JAL-3700 additions and corrections to unit tests

[jalview.git] / src / jalview / datamodel / AlignedCodonFrame.java

diff --git a/src/jalview/datamodel/AlignedCodonFrame.java b/src/jalview/datamodel/AlignedCodonFrame.java
index 7fa8b29..aca523e 100644 (file)
--- a/src/jalview/datamodel/AlignedCodonFrame.java
+++ b/src/jalview/datamodel/AlignedCodonFrame.java
@@ -20,13 +20,13 @@
  */
 package jalview.datamodel;
 
-import jalview.util.MapList;
-import jalview.util.MappingUtils;
-
 import java.util.AbstractList;
 import java.util.ArrayList;
 import java.util.List;
 
+import jalview.util.MapList;
+import jalview.util.MappingUtils;
+
 /**
  * Stores mapping between the columns of a protein alignment and a DNA alignment
  * and a list of individual codon to amino acid mappings between sequences.
@@ -134,7 +134,7 @@ public class AlignedCodonFrame
       }
 
       /*
-       * check that each mapped range lieS with the sequence range
+       * check that each mapped range lies within the sequence range
        * (necessary for circular CDS - example EMBL:J03321:AAA91567)
        * and mapped length covers (at least) sequence length
        */
@@ -311,8 +311,8 @@ public class AlignedCodonFrame
 
   /**
    * Return the corresponding aligned or dataset dna sequence for given amino
-   * acid sequence, or null if not found. returns the sequence from
-   * the first mapping found that involves the protein sequence.
+   * acid sequence, or null if not found. returns the sequence from the first
+   * mapping found that involves the protein sequence.
    * 
    * @param aaSeqRef
    * @return
@@ -819,7 +819,7 @@ public class AlignedCodonFrame
    * Two AlignedCodonFrame objects are equal if they hold the same ordered list
    * of mappings
    * 
-   * @see SequenceToSequenceMapping#
+   * @see SequenceToSequenceMapping#equals
    */
   @Override
   public boolean equals(Object obj)
@@ -836,12 +836,20 @@ public class AlignedCodonFrame
     return mappings;
   }
 
-  public SequenceToSequenceMapping getCoveringMapping(SequenceI cds,
-          SequenceI peptide)
+  /**
+   * Returns the first mapping found which is between the two given sequences,
+   * and covers the full extent of both.
+   * 
+   * @param seq1
+   * @param seq2
+   * @return
+   */
+  public SequenceToSequenceMapping getCoveringMapping(SequenceI seq1,
+          SequenceI seq2)
   {
     for (SequenceToSequenceMapping mapping : mappings)
     {
-      if (mapping.covers(peptide) && mapping.covers(cds))
+      if (mapping.covers(seq2) && mapping.covers(seq1))
       {
         return mapping;
       }