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BioLegato - Bugs and Workarounds

September 1, 2021

Workarounds

1. Circular sequences

Problem: Aside from GenBank format, virtually none of the common file formats has a mechanism to designate whether a DNA/RNA sequence is circular or linear. 

Workarounds:

• Reading files: Read the sequence in using File --> Open, NOT Import Foreign Format.
• Changing topology: Edit --> GetInfo. Set topology to Circular or Linear. Click on "Update".
  
• Use File --> Save SELECTION As to export to a format that explicitly allows for specification of a circular topology. Only GenBank or EMBL formats have the ability to specify topology. Enter a Filename and click on Save.
  Note: If the original sequence was in a format other than GenBank or EMBL, it will not have any annotation except a definition line. The saved file will therefore not contain any annotation, and would be better referred to as a pseudo GenBank file.  

In some cases, when blreads completes a task and refreshes the list of files to reflect files created, a Java error message is printed that begins

BioPCD: Command executed successfully, return status: 0 Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 2 >= 0 at java.util.Vector.elementAt(Vector.java:477) at javax.swing.table.DefaultTableModel.getValueAt(DefaultTableModel.java:648) at javax.swing.JTable.getValueAt(JTable.java:2717) ...

Extensive testing has determined that this bug can be ignored safely. It should be resolved in a future release.

BUGS, Issues and Improvements

The BIRCH Bugzilla is the official site for listing and reporting bugs .

Also see the Release Notes for the current version of BIRCH