JAL-1693 make exon alignment for get-xref splitframe (with CDS xref)

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 482df7f..81046f1 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -20,10 +20,6 @@
  */
 package jalview.datamodel;
 
-import jalview.analysis.AlignmentUtils;
-import jalview.io.FastaFile;
-import jalview.util.MessageManager;
-
 import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.HashSet;
@@ -34,6 +30,10 @@ import java.util.Map;
 import java.util.Set;
 import java.util.Vector;
 
+import jalview.analysis.AlignmentUtils;
+import jalview.io.FastaFile;
+import jalview.util.MessageManager;
+
 /**
  * Data structure to hold and manipulate a multiple sequence alignment
  */
@@ -1664,8 +1664,8 @@ public class Alignment implements AlignmentI
    * identically. If this is nucleotide and the other is protein, make 3 gaps
    * for each gap in the protein sequences. If this is protein and the other is
    * nucleotide, insert a gap for each 3 gaps (or part thereof) between
-   * nucleotide bases. Does nothing if alignment of protein from cDNA is
-   * requested (not yet implemented).
+   * nucleotide bases. If this is protein and the other is nucleotide, gaps
+   * protein to match the relative ordering of codons in the nucleotide.
    * 
    * Parameters control whether gaps in exon (mapped) and intron (unmapped)
    * regions are preserved. Gaps that connect introns to exons are treated
@@ -1697,6 +1697,9 @@ public class Alignment implements AlignmentI
             { thisGapChar, thisGapChar, thisGapChar }) : String
             .valueOf(thisGapChar);
 
+    // TODO handle intron regions? Needs a 'holistic' alignment of dna,
+    // not just sequence by sequence. But how to 'gap' intron regions?
+
     /*
      * Get mappings from 'that' alignment's sequences to this.
      */