Changes between Version 6 and Version 7 of BioPerlRoundTripSecondPass

Timestamp:

2008/02/13 17:09:13 (16 years ago)

Author:

heikki

Comment:

--

BioPerlRoundTripSecondPass

@@ -51 +51 @@
  * ~~MAJOR: line BASE not present in recent genbank format, but it is still generated by !BioPerl~~
    * This should be safe line to drop, because GenPept has never had it and all (most?) parsers can deal with both.
-   * fixed SVN revision 14503.
+   * fixed: SVN revision 14503.
  * minor: features are not returned in order
 
 == swiss-prot ==
 
- * minor: No full stop at the end of the DT lines
- * MAJOR: GN line returning only value from key/value pairs (e.g.
+ * ~~MAJOR: No full stop at the end of the DT lines~~
+   * This is actually important to have. The parser will not grab the sequence version without the stop character.
+   * Changed the parser to work regardless of the end stop character
+   * write_seq now writes out the stops
+   * fixed: SVN revision 14504.
+ * ~~MAJOR: PE (evidence) line returned between CC and DR lines when it should be between DR and KW lines~~
+   * fixed: SVN revision 14505.
+ * ~~MAJOR: RX line:DOI key/value pair lost~~
+   * The parser rexerps depend on the order of references. It will be easier to maintain without this restriction.
+   * The parser does not take into account that any of the refs can be missing
+   * Rewrote RX line parsing and writing
+   * fixed: SVN revision 14505.
+ * MAJOR: GN line returning only values from key/value pairs (e.g.
 {{{
 GN   Name=DOF3.7; Synonyms=BBFA, DAG1;...   
@@ -63 +74 @@
 GN   DOF3.7 OR BBFA OR DAG1 ...
 }}}
+ * MAJOR: Extra spaces and a stop added to FT HELIX and STRAND lines:
+{{{
+FT   STRAND      910    913
+->
+FT   STRAND      910    913       .
+}}}
  * minor: OC line word wrapping differences
  * minor: extra spaces at the end of the first RT line when there are more than one of them
- * MAJOR: RX line:DOI key/value pair lost
- * MAJOR: PE (evidence) line returned between CC and DR lines when it should be between DR and KW lines
  * minor: extra space after first FT line
  * minor: FTid sometimes not written on its own line
  * minor: extra space written to the end of the sequence line
+   *'''Note:''' All these extra spaces at the end of the line  come from _write_line_swissprot_regex(). Check if this can be fixed!