Some more in the documentation...
Package org.biojava.bio.seq.impl
Class AssembledSymbolList
(original)
Support class for applications which need to patch together sections of
sequence into a single SymbolList
(suggested corrections)
either
... sections of *a* sequence into a single SymbolList
or
... sections of *multiple sequences* into a single SymbolList
(not sure if the 2nd alternative makes sense)
Class SimpleFramedFeature
Documentation doesn't quite follow other standards -
eg. Title: SimpleFramedFeature
This doesn't normally appear.
(Original)
Description: A no frills implementation of FramedFeature
(suggested correction)
A no frills implementation of FramedFeature
Package org.biojava.utils
Interface ActivityListener
(original)
Interface for object which monitor long-running activities
(suggested correction)
Interface for *objects* which monitor long-running activities
method activityProgress
(original)
Estimated progress of an activity. This indicated that
current parts of the activity
have been completed, out of
a target target
(suggested correction)
Estimated progress of an activity. This *indicates* that
current parts of the activity
have been completed, out of a target
target
Interface Changeable
method removeChangeListener
(original)
Remove a listener that was interested in a specific types of
changes
(suggested correction)
Remove a listener that was interested in a specific *type* of
*change*
Class ChangeEvent
method getChange
(original)
May return null is this is not
meaningful.
(suggested correction)
May return null *if* this is not
meaningful.
(ditto on getPrevious)
Class ChangeType
Field Detail
(original)
... This is the fallback for when you realy don't know what else to
do
(suggested correction)
...This is the fallback for when you *really* don't know what else to
do
Class NestedException
(Original)
A general perpose Exception that can wrap another exception
(suggested correction)
A general *purpose* Exception that can wrap another exception
(also)
It is common practice in BioJava to throw a NestedException or a subclass
of it when something goes wrong. The exception can be used to catch
another throwable, thus keeping a complete record of where the original
error originated while adding annotation to the stack-trace. It also
affords a neat way to avoid exception-bloat on method calls, particularly
when objects are composed from several objects from different
packages
(suggested changes)
... The exception can be used to catch another throwable, thus keeping a
complete record of where the *error originated* while adding annotation
to the stack-trace. It also affords a neat way to avoid exception-bloat
on method calls, particularly when objects are composed *of* several
objects from different packages.
Class NestedRuntimeException
(original)
A general perpose RuntimeException that can wrap another
exception
(suggested correction)
A general *purpose* RuntimeException that can wrap another
exception
Class ParserException
method toString
(original)
Represent this exception as a string. This includes the default exception
toString representation, followed by details of the location where the
error occured, if they were supplied when constructing this
exception
(suggested correction)
..., followed by details of the location where the error *occurred*, if
they were supplied ...
Hope this helps.
Cheers
