
+  public static final String VARIANT_ID = "id";
 
   /**
    * A data model to hold the 'normal' base value at a position, and an optional
@@ -1932,7 +1935,7 @@ public class AlignmentUtils
             .findMappingsForSequence(proteinProduct, mappings);
     for (AlignedCodonFrame acf : mappingsToPeptide)
     {
-      for (SequenceToSequenceMapping map : acf.getMappings())
+      for (SequenceMapping map : acf.getMappings())
       {
         Mapping mapping = map.getMapping();
         if (mapping != aMapping
@@ -2425,7 +2428,8 @@ public class AlignmentUtils
   static int computePeptideVariants(SequenceI peptide, int peptidePos,
           List<DnaVariant>[] codonVariants)
   {
-    String residue = String.valueOf(peptide.getCharAt(peptidePos - 1));
+    String residue = String
+            .valueOf(peptide.getCharAt(peptidePos - peptide.getStart()));
     int count = 0;
     String base1 = codonVariants[0].get(0).base;
     String base2 = codonVariants[1].get(0).base;
@@ -2575,15 +2579,15 @@ public class AlignmentUtils
             peptidePos, var.getSource());
 
     StringBuilder attributes = new StringBuilder(32);
-    String id = (String) var.variant.getValue(ID);
+    String id = (String) var.variant.getValue(VARIANT_ID);
     if (id != null)
     {
       if (id.startsWith(SEQUENCE_VARIANT))
       {
         id = id.substring(SEQUENCE_VARIANT.length());
       }
-      sf.setValue(ID, id);
-      attributes.append(ID).append("=").append(id);
+      sf.setValue(VARIANT_ID, id);
+      attributes.append(VARIANT_ID).append("=").append(id);
       // TODO handle other species variants JAL-2064
       StringBuilder link = new StringBuilder(32);
       try