mungo merge

[jalview.git] / src / jalview / io / AlignFile.java

diff --git a/src/jalview/io/AlignFile.java b/src/jalview/io/AlignFile.java
index 7e0cabd..984eff6 100755 (executable)
--- a/src/jalview/io/AlignFile.java
+++ b/src/jalview/io/AlignFile.java
@@ -47,7 +47,8 @@ public abstract class AlignFile extends FileParse
   int maxLength = 0;
 
   /**
-   * Sequences to be added to form a new alignment.
+   * Sequences to be added to form a new alignment. TODO: remove vector in this
+   * class
    */
   protected Vector<SequenceI> seqs;
 
@@ -351,7 +352,15 @@ public abstract class AlignFile extends FileParse
     if (space > -1)
     {
       seq = new Sequence(id.substring(0, space), "");
-      seq.setDescription(id.substring(space + 1));
+      String desc = id.substring(space + 1);
+      seq.setDescription(desc);
+
+      /*
+       * it is tempting to parse Ensembl style gene description e.g.
+       * chromosome:GRCh38:7:140696688:140721955:1 and set the
+       * start position of the sequence, but this causes much confusion
+       * for reverse strand feature locations
+       */
     }
     else
     {